WorldWideScience

Sample records for mapping gene structure

  1. Chromosomal mapping, gene structure and characterization of the human and murine RAB27B gene

    Directory of Open Access Journals (Sweden)

    Huxley Clare

    2001-02-01

    Full Text Available Abstract Background Rab GTPases are regulators of intracellular membrane traffic. The Rab27 subfamily consists of Rab27a and Rab27b. Rab27a has been recently implicated in Griscelli Disease, a disease combining partial albinism with severe immunodeficiency. Rab27a plays a key role in the function of lysosomal-like organelles such as melanosomes in melanocytes and lytic granules in cytotoxic T lymphocytes. Little is known about Rab27b. Results The human RAB27B gene is organised in six exons, spanning about 69 kb in the chromosome 18q21.1 region. Exon 1 is non-coding and is separated from the others by 49 kb of DNA and exon 6 contains a long 3' untranslated sequence (6.4 kb. The mouse Rab27b cDNA shows 95% identity with the human cDNA at the protein level and maps to mouse chromosome 18. The mouse mRNA was detected in stomach, large intestine, spleen and eye by RT-PCR, and in heart, brain, spleen and kidney by Northern blot. Transient over-expression of EGF-Rab27b fusion protein in cultured melanocytes revealed that Rab27b is associated with melanosomes, as observed for EGF-Rab27a. Conclusions Our results indicate that the Rab27 subfamily of Ras-like GTPases is highly conserved in mammals. There is high degree of conservation in sequence and gene structure between RAB27A and RAB27B genes. Exogenous expression of Rab27b in melanocytes results in melanosomal association as observed for Rab27a, suggesting the two Rab27 proteins are functional homologues. As with RAB27A in Griscelli Disease, RAB27B may be also associated with human disease mapping to chromosome 18.

  2. Gene structure of the human DDX3 and chromosome mapping of its related sequences.

    Science.gov (United States)

    Kim, Y S; Lee, S G; Park, S H; Song, K

    2001-10-31

    The human DDX3 gene (GenBank accession No. U50553) is the human homologue of the mouse Ddx3 gene and is a member of the gene family that contains DEAD motifs. Previously, we mapped the gene to the Xp11.3-11.23. In this report, we describe the structural organization of the human DDX3 gene. It consisted of 17 exons that span approximately 16 kb. An Alu element was present in the intron 13. Its organization was the same as that of the human DBY gene, a closely related sequence present on the Y chromosome. We also identified two processed pseudogenes (DDX3) with a sequence that is highly homologous to those of DDX3 cDNAs, but contain a translation termination codon within its open-reading frame. Pseudogenes are mapped on human chromosomes 4 and X, respectively. In this paper, we discuss the relationships between DDX3 and its related sequences that have been isolated.

  3. Morphological Structure and Genetic Mapping of New Leaf-Color Mutant Gene in Rice (Oryza sativa)

    Institute of Scientific and Technical Information of China (English)

    LI Yu-hong; WANG Bao-he; DAI Zheng-yuan; LI Ai-hong; LIU Guang-qing; ZUO Shi-min; ZHANG Hong-xi; PAN Xue-biao

    2012-01-01

    Leaf-color mutations are a widely-observed class of mutations,playing an important role in the study of chlorophyll biosynthesis and plant chloroplast structure,function,genetics and development.A naturally-occurring leaf-color rice mutant,Baihuaidao 7,was analyzed.Mutant plants typically exhibited a green-white-green leaf-color progression,but this phenotype was only expressed in the presence of a stress signal induced by mechanical scarification such as transplantation.Prior to the appearance of white leaves,mutant plant growth,leaf color,chlorophyll content,and chloroplast ultrastructure appeared to be identical to those of the wild type.After the changeover to white leaf color,an examination of the mutated leaves revealed a decrease in total chlorophyll,chlorophyll a,chlorophyll b,and carotenoid content,a reduction in the number of chloroplast grana lamella and grana,and a gradual degradation of the thylakoid lamellas.At maturity,the mutant plant was etiolated and dwarfed compared with wild-type plants.Genetic analysis indicated that the leaf mutant character is controlled by a recessive nuclear gene.Genetic mapping of the mutant gene was performed using an F2 population derived from a Baihuaidao 7 ×Jiangxi 1587 cross.The mutant gene was mapped to rice chromosome 11,positioned between InDel markers L59.2-7 and L64.8-11,which are separated by approximately 740.5 kb.The mutant gene is believed to be a new leaf-color mutant gene in rice,and is tentatively designated as gwgl.

  4. Molecular structure and chromosomal mapping of the human homolog of the agouti gene

    Energy Technology Data Exchange (ETDEWEB)

    Kwon, H.Y.; Woychik, R.P. [Oak Ridge National Lab., TN (United States); Bultman, S.J. [Oak Ridge National Lab., TN (United States)]|[Univ. of Tennessee, Oak Ridge, TN (United States); Loeffler, C.; Hansmann, I. [Universitaet Goettingen (Germany); Chen, W.J.; Furdon, P.J.; Wilkison, W. [Glaxo Research Institute, Research Triangle Park, NC (United States); Powell, J.G.; Usala, A.L. [Eastern Carolina Univ., Greenville, NC (United States)

    1994-10-11

    The agouti (a) locus in mouse chromosome 2 normally regulates coat color pigmentation. The mouse agouti gene was recently cloned and shown to encode a distinctive 131-amino acid protein with a consensus signal peptide. Here the authors describe the cloning of the human homolog of the mouse agouti gene using an interspecies DNA-hybridization approach. Sequence analysis revealed that the coding region of the human agouti gene is 85% identical to the mouse gene and has the potential to encode a protein of 132 amino acids with a consensus signal peptide. Chromosomal assignment using somatic-cell-hybrid mapping panels and fluorescence in situ hybridization demonstrated that the human agouti gene maps to chromosome band 20q11.2. This result revealed that the human agouti gene is closely linked to several traits, including a locus called MODY (for maturity onset diabetes of the young) and another region that is associated with the development of myeloid leukemia. Initial expression studies with RNA from several adult human tissues showed that the human agouti gene is expressed in adipose tissue and testis.

  5. Cloning, structural organization, and chromosomal mapping of the human phenol sulfotransferase STP2 gene

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    Gaedigk, A.; Beatty, B.G.; Grant, D.M. [Hospital for Sick Children, Toronto, Ontario (Canada)

    1997-03-01

    Phenol- and monoamine-metabolizing sulfotransferases (STP and STM, respectively) are members of a superfamily of enzymes that add sulfate to a variety of xenobiotics and endobiotics containing hydroxyl or amino functional groups. To characterize related sulfotransferase genes further, we used extra-long PCR (XL-PCR) to generate three distinct sizes of amplification products from human genomic DNA or from genomic phage library clones, each of which contained sulfotransferase gene sequences. One of the PCR fragments contained a new sulfotransferase gene, STP2, corresponding to a recently published cDNA clone that encodes a sulfotransferase with catalytic specificity distinct from that of the previously described STP1 and STM. Additional upstream sequence information was obtained using a second STP2-specific XL-PCR-based approach. The STP2 gene is composed of eight exons and seven introns, with exon sizes ranging from 95 to 181 bp. Protein-coding exon lengths and locations of the splice junctions were identical to those in both the STM gene and an STP2 gene published independently by another group recently. The STP2 gene maps to a chromosomal location (16p11.2-p1.2) that is the same as that previously determined for both STP1 and STM. The characterization of the STP2 gene provides further insight into the organization, regulation, and multiplicity of the sulfotransferase supergene family. 27 refs., 3 figs.

  6. Genomic structure and mapping of precerebellin and a precerebellin-related gene.

    Science.gov (United States)

    Kavety, B; Jenkins, N A; Fletcher, C F; Copeland, N G; Morgan, J I

    1994-11-01

    The cerebellum-specific hexadecapeptide, cerebellin, is derived from a larger precursor, precerebellin, that has sequence homology to the complement component C1qB. We report the cloning of the murine homolog of precerebellin, Cbln1, and a closely related gene, Cbln2. Amino acid comparison of Cbln1 with Cbln2 revealed that Cbln2 is 88% identical to the carboxy terminal region of Cbln1. That these are independent genes was confirmed by Southern analysis and genome mapping. Cbln1 was positioned to the central region of mouse chromosome 8, 2.3 cM distal of JunB and 6.0 cM proximal of Mt1, while Cbln2 mapped to the distal end of mouse chromosome 18, 1.7 cM telomeric of Mbp.

  7. Chromosomal mapping of the structural gene coding for the mouse cell adhesion molecule uvomorulin

    Energy Technology Data Exchange (ETDEWEB)

    Eistetter, H.R.; Adolph, S.; Ringwald, M.; Simon-Chazottes, D.; Schuh, R.; Guenet, J.L.; Kemler, R. (Max-Planck-Gesellschaft, Tuebingen (West Germany))

    1988-05-01

    The gene coding for the mouse cell adhesion molecule uvomorulin has been mapped to chromosome 8. Uvomorulin cDNA clone F5H3 identified restriction fragment length polymorphisms in Southern blots of genomic DNA from mouse species Mus musculus domesticus and Mus spretus. By analyzing the segregation pattern of the gene in 75 offspring from an interspecific backcross a single genetic locus, Um, was defined on chromosome 8. Recombination frequency between Um and the co-segregating loci serum esterase 1 (Es-1) and tyrosine aminotransferase (Tat) places Um about 14 centimorgan (cM) distal to Es-1, and 5 cM proximal to Tat. In situ hybridization of uvomorulin ({sup 3}H)cDNA to mouse metaphase chromosomes located the Um locus close to the distal end of chromosome 8 (bands C3-E1). Since uvomorulin is evolutionarily highly conserved, its chromosomal assignment adds an important marker to the mouse genetic map.

  8. Iconicity as structure mapping.

    Science.gov (United States)

    Emmorey, Karen

    2014-09-19

    Linguistic and psycholinguistic evidence is presented to support the use of structure-mapping theory as a framework for understanding effects of iconicity on sign language grammar and processing. The existence of structured mappings between phonological form and semantic mental representations has been shown to explain the nature of metaphor and pronominal anaphora in sign languages. With respect to processing, it is argued that psycholinguistic effects of iconicity may only be observed when the task specifically taps into such structured mappings. In addition, language acquisition effects may only be observed when the relevant cognitive abilities are in place (e.g. the ability to make structural comparisons) and when the relevant conceptual knowledge has been acquired (i.e. information key to processing the iconic mapping). Finally, it is suggested that iconicity is better understood as a structured mapping between two mental representations than as a link between linguistic form and human experience.

  9. Mapping gene clusters within arrayed metagenomic libraries to expand the structural diversity of biomedically relevant natural products.

    Science.gov (United States)

    Owen, Jeremy G; Reddy, Boojala Vijay B; Ternei, Melinda A; Charlop-Powers, Zachary; Calle, Paula Y; Kim, Jeffrey H; Brady, Sean F

    2013-07-16

    Complex microbial ecosystems contain large reservoirs of unexplored biosynthetic diversity. Here we provide an experimental framework and data analysis tool to facilitate the targeted discovery of natural-product biosynthetic gene clusters from the environment. Multiplex sequencing of barcoded PCR amplicons is followed by sequence similarity directed data parsing to identify sequences bearing close resemblance to biosynthetically or biomedically interesting gene clusters. Amplicons are then mapped onto arrayed metagenomic libraries to guide the recovery of targeted gene clusters. When applied to adenylation- and ketosynthase-domain amplicons derived from saturating soil DNA libraries, our analysis pipeline led to the recovery of biosynthetic clusters predicted to encode for previously uncharacterized glycopeptide- and lipopeptide-like antibiotics; thiocoraline-, azinomycin-, and bleomycin-like antitumor agents; and a rapamycin-like immunosuppressant. The utility of the approach is demonstrated by using recovered eDNA sequences to generate glycopeptide derivatives. The experiments described here constitute a systematic interrogation of a soil metagenome for gene clusters capable of encoding naturally occurring derivatives of biomedically relevant natural products. Our results show that previously undetected biosynthetic gene clusters with potential biomedical relevance are very common in the environment. This general process should permit the routine screening of environmental samples for gene clusters capable of encoding the systematic expansion of the structural diversity seen in biomedically relevant families of natural products.

  10. Physical mapping of the Escherichia coli D-serine deaminase region: contiguity of the dsd structural and regulatory genes.

    Science.gov (United States)

    Carothers, A M; McFall, E; Palchaudhuri, S

    1980-04-01

    The genes dsdA, dsdO, and dsdC have been located on a 3.0-kilobase pair (kb) fragment of the Escherichia coli chromosome by a combination of techniques. The loci were first cloned onto lambda and various plasmid vectors. dsd hybrid plasmids were then digested with restriction enzymes, and the fragments were recloned to test for the presence of dsdC or dsdA. In one case, a 4.2-kb restriction fragment containing the dsdA operon was used to form a heteroduplex with a well-defined lambda dsd deoxyribonucleic acid. The results show that dsdA, dsdO, and at least 0.6 kb of dsdC are present on this piece of deoxyribonucleic acid. On the basis of the mapping analysis and the molecular weight of D-serine deaminase, 1.9 kb of the 4.2-kb fragment is accounted for by the three dsd loci. We conclude that dsdO and dsdC are contiguous. A detailed dsd restriction map is presented.

  11. New Technology Makes Gene Mapping Cheaper, Faster

    Science.gov (United States)

    ... https://medlineplus.gov/news/fullstory_164255.html New Technology Makes Gene Mapping Cheaper, Faster: Study Researchers decoded ... they've developed a much cheaper and faster technology for mapping the genetic makeup of a living ...

  12. Structure and genetic mapping of the Cytochrome P450 gene (CYP1A5) in the turkey (Meleagris gallopavo).

    Science.gov (United States)

    Reed, K M; Mendoza, K M; Coulombe, R A

    2007-01-01

    Cytochromes P450 (P450) are a superfamily of membrane-bound hemoproteins that oxidize a large number of endogenous and exogenous compounds. The recently cloned P450 gene (CYP1A5) encodes the primary protein responsible for epoxidation of aflatoxin B(1) (AFB(1)) in the turkey, an animal extremely sensitive to this mycotoxin. Hypersensitivity of turkeys to AFB(1) was first demonstrated by association with 'Turkey X Disease' which caused widespread deaths of turkeys and other poultry throughout Europe in the 1960s, later shown to be caused by AFB(1)-contaminated feed. In this study, comparative genomic approaches were used to selectively amplify and sequence the introns and 3' flanking region of CYP1A5. The structure of the CYP1A5 gene in the turkey is shown to be equivalent to that of the human CYP1A genes with seven exons of 38, 858, 127, 90, 124, 87 and 307 bp, respectively, and six introns. A single nucleotide polymorphism (SNP) in the 3' UTR was used to assign CYP1A5 to turkey linkage group M16 (equivalent to chicken chromosome 10). The results of this study provide the framework for identifying allelic variants of this biochemically important P450 gene in poultry.

  13. A fruit quality gene map of Prunus

    National Research Council Canada - National Science Library

    Ogundiwin, Ebenezer A; Peace, Cameron P; Gradziel, Thomas M; Parfitt, Dan E; Bliss, Fredrick A; Crisosto, Carlos H

    2009-01-01

    ... to marketing and consumption. Here we present an integrated fruit quality gene map of Prunus containing 133 genes putatively involved in the determination of fruit texture, pigmentation, flavor, and chilling injury resistance...

  14. cDNA sequence, gene structure, and cholinesterase-like domains of an esterase from Caenorhabditis elegans mapped to chromosome V.

    Science.gov (United States)

    Fedon, Y; Cousin, X; Toutant, J P; Thierry-Mieg, D; Arpagaus, M

    1993-01-01

    The structure of an esterase gene from Caenorhabditis elegans has been determined by comparison of the sequences in genomic and cDNA clones. The gene was mapped close to the center of chromosome V (1.7 centimorgans to the left of dpy-11) and is therefore distinct from the gut esterase gene ges-1. It possessed 7 short introns. The 5' splice site of intron 3 presented the sequence GC instead of the usual GT that was found in the other six introns. The cDNA was trans-spliced with the short leader SL1. The open reading frame indicated that a protein of 557 aminoacids was encoded. The deduced aminoacid sequence did not present a signal peptide at the N-terminal but a potential N-myristoylation site (GXXXS) provided that the initiator methionine was removed. This protein should therefore remain intracellular. Comparison of this C. elegans sequence to other protein sequences in databases, as well as the analysis of the secondary structure in the protein showed that it belongs to the subgroup of esterases in the alpha/beta hydrolase fold family.

  15. A fruit quality gene map of Prunus

    Directory of Open Access Journals (Sweden)

    Bliss Fredrick A

    2009-12-01

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

  16. Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley: implications for association mapping in germplasm arrays varying in size and structure

    Directory of Open Access Journals (Sweden)

    Muehlbauer Gary J

    2010-12-01

    Full Text Available Abstract Background Considerations in applying association mapping (AM to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Both are under complex genetic control: growth habit is controlled by the epistatic interactions of several genes. For inflorescence type, multiple loss-of-function alleles in one gene lead to the same phenotype. We used these two traits as models for assessing the effectiveness of AM. This research was initiated using the CAP Core germplasm array (n = 102 assembled at the start of the Barley Coordinated Agricultural Project (CAP. This array was genotyped with 4,608 SNPs and we re-sequenced genes involved in morphology, growth and development. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project. This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608. Results Significant associations with SNPs located in the vicinity of the loci involved in growth habit and inflorescence type were found in the CAP Core. Differentiation of true and spurious associations was not possible without a priori knowledge of the candidate genes, based on re-sequencing. The re-sequencing data were used to define allele types of the determinant genes based on functional polymorphisms. In a second round of association mapping, these synthetic markers based on allele types gave the most significant associations. When the synthetic markers were used as anchor points for analysis of interactions, we detected other known-function genes and candidate loci involved in the control of growth habit and inflorescence type. We

  17. Consensus maps of cloned plant cuticle genes

    Institute of Scientific and Technical Information of China (English)

    Eviatar; Nevo

    2010-01-01

    Plant cuticle,which covers the plant surface,consists of waxes and cutins,and is associated with plant drought,cold,and salt resistance.Hitherto,at least 47 genes participating in the formation of plant cuticle have been cloned from Arabidopsis thaliana,Oryza sativa,Zea mays,Ricinus communis,Brassica napus,and Medicago truncatula;and about 85% of them encode proteins sharing above 50% identities with their rice homologous sequences.These cloned cuticle genes were mapped in silico on different chromosomes of rice and Arabidopsis,respectively.The mapping results revealed that plant cuticle genes were not evenly distributed in both genomes.About 40% of the mapped cuticle genes were located on chromosome 1 in Arabidopsis,while 20% of the mapped cuticle genes were located on chromosome 2 but none on chromosome 12 in rice.Some cloned plant cuticle genes have several rice homologous sequences,which might be produced by chromosomal segment duplication.The consensus map of cloned plant cuticle genes will provide important clues for the selection of candidate genes in a positional cloning of an unknown cuticle gene in plants.

  18. Design Process Optimization Based on Design Process Gene Mapping

    Institute of Scientific and Technical Information of China (English)

    LI Bo; TONG Shu-rong

    2011-01-01

    The idea of genetic engineering is introduced into the area of product design to improve the design efficiency. A method towards design process optimization based on the design process gene is proposed through analyzing the correlation between the design process gene and characteristics of the design process. The concept of the design process gene is analyzed and categorized into five categories that are the task specification gene, the concept design gene, the overall design gene, the detailed design gene and the processing design gene in the light of five design phases. The elements and their interactions involved in each kind of design process gene signprocess gene mapping is drawn with its structure disclosed based on its function that process gene.

  19. Analysis of multiplex gene expression maps obtained by voxelation

    Directory of Open Access Journals (Sweden)

    Smith Desmond J

    2009-04-01

    Full Text Available Abstract Background Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions. Results To analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in

  20. Structure, genetic mapping, and function of the cytochrome P450 3A37 gene in the turkey (Meleagris gallopavo).

    Science.gov (United States)

    Rawal, S; Mendoza, K M; Reed, K M; Coulombe, R A

    2009-01-01

    Cytochromes P450 (P450 for protein; CYP for gene) are a superfamily of membrane-bound hemoproteins that oxidize a large number of endogenous and exogenous compounds. Through oxidation reactions, these enzymes are often responsible for the toxic and carcinogenic effects of natural food-borne toxicants, such as the mycotoxin aflatoxin B1 (AFB1). Previous studies in our laboratory have shown that the extreme sensitivity of turkeys to AFB1 is in part explained by efficient hepatic P450-mediated epoxidation to the toxic and reactive metabolite the exo-AFB1-8,9-epoxide (AFBO). Using 3'-5'-rapid amplification of cDNA ends (RACE), we amplified CYP3A37 from turkey liver RNA, the E. coli-expressed protein which efficiently epoxidates AFB(1). Turkey CYP3A37 has an ORF of 1512 bp, and the protein is predicted to be 504 amino acids with 97% homology to chicken CYP3A37. The turkey gene is organized into 13 exons and 12 introns. A single nucleotide polymorphism in the 11th intron was used to assign CYP3A37 to turkey linkage group 10 (corresponding to chicken chromosome 14, GGA14). Because of the important role of P450s in the extreme sensitivity of turkeys to the toxic effects of AFB(1), this study will contribute to the identifying allelic variants of this important gene in poultry. Copyright 2009 S. Karger AG, Basel.

  1. Mapping genes on human chromosome 20

    Energy Technology Data Exchange (ETDEWEB)

    Keith, T.; Phipps, P.; Serino, K. [Collaborative Research, Inc., Waltham, MA (United States)] [and others

    1994-09-01

    While a substantial number of genes have been physically localized to human chromosome 20, few have been genetically mapped. In the process of developing a genetic linkage map of chromosome 20, we have mapped microsatellite polymorphisms associated with six genes. Three of these had highly informative polymorphisms (greater than 0.70) that were originally identified by other investigators. These include avian sarcoma oncogene homolog (SRC), ribophorin II (RPN2), and phosphoenolpyruvate carboxykinase (PCK1). Polymorphisms associated with two genes were determined following a screen of their DNA sequences in GenBank. These include dinucleotide polymorphisms in introl II of cystatin c (CST3) and in the promoter region of neuroendocrine convertase 2 (NEC2) with heterozygosities of 0.52 and 0.54, respectively. A sixth gene, prodynorphin (PDYN) was mapped following the identification of a dinucleotide repeat polymorphism (heterozygosity of 0.35) in a cosmid subclone from a YAC homologous to the original phage clone. CA-positive cosmid subclones from a YAC for an additional gene, guanine nucleotide binding protein, alpha (GNAS10), have been identified and sequencing is in progress. Similar efforts were utilized to identify a microsatellite polymorphism from a half-YAC cloned by W. Brown and localized by FISH to 20pter. This polymorphism is highly informative, with a heterozygosity of 0.83, and serves to delimit the genetic map of the short arm of this chromosome.

  2. Physical mapping of the Escherichia coli D-serine deaminase region: contiguity of the dsd structural and regulatory genes.

    OpenAIRE

    Carothers, A M; McFall, E; Palchaudhuri, S

    1980-01-01

    The genes dsdA, dsdO, and dsdC have been located on a 3.0-kilobase pair (kb) fragment of the Escherichia coli chromosome by a combination of techniques. The loci were first cloned onto lambda and various plasmid vectors. dsd hybrid plasmids were then digested with restriction enzymes, and the fragments were recloned to test for the presence of dsdC or dsdA. In one case, a 4.2-kb restriction fragment containing the dsdA operon was used to form a heteroduplex with a well-defined lambda dsd deox...

  3. Mutated Genes in Schizophrenia Map to Brain Networks

    Science.gov (United States)

    ... Matters NIH Research Matters August 12, 2013 Mutated Genes in Schizophrenia Map to Brain Networks Schizophrenia networks in the ... in People with Serious Mental Illness Clues for Schizophrenia in Rare Gene Glitch Recognizing Schizophrenia: Seeking Clues to a Difficult ...

  4. A physical map of 30,000 human genes.

    Science.gov (United States)

    Deloukas, P; Schuler, G D; Gyapay, G; Beasley, E M; Soderlund, C; Rodriguez-Tomé, P; Hui, L; Matise, T C; McKusick, K B; Beckmann, J S; Bentolila, S; Bihoreau, M; Birren, B B; Browne, J; Butler, A; Castle, A B; Chiannilkulchai, N; Clee, C; Day, P J; Dehejia, A; Dibling, T; Drouot, N; Duprat, S; Fizames, C; Fox, S; Gelling, S; Green, L; Harrison, P; Hocking, R; Holloway, E; Hunt, S; Keil, S; Lijnzaad, P; Louis-Dit-Sully, C; Ma, J; Mendis, A; Miller, J; Morissette, J; Muselet, D; Nusbaum, H C; Peck, A; Rozen, S; Simon, D; Slonim, D K; Staples, R; Stein, L D; Stewart, E A; Suchard, M A; Thangarajah, T; Vega-Czarny, N; Webber, C; Wu, X; Hudson, J; Auffray, C; Nomura, N; Sikela, J M; Polymeropoulos, M H; James, M R; Lander, E S; Hudson, T J; Myers, R M; Cox, D R; Weissenbach, J; Boguski, M S; Bentley, D R

    1998-10-23

    A map of 30,181 human gene-based markers was assembled and integrated with the current genetic map by radiation hybrid mapping. The new gene map contains nearly twice as many genes as the previous release, includes most genes that encode proteins of known function, and is twofold to threefold more accurate than the previous version. A redesigned, more informative and functional World Wide Web site (www.ncbi.nlm.nih.gov/genemap) provides the mapping information and associated data and annotations. This resource constitutes an important infrastructure and tool for the study of complex genetic traits, the positional cloning of disease genes, the cross-referencing of mammalian genomes, and validated human transcribed sequences for large-scale studies of gene expression.

  5. MapGene2Chrom, a tool to draw gene physical map based on Perl and SVG languages.

    Science.gov (United States)

    Jiangtao, Chao; Yingzhen, Kong; Qian, Wang; Yuhe, Sun; Daping, Gong; Jing, Lv; Guanshan, Liu

    2015-01-01

    Genetic linkage map is helpful for analysis on heredity of some gene families and map-based gene cloning because of its simple and elegant manifestation. One software is in need to draw a gene physical map, which shows a manner similar to the genetic linkage map, based on the relative physical distance between genes. Although some tools like GBrowse and MapViewer etc. are available to draw gene physical map, there are obvious limitations for them: (1) the data need to be decorated in advance; (2) users can't modify results. Therefore, we developed a bio-assisted mapping software--MapGene2Chrom with PC and web versions, which is based on Perl and SVG languages. The software can be used to draw the corresponding physical map quickly in SVG format based on the input data. It will become a useful tool for drawing gene physical map with the advantages of simple input data format, easily modified output and very good portability.

  6. HapMap and mapping genes for cardiovascular disease.

    Science.gov (United States)

    Musunuru, Kiran; Kathiresan, Sekar

    2008-10-01

    A key goal of biomedical science is to understand why individuals differ in their susceptibility to disease. Family history is among the established risk factors for most forms of cardiovascular disease, in part because inherited DNA sequence variants play a causal role in disease susceptibility. Consequently, the search for these variants has intensified over the past decade. One class of DNA sequence variants takes the form of single nucleotide changes(single nucleotide polymorphisms, or SNPs), usually with two variants or alleles for each SNP. SNPs are scattered throughout the 23 pairs of chromosomes of the human genome, and roughly 11 million common polymorphisms (ie,those > 1% frequency) are estimated to exist. A combination of SNP alleles along a chromosome is termed a haplotype. The International Haplotype Map Project was designed to create a public genome-wide database of common SNPs and, consequently, enable systematic studies of most common SNPs for their potential role in human disease. We review the following: (1) the concept of linkage disequilibrium orallelic association, (2) the HapMap project, and (3) several examples of the utility of HapMap data in genetic mapping for cardiovascular disease phenotypes.

  7. Assessing the Structure of a Concept Map

    Science.gov (United States)

    Giouvanakis, Thanasis; Samaras, Haido; Kehris, Evangelos; Mpakavos, Asterios

    2013-01-01

    This paper presents a framework for the evaluation of concept maps. We focus on supporting the student in dealing with ill-structured and complex problems. We argue that these problems require the application of "the modularity approach." In view of this, the paper describes ways of providing student support for the implementation of…

  8. Saliency Mapping Enhanced by Structure Tensor

    Directory of Open Access Journals (Sweden)

    Zhiyong He

    2015-01-01

    Full Text Available We propose a novel efficient algorithm for computing visual saliency, which is based on the computation architecture of Itti model. As one of well-known bottom-up visual saliency models, Itti method evaluates three low-level features, color, intensity, and orientation, and then generates multiscale activation maps. Finally, a saliency map is aggregated with multiscale fusion. In our method, the orientation feature is replaced by edge and corner features extracted by a linear structure tensor. Following it, these features are used to generate contour activation map, and then all activation maps are directly combined into a saliency map. Compared to Itti method, our method is more computationally efficient because structure tensor is more computationally efficient than Gabor filter that is used to compute the orientation feature and our aggregation is a direct method instead of the multiscale operator. Experiments on Bruce’s dataset show that our method is a strong contender for the state of the art.

  9. 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.

  10. Mapping Mammary Carcinoma Suppressor Genes in the Laboratory Rat

    Science.gov (United States)

    1997-07-01

    AD GRANT NUMBER DAMDI7-94-J-4040 TITLE: Mapping Mammary Carcinoma Suppressor Genes in the Laboratory Rat PRINCIPAL INVESTIGATOR: Michael Gould, Ph.D...Carcinoma Suppressor Genes in the Laboratory Rat DAMDI7-94-J-4040 6. AUTHOR(S) Michael Gould, Ph.D. Hong Lan, Ph.D. 7. PERFORMING ORGANIZATION NAME(S) AND

  11. Mapping of the Mouse Actin Capping Protein Beta Subunit Gene

    Directory of Open Access Journals (Sweden)

    Cooper John A

    2000-07-01

    Full Text Available Abstract Background Capping protein (CP, a heterodimer of α and β subunits, is found in all eukaryotes. CP binds to the barbed ends of actin filaments in vitro and controls actin assembly and cell motility in vivo. Vertebrates have three isoforms of CPβ produced by alternatively splicing from one gene; lower organisms have one gene and one isoform. Results We isolated genomic clones corresponding to the β subunit of mouse CP and identified its chromosomal location by interspecies backcross mapping. Conclusions The CPβ gene (Cappb1 mapped to Chromosome 4 between Cdc42 and D4Mit312. Three mouse mutations, snubnose, curly tail, and cribriform degeneration, map in the vicinity of the β gene.

  12. Methodology optimizing SAGE library tag-to-gene mapping: application to Leishmania

    Directory of Open Access Journals (Sweden)

    Smandi Sondos

    2012-01-01

    Full Text Available Abstract Background Leishmaniasis are widespread parasitic-diseases with an urgent need for more active and less toxic drugs and for effective vaccines. Understanding the biology of the parasite especially in the context of host parasite interaction is a crucial step towards such improvements in therapy and control. Several experimental approaches including SAGE (Serial analysis of gene expression have been developed in order to investigate the parasite transcriptome organisation and plasticity. Usual SAGE tag-to-gene mapping techniques are inadequate because almost all tags are normally located in the 3'-UTR outside the CDS, whereas most information available for Leishmania transcripts is restricted to the CDS predictions. The aim of this work is to optimize a SAGE libraries tag-to-gene mapping technique and to show how this development improves the understanding of Leishmania transcriptome. Findings The in silico method implemented herein was based on mapping the tags to Leishmania genome using BLAST then mapping the tags to their gene using a data-driven probability distribution. This optimized tag-to-gene mappings improved the knowledge of Leishmania genome structure and transcription. It allowed analyzing the expression of a maximal number of Leishmania genes, the delimitation of the 3' UTR of 478 genes and the identification of biological processes that are differentially modulated during the promastigote to amastigote differentiation. Conclusion The developed method optimizes the assignment of SAGE tags in trypanosomatidae genomes as well as in any genome having polycistronic transcription and small intergenic regions.

  13. Mapping the semantic structure of cognitive neuroscience.

    Science.gov (United States)

    Beam, Elizabeth; Appelbaum, L Gregory; Jack, Jordynn; Moody, James; Huettel, Scott A

    2014-09-01

    Cognitive neuroscience, as a discipline, links the biological systems studied by neuroscience to the processing constructs studied by psychology. By mapping these relations throughout the literature of cognitive neuroscience, we visualize the semantic structure of the discipline and point to directions for future research that will advance its integrative goal. For this purpose, network text analyses were applied to an exhaustive corpus of abstracts collected from five major journals over a 30-month period, including every study that used fMRI to investigate psychological processes. From this, we generate network maps that illustrate the relationships among psychological and anatomical terms, along with centrality statistics that guide inferences about network structure. Three terms--prefrontal cortex, amygdala, and anterior cingulate cortex--dominate the network structure with their high frequency in the literature and the density of their connections with other neuroanatomical terms. From network statistics, we identify terms that are understudied compared with their importance in the network (e.g., insula and thalamus), are underspecified in the language of the discipline (e.g., terms associated with executive function), or are imperfectly integrated with other concepts (e.g., subdisciplines like decision neuroscience that are disconnected from the main network). Taking these results as the basis for prescriptive recommendations, we conclude that semantic analyses provide useful guidance for cognitive neuroscience as a discipline, both by illustrating systematic biases in the conduct and presentation of research and by identifying directions that may be most productive for future research.

  14. Simultaneous mapping of multiple gene loci with pooled segregants.

    Directory of Open Access Journals (Sweden)

    Jürgen Claesen

    Full Text Available The analysis of polygenic, phenotypic characteristics such as quantitative traits or inheritable diseases remains an important challenge. It requires reliable scoring of many genetic markers covering the entire genome. The advent of high-throughput sequencing technologies provides a new way to evaluate large numbers of single nucleotide polymorphisms (SNPs as genetic markers. Combining the technologies with pooling of segregants, as performed in bulked segregant analysis (BSA, should, in principle, allow the simultaneous mapping of multiple genetic loci present throughout the genome. The gene mapping process, applied here, consists of three steps: First, a controlled crossing of parents with and without a trait. Second, selection based on phenotypic screening of the offspring, followed by the mapping of short offspring sequences against the parental reference. The final step aims at detecting genetic markers such as SNPs, insertions and deletions with next generation sequencing (NGS. Markers in close proximity of genomic loci that are associated to the trait have a higher probability to be inherited together. Hence, these markers are very useful for discovering the loci and the genetic mechanism underlying the characteristic of interest. Within this context, NGS produces binomial counts along the genome, i.e., the number of sequenced reads that matches with the SNP of the parental reference strain, which is a proxy for the number of individuals in the offspring that share the SNP with the parent. Genomic loci associated with the trait can thus be discovered by analyzing trends in the counts along the genome. We exploit the link between smoothing splines and generalized mixed models for estimating the underlying structure present in the SNP scatterplots.

  15. Differential Measurement Periodontal Structures Mapping System

    Science.gov (United States)

    Companion, John A. (Inventor)

    1998-01-01

    This invention relates to a periodontal structure mapping system employing a dental handpiece containing first and second acoustic sensors for locating the Cemento-Enamel Junction (CEJ) and measuring the differential depth between the CEJ and the bottom of the periodontal pocket. Measurements are taken at multiple locations on each tooth of a patient, observed, analyzed by an optical analysis subsystem, and archived by a data storage system for subsequent study and comparison with previous and subsequent measurements. Ultrasonic transducers for the first and second acoustic sensors are contained within the handpiece and in connection with a control computer. Pressurized water is provided for the depth measurement sensor and a linearly movable probe sensor serves as the sensor for the CEJ finder. The linear movement of the CEJ sensor is obtained by a control computer actuated by the prober. In an alternate embodiment, the CEJ probe is an optical fiber sensor with appropriate analysis structure provided therefor.

  16. Mapping and localization of susceptible genes in asthma

    Institute of Scientific and Technical Information of China (English)

    GU Ming-liang; ZHAO Jing

    2011-01-01

    Objective To elucidate the development of mapping and localization of susceptible genes on chromosomes to asthma related phenotypes.Data sources Published articles about susceptibility genes for asthma related phenotypes were selected using PubMed.Study selection Using methods of candidate gene positional clone and genome-wide scan with linkage and association analysis to determine the location in the genome of susceptibility genes to asthma and asthma related phenotypes.Results There are multiple regions in the genome harboring susceptibility genes to asthma and asthma relatedphenotypes, including chromosomes 5, 11, 12, 6, 2, 3, 13, 7, 14, 9, 19 and 17. Many of these regions contain candidate genes involved in asthma development and progression. Some susceptible genes may affect the phenotype expression or response to therapy. In addition, the interaction of multiple genes with the environment may contribute to the susceptibility to asthma.Conclusions As an essential step toward cloning the susceptible genes to asthma, fine mapping and localization onchromosomes are definitely needed. Novel powerful tools for gene discovery and the integration of genetics, biology and bioinformatics should be pursued.

  17. Mapping Interactive Cancer Susceptibility Genes in Prostate Cancer

    Science.gov (United States)

    2007-04-01

    further analysis around this FHIT marker. Under the assumption of a recessive model, we attempted to narrow the disease interval by examining key meiotic ...examining key meiotic recombinants. A and B, physical map illustrating marker and FHIT exon locations. Solid bar, FHIT gene boundary; vertical bars, exons 5...gene, spanning the chromosome 3p14.2 fragile site and renal carcinoma-associated t(3;8) breakpoint, is abnormal in digestive tract cancers. Cell 1996;84

  18. 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.

  19. Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

    Directory of Open Access Journals (Sweden)

    2006-05-01

    Full Text Available Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such studies, we summarize here results of an investigation of one of the first of these technologies to be publicly available, the Affymetrix GeneChip Human Mapping 100K set of single nucleotide polymorphisms (SNPs. In a systematic analysis of the pattern and distribution of SNPs in the Mapping 100K set, we find that SNPs in this set are undersampled from coding regions (both nonsynonymous and synonymous and oversampled from regions outside genes, relative to SNPs in the overall HapMap database. In addition, we utilize a novel multilocus linkage disequilibrium (LD coefficient based on information content (analogous to the information content scores commonly used for linkage mapping that is equivalent to the familiar measure r2 in the special case of two loci. Using this approach, we are able to summarize for any subset of markers, such as the Affymetrix Mapping 100K set, the information available for association mapping in that subset, relative to the information available in the full set of markers included in the HapMap, and highlight circumstances in which this multilocus measure of LD provides substantial additional insight about the haplotype structure in a region over pairwise measures of LD.

  20. How-to-Do-It. An Exercise in Gene Mapping.

    Science.gov (United States)

    Seidel-Rogol, Bonnie L.

    1990-01-01

    Described is a laboratory exercise designed to introduce students to the theory and practice of gene mapping including RNA extraction, sucrose density gradient centrifugation, labelling of nucleic acids in vitro, DNA extraction, digestion of DNA with restriction enzymes, and the southern hybridization analysis. Procedures and sample results are…

  1. Fish on avian lampbrush chromosomes produces higher resolution gene mapping

    NARCIS (Netherlands)

    Galkina, S.A.; Deryusheva, S.; Fillon, V.; Vignal, A.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Rodionov, A.V.; Gaginskaya, E.

    2006-01-01

    Giant lampbrush chromosomes, which are characteristic of the diplotene stage of prophase I during avian oogenesis, represent a very promising system for precise physical gene mapping. We applied 35 chicken BAC and 4 PAC clones to both mitotic metaphase chromosomes and meiotic lampbrush chromosomes

  2. Fish on avian lampbrush chromosomes produces higher resolution gene mapping

    NARCIS (Netherlands)

    Galkina, S.A.; Deryusheva, S.; Fillon, V.; Vignal, A.; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Rodionov, A.V.; Gaginskaya, E.

    2006-01-01

    Giant lampbrush chromosomes, which are characteristic of the diplotene stage of prophase I during avian oogenesis, represent a very promising system for precise physical gene mapping. We applied 35 chicken BAC and 4 PAC clones to both mitotic metaphase chromosomes and meiotic lampbrush chromosomes o

  3. Mapping of the silver gene in mink and its association with the dilution gene in dog

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Christensen, Knud

    2007-01-01

    recessive mutations within mink fur farming being part of some of the popular color types which combine more recessive mutations. We report there the mapping of the 'silver' gene on MVI3 by means of the first linkage genetic map in the American mink (Mustela vison). A Canis familiaris BAC clone containing...

  4. Linkage mapping of the human CSF2 and IL3 genes

    Energy Technology Data Exchange (ETDEWEB)

    Frolova, E.I.; Dolganov, G.M.; Mazo, I.A.; Smirnov, D.V. (M.M. Shemyakin Inst. of Bio-organic Chemistry, Moscow (USSR)); Copeland, P.; Stewart, C.; Dean, M. (Program Resources, Inc./DynCorp., Research Triangle Park, NC (United States)); O' Brien, S.J. (National Cancer Inst., Frederick, MD (United States))

    1991-06-01

    Interleukin 3 (encoded by the IL3 gene) and granulocyte-macrophage colony-stimulating factor (encoded by the CSF2 gene) are small secreted polypeptides that bind to specific cell surface receptors and regulate the growth, gene expression, and differentiation of many of the hematopoietic cell lineages, particularly nonlymphoid cells. The IL3 and CSF2 genes have been cloned and mapped to human chromosome bands 5q23-31. Only 10 kilobases of dna separates the two genes, suggesting that they have a common origin and/or regulation. The authors have cloned 70 kilobases of genomic DNA that includes the IL3 and CSF2 genes, as well as flanking sequences, and report a physical map of this region. Several unique-sequence DNA segments have been identified in this region, and one of these fragments detects two restriction fragment length polymorphisms in DNA from unrelated Caucasians. Segregation of these DNA polymorphisms was followed in the Centre Etude du Polymorphisme Humaine (CEPH) panel of 40 large three-generation pedigrees, and linkage was detected with 17 genetic markers previously typed in these families. Multipoint linkage analysis permits the placement of the region containing the IL3 and CSF2 structural genes on the recombination-genetic linkage map of chromosome 5q and thereby allows the role of these genes in leukemogenesis to be more critically examined.

  5. Chromatin structure regulates gene conversion.

    Directory of Open Access Journals (Sweden)

    W Jason Cummings

    2007-10-01

    Full Text Available Homology-directed repair is a powerful mechanism for maintaining and altering genomic structure. We asked how chromatin structure contributes to the use of homologous sequences as donors for repair using the chicken B cell line DT40 as a model. In DT40, immunoglobulin genes undergo regulated sequence diversification by gene conversion templated by pseudogene donors. We found that the immunoglobulin Vlambda pseudogene array is characterized by histone modifications associated with active chromatin. We directly demonstrated the importance of chromatin structure for gene conversion, using a regulatable experimental system in which the heterochromatin protein HP1 (Drosophila melanogaster Su[var]205, expressed as a fusion to Escherichia coli lactose repressor, is tethered to polymerized lactose operators integrated within the pseudo-Vlambda donor array. Tethered HP1 diminished histone acetylation within the pseudo-Vlambda array, and altered the outcome of Vlambda diversification, so that nontemplated mutations rather than templated mutations predominated. Thus, chromatin structure regulates homology-directed repair. These results suggest that histone modifications may contribute to maintaining genomic stability by preventing recombination between repetitive sequences.

  6. High-resolution gene mapping using admixture linkage disequilibrium

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    This note reports simulation study on the rate of decay in linkage dis equilibrium (LD) in mixed populations over multiple discrete generations and explores the usefulness of the LD analysis in high-resolution gene mapping. The results indicate that the smaller the recombination fraction and the fewer generati ons since admixtureevent, the higher power of the approach in gene mapping. The expected estimate of recombination fraction would give an estimate that is slig htly biased upwards, if relevant genes are in tight linkage. The estimated recom bination fraction is usually larger than the true value within 2-5 generations. From generations 10-20, the mean estimates are in good agreement with the true value. The method presented here enables estimation of means and corresponding confidence intervals of the recombination fraction at any number of generations.

  7. Structure-mapping in metaphor comprehension.

    Science.gov (United States)

    Wolff, Phillip; Gentner, Dedre

    2011-01-01

    Metaphor has a double life. It can be described as a directional process in which a stable, familiar base domain provides inferential structure to a less clearly specified target. But metaphor is also described as a process of finding commonalities, an inherently symmetric process. In this second view, both concepts may be altered by the metaphorical comparison. Whereas most theories of metaphor capture one of these aspects, we offer a model based on structure-mapping that captures both sides of metaphor processing. This predicts (a) an initial processing stage of symmetric alignment; and (b) a later directional phase in which inferences are projected to the target. To test these claims, we collected comprehensibility judgments for forward (e.g., "A rumor is a virus") and reversed ("A virus is a rumor") metaphors at early and late stages of processing, using a deadline procedure. We found an advantage for the forward direction late in processing, but no directional preference early in processing. Implications for metaphor theory are discussed.

  8. Expression and mapping of anthocyanin biosynthesis genes in carrot.

    Science.gov (United States)

    Yildiz, Mehtap; Willis, David K; Cavagnaro, Pablo F; Iorizzo, Massimo; Abak, Kazim; Simon, Philipp W

    2013-07-01

    Anthocyanin gene expression has been extensively studied in leaves, fruits and flowers of numerous plants. Little, however, is known about anthocyanin accumulation in roots of carrots or other species. We quantified expression of six anthocyanin biosynthetic genes [phenylalanine ammonia-lyase (PAL3), chalcone synthase (CHS1), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR1), leucoanthocyanidin dioxygenase (LDOX2), and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT)] in three carrot inbreds with contrasting root color: solid purple (phloem and xylem); purple outer phloem/orange xylem; and orange phloem and xylem. Transcripts for five of these genes (CHS1, DFR1, F3H, LDOX2, PAL3) accumulated at high levels in solid purple carrots, less in purple-orange carrot, and low or no transcript in orange carrots. Gene expression coincided with anthocyanin accumulation. In contrast, UFGT expression was comparable in purple and orange carrots and relatively unchanged during root development. In addition, five anthocyanin biosynthesis genes [FLS1 (flavonol synthase), F3H, LDOX2, PAL3, and UFGT] and three anthocyanin transcription factors (DcEFR1, DcMYB3 and DcMYB5) were mapped in a population segregating for the P 1 locus that conditions purple root color. P 1 mapped to chromosome 3 and of the eight anthocyanin biosynthesis genes, only F3H and FLS1 were linked to P 1. The gene expression and mapping data suggest a coordinated regulatory control of anthocyanin expression in carrot root and establish a framework for studying the anthocyanin pathway in carrots, and they also suggest that none of the genes evaluated is a candidate for P 1.

  9. Tag SNP selection for candidate gene association studies using HapMap and gene resequencing data.

    Science.gov (United States)

    Xu, Zongli; Kaplan, Norman L; Taylor, Jack A

    2007-10-01

    HapMap provides linkage disequilibrium (LD) information on a sample of 3.7 million SNPs that can be used for tag SNP selection in whole-genome association studies. HapMap can also be used for tag SNP selection in candidate genes, although its performance has yet to be evaluated against gene resequencing data, where there is near-complete SNP ascertainment. The Environmental Genome Project (EGP) is the largest gene resequencing effort to date with over 500 resequenced genes. We used HapMap data to select tag SNPs and calculated the proportions of common SNPs (MAF>or=0.05) tagged (rho2>or=0.8) for each of 127 EGP Panel 2 genes where individual ethnic information was available. Median gene-tagging proportions are 50, 80 and 74% for African, Asian, and European groups, respectively. These low gene-tagging proportions may be problematic for some candidate gene studies. In addition, although HapMap targeted nonsynonymous SNPs (nsSNPs), we estimate only approximately 30% of nonsynonymous SNPs in EGP are in high LD with any HapMap SNP. We show that gene-tagging proportions can be improved by adding a relatively small number of tag SNPs that were selected based on resequencing data. We also demonstrate that ethnic-mixed data can be used to improve HapMap gene-tagging proportions, but are not as efficient as ethnic-specific data. Finally, we generalized the greedy algorithm proposed by Carlson et al (2004) to select tag SNPs for multiple populations and implemented the algorithm into a freely available software package mPopTag.

  10. STRUCTURE OF KELLER MAPPINGS, TWO-DIMENSIONAL CASE

    Directory of Open Access Journals (Sweden)

    V. V. Starkov

    2017-06-01

    Full Text Available A Keller map is a polynomial mapping ƒ : Rⁿ → Rⁿ (or Cⁿ → Cⁿ with the Jacobian J_ƒ ≡ const ≠ 0. The Jacobian conjecture was first formulated by O. N. Keller in 1939. In the modern form it supposes injectivity of a Keller map. Earlier, in the case n = 2, the author gave a complete description of Keller maps with deg ƒ ≤ 3. This paper is devoted to the description of Keller maps for which deg ƒ ≤ 4. Significant differences between these two cases are revealed, which, in particular, indicate the irregular structure of Keller maps even in the case of n = 2.

  11. Chromosome mapping of dragline silk genes in the genomes of widow spiders (Araneae, Theridiidae.

    Directory of Open Access Journals (Sweden)

    Yonghui Zhao

    Full Text Available With its incredible strength and toughness, spider dragline silk is widely lauded for its impressive material properties. Dragline silk is composed of two structural proteins, MaSp1 and MaSp2, which are encoded by members of the spidroin gene family. While previous studies have characterized the genes that encode the constituent proteins of spider silks, nothing is known about the physical location of these genes. We determined karyotypes and sex chromosome organization for the widow spiders, Latrodectus hesperus and L. geometricus (Araneae, Theridiidae. We then used fluorescence in situ hybridization to map the genomic locations of the genes for the silk proteins that compose the remarkable spider dragline. These genes included three loci for the MaSp1 protein and the single locus for the MaSp2 protein. In addition, we mapped a MaSp1 pseudogene. All the MaSp1 gene copies and pseudogene localized to a single chromosomal region while MaSp2 was located on a different chromosome of L. hesperus. Using probes derived from L. hesperus, we comparatively mapped all three MaSp1 loci to a single region of a L. geometricus chromosome. As with L. hesperus, MaSp2 was found on a separate L. geometricus chromosome, thus again unlinked to the MaSp1 loci. These results indicate orthology of the corresponding chromosomal regions in the two widow genomes. Moreover, the occurrence of multiple MaSp1 loci in a conserved gene cluster across species suggests that MaSp1 proliferated by tandem duplication in a common ancestor of L. geometricus and L. hesperus. Unequal crossover events during recombination could have given rise to the gene copies and could also maintain sequence similarity among gene copies over time. Further comparative mapping with taxa of increasing divergence from Latrodectus will pinpoint when the MaSp1 duplication events occurred and the phylogenetic distribution of silk gene linkage patterns.

  12. A brain region-specific predictive gene map for autism derived by profiling a reference gene set.

    Directory of Open Access Journals (Sweden)

    Ajay Kumar

    Full Text Available Molecular underpinnings of complex psychiatric disorders such as autism spectrum disorders (ASD remain largely unresolved. Increasingly, structural variations in discrete chromosomal loci are implicated in ASD, expanding the search space for its disease etiology. We exploited the high genetic heterogeneity of ASD to derive a predictive map of candidate genes by an integrated bioinformatics approach. Using a reference set of 84 Rare and Syndromic candidate ASD genes (AutRef84, we built a composite reference profile based on both functional and expression analyses. First, we created a functional profile of AutRef84 by performing Gene Ontology (GO enrichment analysis which encompassed three main areas: 1 neurogenesis/projection, 2 cell adhesion, and 3 ion channel activity. Second, we constructed an expression profile of AutRef84 by conducting DAVID analysis which found enrichment in brain regions critical for sensory information processing (olfactory bulb, occipital lobe, executive function (prefrontal cortex, and hormone secretion (pituitary. Disease specificity of this dual AutRef84 profile was demonstrated by comparative analysis with control, diabetes, and non-specific gene sets. We then screened the human genome with the dual AutRef84 profile to derive a set of 460 potential ASD candidate genes. Importantly, the power of our predictive gene map was demonstrated by capturing 18 existing ASD-associated genes which were not part of the AutRef84 input dataset. The remaining 442 genes are entirely novel putative ASD risk genes. Together, we used a composite ASD reference profile to generate a predictive map of novel ASD candidate genes which should be prioritized for future research.

  13. Mapping and annotating obesity-related genes in pig and human genomes.

    Science.gov (United States)

    Martelli, Pier Luigi; Fontanesi, Luca; Piovesan, Damiano; Fariselli, Piero; Casadio, Rita

    2014-01-01

    Background. Obesity is a major health problem in both developed and emerging countries. Obesity is a complex disease whose etiology involves genetic factors in strong interplay with environmental determinants and lifestyle. The discovery of genetic factors and biological pathways underlying human obesity is hampered by the difficulty in controlling the genetic background of human cohorts. Animal models are then necessary to further dissect the genetics of obesity. Pig has emerged as one of the most attractive models, because of the similarity with humans in the mechanisms regulating the fat deposition. Results. We collected the genes related to obesity in humans and to fat deposition traits in pig. We localized them on both human and pig genomes, building a map useful to interpret comparative studies on obesity. We characterized the collected genes structurally and functionally with BAR+ and mapped them on KEGG pathways and on STRING protein interaction network. Conclusions. The collected set consists of 361 obesity related genes in human and pig genomes. All genes were mapped on the human genome, and 54 could not be localized on the pig genome (release 2012). Only for 3 human genes there is no counterpart in pig, confirming that this animal is a good model for human obesity studies. Obesity related genes are mostly involved in regulation and signaling processes/pathways and relevant connection emerges between obesity-related genes and diseases such as cancer and infectious diseases.

  14. The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science.

    Science.gov (United States)

    Klie, Sebastian; Nikoloski, Zoran

    2012-01-01

    Since the introduction of the Gene Ontology (GO), the analysis of high-throughput data has become tightly coupled with the use of ontologies to establish associations between knowledge and data in an automated fashion. Ontologies provide a systematic description of knowledge by a controlled vocabulary of defined structure in which ontological concepts are connected by pre-defined relationships. In plant science, MapMan and GO offer two alternatives for ontology-driven analyses. Unlike GO, initially developed to characterize microbial systems, MapMan was specifically designed to cover plant-specific pathways and processes. While the dependencies between concepts in MapMan are modeled as a tree, in GO these are captured in a directed acyclic graph. Therefore, the difference in ontologies may cause discrepancies in data reduction, visualization, and hypothesis generation. Here provide the first systematic comparative analysis of GO and MapMan for the case of the model plant species Arabidopsis thaliana (Arabidopsis) with respect to their structural properties and difference in distributions of information content. In addition, we investigate the effect of the two ontologies on the specificity and sensitivity of automated gene function prediction via the coupling of co-expression networks and the guilt-by-association principle. Automated gene function prediction is particularly needed for the model plant Arabidopsis in which only half of genes have been functionally annotated based on sequence similarity to known genes. The results highlight the need for structured representation of species-specific biological knowledge, and warrants caution in the design principles employed in future ontologies.

  15. The choice between MapMan and Gene Ontology for automated gene function prediction in plant science

    Directory of Open Access Journals (Sweden)

    Sebastian eKlie

    2012-06-01

    Full Text Available Since the introduction of the Gene Ontology (GO, the analysis of high-throughput data has become tightly coupled with the use of ontologies to establish associations between knowledge and data in an automated fashion. Ontologies provide a systematic description of knowledge by a controlled vocabulary of defined structure in which ontological concepts are connected by pre-defined relationships. In plant science, MapMan and GO offer two alternatives for ontology-driven analyses. Unlike GO, initially developed to characterize microbial systems, MapMan was specifically designed to cover plant-specific pathways and processes. While the dependencies between concepts in MapMan are modeled as a tree, in GO these are captured in a directed acyclic graph. Therefore, the difference in ontologies may cause discrepancies in data reduction, visualization, and hypothesis generation. Here provide the first systematic comparative analysis of GO and MapMan for the case of the model plant species Arabidopsis thaliana (Arabidopsis with respect to their structural properties and difference in distributions of information content. In addition, we investigate the effect of the two ontologies on the specificity and sensitivity of automated gene function prediction via the coupling of coexpression networks and the guilt-by-association principle. Automated gene function prediction is particularly needed for the model plant Arabidopsis in which only half of genes have been functionally annotated based on sequence similarity to known genes. The results highlight the need for structured representation of species-specific biological knowledge, and warrants caution in the design principles employed in future ontologies.

  16. Mapping the structure of animal behavior

    Science.gov (United States)

    Berman, Gordon; Choi, Daniel; Bialek, William; Shaevitz, Joshua

    2014-03-01

    Most animals possess the ability to actuate a vast diversity of movements, ostensibly constrained only by morphology and physics. In practice, however, a frequent assumption in behavioral science is that most of an animal's activities can be described in terms of a small set of stereotyped motifs. Here we introduce a method for mapping the behavioral space of organisms, relying only upon the underlying structure of postural movement data to organize and classify behaviors. Applying our method to movies of size closely-related species of freely-behaving fruit flies, we find a wide variety of non-stereotyped and stereo-typed behaviors, spanning a wide range of time scales. We observe subtle behavioral differences between these species, identifying the some of the effects of phylogenic history on behavior. Moreover, we find that the transitions between the observed behaviors display a hierarchical syntax, with similar behaviors likely to transition between each other, but with a long time scale of memory. These results suggest potential mechanisms for the evolution of behavior and for the neural control of movements.

  17. Bifurcation Structures in a Bimodal Piecewise Linear Map

    Directory of Open Access Journals (Sweden)

    Anastasiia Panchuk

    2017-05-01

    Full Text Available In this paper we present an overview of the results concerning dynamics of a piecewise linear bimodal map. The organizing principles of the bifurcation structures in both regular and chaotic domains of the parameter space of the map are discussed. In addition to the previously reported structures, a family of regions closely related to the so-called U-sequence is described. The boundaries of distinct regions belonging to these structures are obtained analytically using the skew tent map and the map replacement technique.

  18. Fast Mapping Verb Meaning from Argument Structure

    Science.gov (United States)

    Johnson, Valerie E.

    2010-01-01

    Purpose: To examine lexical knowledge in children through a fast mapping task. Method: This study compared the performance of 60 African American English-speaking and general American English-speaking children between the ages of 4 and 6 years. They were presented with a comprehension task involving the fast mapping of novel verbs in 4 different…

  19. Identification and Gene Mapping of Completely Dominant Earliness in Rice

    Institute of Scientific and Technical Information of China (English)

    DENG Xiao-jian; ZHOU Kai-da; LI Ren-duan; CHUN Ze; LI Ping; WANG Wen-ming; ZHAI Wen-xue; ZHU Li-huang

    2002-01-01

    The completely dominant earliness was identified in a genic male-sterile and early maturing indica line 6442S-7. F1 progenies from 6442S-7 crossed with thirteen various types of medium- or latematuring varieties, shared the same heading date as 6442S-7. The segregation of heading date in the F2 and B1F1 populations showed that the earliness of 6442S-7 is mainly controlled by two dominant major genes. The local linkage map of one dominant earliness gene harbored in 6442S-7 was constructed with F2 population and four kinds of molecular marker techniques. The results showed that the gene was located between a RFLPmarker C515 and a RAPD marker OPI 11. 557 on the terminal region of short arm of rice chromosome 3,10.9cM and 1.5 cM from C515 and OPI11. 557, respectively. The genetic distances from the target gene to twoSSR markers, RM22 and RM231, and one AFLP marker, PT671, were 3.0, 6.7 and 12.4 cM, respectively. This gene, being identified and mapped first, is designated tentatively as Ef-cd (t). As a new genetic resource of completely dominant earliness, 6442S-7 has splendid future in rice improvement.

  20. Mapping of the apple scab-resistance gene Vb.

    Science.gov (United States)

    Erdin, N; Tartarini, S; Broggini, G A L; Gennari, F; Sansavini, S; Gessler, C; Patocchi, A

    2006-10-01

    Apple scab, caused by the fungus Venturia inaequalis, is the major production constraint in temperate zones with humid springs. Normally, its control relies on frequent and regular fungicide applications. Because this control strategy has come under increasing criticism, major efforts are being directed toward the breeding of scab-resistant apple cultivars. Modern apple breeding programs include the use of molecular markers, making it possible to combine several different scab-resistance genes in 1 apple cultivar (pyramiding) and to speed up the breeding process. The apple scab-resistance gene Vb is derived from the Siberian crab apple 'Hansen's baccata #2', and is 1 of the 6 "historical" major apple scab-resistance genes (Vf, Va, Vr, Vbj, Vm, and Vb). Molecular markers have been published for all these genes, except Vr. In testcross experiments conducted in the 1960s, it was reported that Vb segregated independently from 3 other major resistance genes, including Vf. Recently, however, Vb and Vf have both been mapped on linkage group 1, a result that contrasts with the findings from former testcross experiments. In this study, simple sequence repeat (SSR) markers were used to identify the precise position of Vb in a cross of 'Golden Delicious' (vbvb) and 'Hansen's baccata #2' (Vbvb). A genome scanning approach, a fast method already used to map apple scab-resistance genes Vr2 and Vm, was used, and the Vb locus was identified on linkage group 12, between the SSR markers Hi02d05 and Hi07f01. This finding confirms the independent segregation of Vb from Vf. With the identification of SSR markers linked to Vb, another major apple scab-resistance gene has become available; breeders can use it to develop durable resistant cultivars with several different resistance genes.

  1. GeneRecon Users' Manual — A coalescent based tool for fine-scale association mapping

    DEFF Research Database (Denmark)

    Mailund, T

    2006-01-01

    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample...

  2. Fine mapping and candidate gene analysis of purple pericarp gene Pb in rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Purple rice is a type of rice with anthocyanins deposited in its grain pericarp. The rice Pb gene controlling purple pericarp character is known to be on chromosome 4, and the purple color is dominant over white color. In this study, we fine mapped the Pb gene using two F2 segregating populations, i.e. Pei'ai 64S (white) × Yunanheixiannuo (purple) and Pei'ai 64S × Chuanheinuo (purple). In the first-pass mapping, the Pb gene was located in the region downstream the SSR marker RM3820. In the fine mapping, the candidate region was saturated with InDel and CAPS markers developed specifically for this study. Eventually, the Pb gene was mapped within the 25-kb region delimited by the upstream marker RID3 and the downstream marker RID4. The delimited region contained two annotated genes, Ra and bhlh16 (TIGR Rice Genome, R.5). The former is a homologue of the Myc transcription factor Lc controlling anthocyanin biosynthesis in maize, and the latter is a homologue of the TT8 gene, which is also an Myc transcription factor gene controlling the pericarp pigmentation in Arabidopsis thaliana. Sequence analysis showed that the exon 7 of the Ra gene of Yunanheixiannuo and Chuanheinuo had a 2-bp (GT) deletion compared with those of the white rice varieties Pei'ai 64S, 9311 and Nipponbare. A CAPS marker, CAPSRa, was developed according to the GT deletion for analysis of the two F2 segregating populations and 106 rice lines. The results showed that all F2 plants with white pericarp, and all non-purple rice lines (63 white and 22 red) contained no GT deletion, but all 20 purple rice lines contained the GT deletion. These results suggested that the Ra gene may be the Pb gene and the purple pericarp characteristic of rice is caused by the GT deletion within exon 7 of the Ra gene.

  3. In vitro mapping of Myotonic Dystrophy (DM) gene promoter

    Energy Technology Data Exchange (ETDEWEB)

    Storbeck, C.J.; Sabourin, L. [Univ. of Ottawa (Canada); Baird, S. [Children`s Hospital of Eastern Ontario, Ottawa (Canada)] [and others

    1994-09-01

    The Myotonic Dystrophy Kinase (DMK) gene has been cloned and shared homology to serine/threonine protein kinases. Overexpression of this gene in stably transfected mouse myoblasts has been shown to inhibit fusion into myotubes while myoblasts stably transfected with an antisense construct show increased fusion potential. These experiments, along with data showing that the DM gene is highly expressed in muscle have highlighted the possibility of DMK being involved in myogenesis. The promoter region of the DM gene lacks a consensus TATA box and CAAT box, but harbours numerous transcription binding sites. Clones containing extended 5{prime} upstream sequences (UPS) of DMK only weakly drive the reporter gene chloramphenicol acetyl transferase (CAT) when transfected into C2C12 mouse myoblasts. However, four E-boxes are present in the first intron of the DM gene and transient assays show increased expression of the CAT gene when the first intron is present downstream of these 5{prime} UPS in an orientation dependent manner. Comparison between mouse and human sequence reveals that the regions in the first intron where the E-boxes are located are highly conserved. The mapping of the promoter and the importance of the first intron in the control of DMK expression will be presented.

  4. A gene frequency model for QTL mapping using Bayesian inference

    Directory of Open Access Journals (Sweden)

    Dekkers Jack CM

    2010-06-01

    Full Text Available Abstract Background Information for mapping of quantitative trait loci (QTL comes from two sources: linkage disequilibrium (non-random association of allele states and cosegregation (non-random association of allele origin. Information from LD can be captured by modeling conditional means and variances at the QTL given marker information. Similarly, information from cosegregation can be captured by modeling conditional covariances. Here, we consider a Bayesian model based on gene frequency (BGF where both conditional means and variances are modeled as a function of the conditional gene frequencies at the QTL. The parameters in this model include these gene frequencies, additive effect of the QTL, its location, and the residual variance. Bayesian methodology was used to estimate these parameters. The priors used were: logit-normal for gene frequencies, normal for the additive effect, uniform for location, and inverse chi-square for the residual variance. Computer simulation was used to compare the power to detect and accuracy to map QTL by this method with those from least squares analysis using a regression model (LSR. Results To simplify the analysis, data from unrelated individuals in a purebred population were simulated, where only LD information contributes to map the QTL. LD was simulated in a chromosomal segment of 1 cM with one QTL by random mating in a population of size 500 for 1000 generations and in a population of size 100 for 50 generations. The comparison was studied under a range of conditions, which included SNP density of 0.1, 0.05 or 0.02 cM, sample size of 500 or 1000, and phenotypic variance explained by QTL of 2 or 5%. Both 1 and 2-SNP models were considered. Power to detect the QTL for the BGF, ranged from 0.4 to 0.99, and close or equal to the power of the regression using least squares (LSR. Precision to map QTL position of BGF, quantified by the mean absolute error, ranged from 0.11 to 0.21 cM for BGF, and was better

  5. MADS-box gene evolution - structure and transcription patterns

    DEFF Research Database (Denmark)

    Johansen, Bo; Pedersen, Louise Buchholt; Skipper, Martin;

    2002-01-01

    Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs......Mads-box genes, ABC model, Evolution, Phylogeny, Transcription patterns, Gene structure, Conserved motifs...

  6. A Medaka Gene Map: The Trace of Ancestral Vertebrate Proto-Chromosomes Revealed by Comparative Gene Mapping

    OpenAIRE

    Naruse, Kiyoshi; Tanaka, Minoru; Mita, Kazuei; Shima, Akihiro; Postlethwait, John; Mitani, Hiroshi

    2004-01-01

    The mapping of Hox clusters and many duplicated genes in zebrafish indicated an extra whole-genome duplication in ray-fined fish. However, to reconstruct the preduplication chromosomes (proto-chromosomes), the comparative genomic studies of more distantly related teleosts are essential. Medaka and zebrafish are ideal for this purpose, because their lineages separated from their last common ancestor ∼140 million years ago. To reconstruct ancient vertebrate chromosomes, including the chromosome...

  7. Chromosomal mapping of the human M6 genes

    Energy Technology Data Exchange (ETDEWEB)

    Olinsky, S.; Loop, B.T.; DeKosky, A. [Univ. of Pittsburgh, PA (United States)] [and others

    1996-05-01

    M6 is a neuronal membrane glycoprotein that may have an important role in neural development. This molecule was initially defined by a monoclonal antibody that affected the survival of cultured cerebellar neurons and the outgrowth of neurites. The nature of the antigen was discovered by expression cDNA cloning using this monoclonal antibody. Two distinct murine M6 cDNAs (designated M6a and M6b) whose deduced amino acid sequences were remarkably similar to that of the myelin proteolipid protein human cDNA and genomic clones encoding M6a and M6b and have characterized them by restriction mapping, Southern hybridization with cDNA probes, and sequence analysis. We have localized these genes within the human genome by FISH (fluorescence in situ hybridization). The human M6a gene is located at 4q34, and the M6b gene is located at Xp22.2 A number of human neurological disorders have been mapped to the Xp22 region, including Aicardi syndrome (MIM 304050), Rett syndrome (MIM 312750), X-linked Charcot-Marie-Tooth neuropathy (MIM 302801), and X-linked mental retardation syndromes (MRX1, MIM 309530). This raises the possibility that a defect in the M6b gene is responsible for one of these neurological disorders. 8 refs., 3 figs.

  8. Gene-gene interaction and RNA splicing profiles of MAP2K4 gene in rheumatoid arthritis.

    Science.gov (United States)

    Shchetynsky, Klementy; Protsyuk, Darya; Ronninger, Marcus; Diaz-Gallo, Lina-Marcela; Klareskog, Lars; Padyukov, Leonid

    2015-05-01

    We performed gene-gene interaction analysis, with HLA-DRB1 shared epitope (SE) alleles for 195 SNPs within immunologically important MAP2K, MAP3K and MAP4K gene families, in 2010 rheumatoid arthritis (RA) patients and 2280 healthy controls. We found a significant statistical interaction for rs10468473 with SE alleles in autoantibody-positive RA. Individuals heterozygous for rs10468473 demonstrated higher expression of total MAP2K4 mRNA in blood, compared to A-allele homozygous. We discovered a novel, putatively translated, "cassette exon" RNA splice form of MAP2K4, differentially expressed in peripheral blood mononuclear cells from 88 RA cases and controls. Within the group of RA patients, we observed a correlation of MAP2K4 isoform expression with carried SE alleles, autoantibody, and rheumatoid factor profiles. TNF-dependent modulation of isoform expression pattern was detected in the Jurkat cell line. Our data suggest a genetic interaction between MAP2K4 and HLA-DRB1, and the importance of rs10468473 and MAP2K4 splice variants in the development of autoantibody-positive RA.

  9. Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean.

    Science.gov (United States)

    Galeano, Carlos H; Fernandez, Andrea C; Franco-Herrera, Natalia; Cichy, Karen A; McClean, Phillip E; Vanderleyden, Jos; Blair, Matthew W

    2011-01-01

    Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

  10. Overlapping Structures in Sensory-Motor Mappings

    Science.gov (United States)

    Earland, Kevin; Lee, Mark; Shaw, Patricia; Law, James

    2014-01-01

    This paper examines a biologically-inspired representation technique designed for the support of sensory-motor learning in developmental robotics. An interesting feature of the many topographic neural sheets in the brain is that closely packed receptive fields must overlap in order to fully cover a spatial region. This raises interesting scientific questions with engineering implications: e.g. is overlap detrimental? does it have any benefits? This paper examines the effects and properties of overlap between elements arranged in arrays or maps. In particular we investigate how overlap affects the representation and transmission of spatial location information on and between topographic maps. Through a series of experiments we determine the conditions under which overlap offers advantages and identify useful ranges of overlap for building mappings in cognitive robotic systems. Our motivation is to understand the phenomena of overlap in order to provide guidance for application in sensory-motor learning robots. PMID:24392118

  11. Acquisition of 3-D Map Structures for Mobile Robots

    Science.gov (United States)

    2007-11-02

    U.S.N.A. — Trident Scholar project report; no. 295 (2002) Acquisition of 3-D Map Structures for Mobile Robots by Midshipman Edward H.L. Fong, Class...REPORT TYPE 3. DATES COVERED (FROM - TO) xx-xx-2002 to xx-xx-2002 4. TITLE AND SUBTITLE Acquisition of 3-D Map Structures for Mobile Robots Unclassified...AND SUBTITLE Acquisition of 3-D map structures for mobile robots 6. AUTHOR(S) Fong, Edward H. L. (Edward Hsiang Lung), 1980- 5. FUNDING NUMBERS 7

  12. Clinical and molecular cytogenetics and gene mapping: principles and techniques.

    Science.gov (United States)

    Francke, U

    1995-01-01

    This article reviews the history of human cytogenetics with respect to technical advances from chromosome banding to molecular cytogenetics. Technologies such as in situ hybridization, chromosome painting, comparative genomic hybridization and interphase cytogenetics and their applications are discussed. The assignments of genes to chromosome regions by somatic cell genetics is illustrated by molecular analyses of somatic cell hybrid panels. The generation of complete physical maps of human chromosomes, by radiation hybrid mapping of sequence-tagged sites and establishment of chromosome-specific yeast artificial chromosome (YAC) banks and clone overlaps (contigs), is exemplified by studies of chromosome 18. The last section outlines the recent and future advances in clinical cytogenetics made possible by progress in molecular genetics.

  13. MOLECULAR CHARACTERIZATION OF MAP30 GENE FROM MOMORDICA CHARANTIA L.

    Directory of Open Access Journals (Sweden)

    P Supraja

    2015-07-01

    Full Text Available Natural products especially from plants have been used for the treatment of various diseases. Momordica charantia or bitter melon, grows in the tropical area is popularly consumed as vegetables and has high medicinal values .It is one of the most promising alternative medicines used as anti-HIV, anti-ulcer, antiinflammatory, antileukemic, anti-microbial, anti-diabetic, and anti-tumor. Proteins like momordin, alpha- and betamomorcharin and cucurbitacin B of Momordica charantia were also tested for possible anticancerous effects .Chemical analogs of these proteins have been developed, patented, and named MAP30.The MAP30gene was amplified from Momordica charantia leaves by Polymerase Chain Reaction .The resultant product was amplified

  14. Alternative mapping of probes to genes for Affymetrix chips

    Directory of Open Access Journals (Sweden)

    Friis-Hansen Lennart

    2004-08-01

    Full Text Available Abstract Background Short oligonucleotide arrays have several probes measuring the expression level of each target transcript. Therefore the selection of probes is a key component for the quality of measurements. However, once probes have been selected and synthesized on an array, it is still possible to re-evaluate the results using an updated mapping of probes to genes, taking into account the latest biological knowledge available. Methods We investigated how probes found on recent commercial microarrays for human genes (Affymetrix HG-U133A were matching a recent curated collection of human transcripts: the NCBI RefSeq database. We also built mappings and used them in place of the original probe to genes associations provided by the manufacturer of the arrays. Results In a large number of cases, 36%, the probes matching a reference sequence were consistent with the grouping of probes by the manufacturer of the chips. For the remaining cases there were discrepancies and we show how that can affect the analysis of data. Conclusions While the probes on Affymetrix arrays remain the same for several years, the biological knowledge concerning the genomic sequences evolves rapidly. Using up-to-date knowledge can apparently change the outcome of an analysis.

  15. The active gene that encodes human High Mobility Group 1 protein (HMG1) contains introns and maps to chromosome 13

    Energy Technology Data Exchange (ETDEWEB)

    Ferrari, S. [Dipartimento di Genetica e di Biologia dei Microrganismi, Milan (Italy); Finelli, P.; Rocchi, M. [Istituto di Genetica, Bari (Italy)] [and others

    1996-07-15

    The human genome contains a large number of sequences related to the cDNA for High Mobility Group 1 protein (HMG1), which so far has hampered the cloning and mapping of the active HMG1 gene. We show that the human HMG1 gene contains introns, while the HMG1-related sequences do not and most likely are retrotransposed pseudogenes. We identified eight YACs from the ICI and CEPH libraries that contain the human HMG1 gene. The HMG1 gene is similar in structure to the previously characterized murine homologue and maps to human chromosome 13 and q12, as determined by in situ hybridization. The mouse Hmg1 gene maps to the telomeric region of murine Chromosome 5, which is syntenic to the human 13q12 band. 18 refs., 3 figs.

  16. Highlighting material structure with transmission electron diffraction correlation coefficient maps.

    Science.gov (United States)

    Kiss, Ákos K; Rauch, Edgar F; Lábár, János L

    2016-04-01

    Correlation coefficient maps are constructed by computing the differences between neighboring diffraction patterns collected in a transmission electron microscope in scanning mode. The maps are shown to highlight material structural features like grain boundaries, second phase particles or dislocations. The inclination of the inner crystal interfaces are directly deduced from the resulting contrast.

  17. High-Density Genetic Map Construction and Gene Mapping of Basal Branching Habit and Flowers per Leaf Axil in Sesame

    Science.gov (United States)

    Mei, Hongxian; Liu, Yanyang; Du, Zhenwei; Wu, Ke; Cui, Chengqi; Jiang, Xiaolin; Zhang, Haiyang; Zheng, Yongzhan

    2017-01-01

    A good genetic map can provide the framework for quantitative trait loci (QTL) analysis, map-based gene cloning, and genome sequence assembling. The main objectives of this study were to develop a high-density genetic linkage map using specific length amplified fragment sequencing (SLAF-seq) in sesame. In the result, a high-resolution genetic map with 9,378 SLAF markers and 13 linkage groups (LGs) was constructed. The map spanned a total genetic distance of 1,974.23 cM, and the mean LG length was 151.86 cM, with an average genetic distance of 0.22 cM between adjacent markers. Based on the newly constructed genetic map, genes for basal branching habit (SiBH) and flowers per leaf axil (SiFA) were mapped to LG5 and LG11, respectively. PMID:28496450

  18. Gene-based SNP discovery and genetic mapping in pea.

    Science.gov (United States)

    Sindhu, Anoop; Ramsay, Larissa; Sanderson, Lacey-Anne; Stonehouse, Robert; Li, Rong; Condie, Janet; Shunmugam, Arun S K; Liu, Yong; Jha, Ambuj B; Diapari, Marwan; Burstin, Judith; Aubert, Gregoire; Tar'an, Bunyamin; Bett, Kirstin E; Warkentin, Thomas D; Sharpe, Andrew G

    2014-10-01

    Gene-based SNPs were identified and mapped in pea using five recombinant inbred line populations segregating for traits of agronomic importance. Pea (Pisum sativum L.) is one of the world's oldest domesticated crops and has been a model system in plant biology and genetics since the work of Gregor Mendel. Pea is the second most widely grown pulse crop in the world following common bean. The importance of pea as a food crop is growing due to its combination of moderate protein concentration, slowly digestible starch, high dietary fiber concentration, and its richness in micronutrients; however, pea has lagged behind other major crops in harnessing recent advances in molecular biology, genomics and bioinformatics, partly due to its large genome size with a large proportion of repetitive sequence, and to the relatively limited investment in research in this crop globally. The objective of this research was the development of a genome-wide transcriptome-based pea single-nucleotide polymorphism (SNP) marker platform using next-generation sequencing technology. A total of 1,536 polymorphic SNP loci selected from over 20,000 non-redundant SNPs identified using deep transcriptome sequencing of eight diverse Pisum accessions were used for genotyping in five RIL populations using an Illumina GoldenGate assay. The first high-density pea SNP map defining all seven linkage groups was generated by integrating with previously published anchor markers. Syntenic relationships of this map with the model legume Medicago truncatula and lentil (Lens culinaris Medik.) maps were established. The genic SNP map establishes a foundation for future molecular breeding efforts by enabling both the identification and tracking of introgression of genomic regions harbouring QTLs related to agronomic and seed quality traits.

  19. Drosophila transposon insertions as unknowns for structured inquiry recombination mapping exercises in an undergraduate genetics course.

    Science.gov (United States)

    Marcus, Jeffrey M; Hughes, Tia M

    2009-06-01

    Structured inquiry approaches, in which students receive a Drosophila strain of unknown genotype to analyze and map the constituent mutations, are a common feature of many genetics teaching laboratories. The required crosses frustrate many students because they are aware that they are participating in a fundamentally trivial exercise, as the map locations of the genes are already established and have been recalculated thousands of times by generations of students. We modified the traditional structured inquiry approach to include a novel research experience for the students in our undergraduate genetics laboratories. Students conducted crosses with Drosophila strains carrying P[lacW] transposon insertions in genes without documented recombination map positions, representing a large number of unique, but equivalent genetic unknowns. Using the eye color phenotypes associated with the inserts as visible markers, it is straightforward to calculate recombination map positions for the interrupted loci. Collectively, our students mapped 95 genetic loci on chromosomes 2 and 3. In most cases, the calculated 95% confidence interval for meiotic map location overlapped with the predicted map position based on cytology. The research experience evoked positive student responses and helped students better understand the nature of scientific research for little additional cost or instructor effort.

  20. Mapping strategy, structure, ownership and performance in European corporations : Introduction

    NARCIS (Netherlands)

    Colli, A.; Iversen, M.J.; de Jong, A.

    2011-01-01

    This paper is the introduction to the Business History special issue on European Business Models. The volume presents results of the international project about mapping European corporations, within the strategy, structure, ownership and performance (SSOP) framework. The paper describes the

  1. Mapping Strategy, Structure, Ownership and Performance in European Corporations

    DEFF Research Database (Denmark)

    Iversen, Martin; Colli, Andrea; de Jong, Abe

    2011-01-01

    This paper is the introduction to the Business History special issue on European Business Models. The volume presents results of the international project about mapping European corporations, within the strategy, structure, ownership and performance (SSOP) framework. The paper describes the histo......This paper is the introduction to the Business History special issue on European Business Models. The volume presents results of the international project about mapping European corporations, within the strategy, structure, ownership and performance (SSOP) framework. The paper describes...

  2. HYPERSTATIC STRUCTURE MAPPING MODEL BUILDING AND OPTIMIZING DESIGN

    Institute of Scientific and Technical Information of China (English)

    XU Gening; GAO Youshan; ZHANG Xueliang; YANG Ruigang

    2007-01-01

    Hyperstatic structure plane model being built by structural mechanics is studied. Space model precisely reflected in real stress of the structure is built by finite element method (FEM) analysis commerce software. Mapping model of complex structure system is set up, with convenient calculation just as in plane model and comprehensive information as in space model. Plane model and space model are calculated under the same working condition. Plane model modular construction inner force is considered as input data; Space model modular construction inner force is considered as output data. Thus specimen is built on input data and output data. Character and affiliation are extracted through training specimen, with the employment of nonlinear mapping capability of the artificial neural network. Mapping model with interpolation and extrapolation is gained, laying the foundation for optimum design. The steel structure of high-layer parking system (SSHLPS) is calculated as an instance. A three-layer back-propagation (BP) net including one hidden layer is constructed with nine input nodes and eight output nodes for a five-layer SSHLPS. The three-layer structure optimization result through the mapping model interpolation contrasts with integrity re-analysis, and seven layers structure through the mapping model extrapolation contrasts with integrity re-analysis. Any layer SSHLPS among 1~8 can be calculated with much accuracy. Amount of calculation can also be reduced if it is applied into the same topological structure, with reduced distortion and assured precision.

  3. USGS Structures Overlay Map Service from The National Map - National Geospatial Data Asset (NGDA) USGS National Structures Dataset

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — USGS Structures from The National Map (TNM) consists of data to include the name, function, location, and other core information and characteristics of selected...

  4. The structure of states and maps in quantum theory

    Indian Academy of Sciences (India)

    Sudhavathani Simon; S P Rajagopalan; R Simon

    2009-09-01

    The structure of statistical state spaces in the classical and quantum theories are compared in an interesting and novel manner. Quantum state spaces and maps on them have rich convex structures arising from the superposition principle and consequent entanglement. Communication channels (physical processes) in the quantum scheme of things are in one-to-one correspondence with completely positive maps. Positive maps which are not completely positive do not correspond to physical processes. Nevertheless they prove to be invaluable mathematical tools in establishing or witnessing entanglement of mixed states. We consider some of the recent developments in our understanding of the convex structure of states and maps in quantum theory, particularly in the context of quantum information theory.

  5. Comments on the Bifurcation Structure of 1D Maps

    DEFF Research Database (Denmark)

    Belykh, V.N.; Mosekilde, Erik

    1997-01-01

    The paper presents a complementary view on some of the phenomena related to the bifurcation structure of unimodal maps. An approximate renormalization theory for the period-doubling cascade is developed, and a mapping procedure is established that accounts directly for the box-within-a-box struct......The paper presents a complementary view on some of the phenomena related to the bifurcation structure of unimodal maps. An approximate renormalization theory for the period-doubling cascade is developed, and a mapping procedure is established that accounts directly for the box......-within-a-box structure of the total bifurcation set. This presents a picture in which the homoclinic orbit bifurcations act as a skeleton for the bifurcational set. At the same time, experimental results on continued subharmonic generation for piezoelectrically amplified sound waves, predating the Feigenbaum theory...

  6. Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii.

    Science.gov (United States)

    Jacobson, M R; Brigle, K E; Bennett, L T; Setterquist, R A; Wilson, M S; Cash, V L; Beynon, J; Newton, W E; Dean, D R

    1989-02-01

    Determination of a 28,793-base-pair DNA sequence of a region from the Azotobacter vinelandii genome that includes and flanks the nitrogenase structural gene region was completed. This information was used to revise the previously proposed organization of the major nif cluster. The major nif cluster from A. vinelandii encodes 15 nif-specific genes whose products bear significant structural identity to the corresponding nif-specific gene products from Klebsiella pneumoniae. These genes include nifH, nifD, nifK, nifT, nifY, nifE, nifN, nifX, nifU, nifS, nifV, nifW, nifZ, nifM, and nifF. Although there are significant spatial differences, the identified A. vinelandii nif-specific genes have the same sequential arrangement as the corresponding nif-specific genes from K. pneumoniae. Twelve other potential genes whose expression could be subject to nif-specific regulation were also found interspersed among the identified nif-specific genes. These potential genes do not encode products that are structurally related to the identified nif-specific gene products. Eleven potential nif-specific promoters were identified within the major nif cluster, and nine of these are preceded by an appropriate upstream activator sequence. A + T-rich regions were identified between 8 of the 11 proposed nif promoter sequences and their upstream activator sequences. Site-directed deletion-and-insertion mutagenesis was used to establish a genetic map of the major nif cluster.

  7. Reconstruction of 3D structures from protein contact maps.

    Science.gov (United States)

    Vassura, Marco; Margara, Luciano; Di Lena, Pietro; Medri, Filippo; Fariselli, Piero; Casadio, Rita

    2008-01-01

    The prediction of the protein tertiary structure from solely its residue sequence (the so called Protein Folding Problem) is one of the most challenging problems in Structural Bioinformatics. We focus on the protein residue contact map. When this map is assigned it is possible to reconstruct the 3D structure of the protein backbone. The general problem of recovering a set of 3D coordinates consistent with some given contact map is known as a unit-disk-graph realization problem and it has been recently proven to be NP-Hard. In this paper we describe a heuristic method (COMAR) that is able to reconstruct with an unprecedented rate (3-15 seconds) a 3D model that exactly matches the target contact map of a protein. Working with a non-redundant set of 1760 proteins, we find that the scoring efficiency of finding a 3D model very close to the protein native structure depends on the threshold value adopted to compute the protein residue contact map. Contact maps whose threshold values range from 10 to 18 Angstroms allow reconstructing 3D models that are very similar to the proteins native structure.

  8. Qualitative Mapping of Structural Different Polypeptide Nanotubes

    DEFF Research Database (Denmark)

    Clausen, Casper Hyttel; Jensen, Jason; Castillo, Jaime

    2008-01-01

    that it is possible to distinguish between these three types of structures using this method. Further, an agreement between the detected signal and the structure of the hollow peptide was demonstrated; however only qualitative agreement with the mathematical expressing of the tubes is shown.......Biological self-assembled structures are receiving increasing focus within micro- and nanotechnology, for example, as sensing devices, due to the fact that they are cheap to produce and easy to functionalize. Therefore, methods for the characterization of these structures are much needed...

  9. Genetic regulation of tissue-specific expression of amylase structural genes in Drosophila melanogaster.

    Science.gov (United States)

    Abraham, I; Doane, W W

    1978-01-01

    Laboratory strains of Drosophila melanogaster were screened for spatial variations in adult midgut alpha-amylase (1,4-alpha-D-glucan glucanohydrolase, EC 3.2.1.1) expression. No strain-specific differences were found anteriorly, but three patterns of activity were discerned in the posterior midgut: A, activity throughout most of the region; B, activity in the anterior part of the region; and C, little or no activity. Alleles of a control gene, map, are responsible for this tissue-specific regulation of activity; e.g., mapA homozygotes produce the A pattern and mapC homozygotes the C pattern. The map locus was placed at 2--80 +/- on the genetic map of chromosome 2R, about two crossover units distal to the Amy structural gene region for alpha-amylase. Electrophoretic studies showed that mapA is trans acting in mapA/mapC flies, allowing expression of amylase isozymes coded for by genes on the opposite chromosome. The map gene behaves as a temporal gene that is clearly separable from the tightly linked, duplicated Amy structural genes. Images PMID:100784

  10. Structure of the murine Thy-1 gene

    NARCIS (Netherlands)

    V. Giguere; K-I. Isobe; F.G. Grosveld (Frank)

    1985-01-01

    textabstractWe have cloned the murine Thy-1.1 (AKR) and Thy-1.2 (Balb/c) genes. The complete exon/intron structure and the nucleotide sequence of the Thy-1.2 gene was determined. The gene contains four exons and three intervening sequences. The complete transcriptional unit gives rise to a tissue an

  11. GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology.

    Science.gov (United States)

    Ramsak, Živa; Baebler, Špela; Rotter, Ana; Korbar, Matej; Mozetic, Igor; Usadel, Björn; Gruden, Kristina

    2014-01-01

    GoMapMan (http://www.gomapman.org) is an open web-accessible resource for gene functional annotations in the plant sciences. It was developed to facilitate improvement, consolidation and visualization of gene annotations across several plant species. GoMapMan is based on the MapMan ontology, organized in the form of a hierarchical tree of biological concepts, which describe gene functions. Currently, genes of the model species Arabidopsis and three crop species (potato, tomato and rice) are included. The main features of GoMapMan are (i) dynamic and interactive gene product annotation through various curation options; (ii) consolidation of gene annotations for different plant species through the integration of orthologue group information; (iii) traceability of gene ontology changes and annotations; (iv) integration of external knowledge about genes from different public resources; and (v) providing gathered information to high-throughput analysis tools via dynamically generated export files. All of the GoMapMan functionalities are openly available, with the restriction on the curation functions, which require prior registration to ensure traceability of the implemented changes.

  12. IMPLEMENTATION OF THE NEW CAREER STRUCTURE SCHEME (MAPS)

    CERN Multimedia

    Human Resources Division

    2002-01-01

    This is to inform staff members that the Administrative Circular on MAPS*, announced in the Weekly Bulletin last year, has now been published. It has been sent to each individual staff member and is posted on the HR Division Web site, together with other documents on MAPS, at the following address : Human Resources: Information about the new career structure English and French versions are also available at Divisional Secretariats. Please note that the Annual Interview programme for this first year of implementation of MAPS will not follow the calendar normally foreseen in the Circular. This is to give sufficient time to hold MAPS seminars for supervisors in January and February. Consequently, individual interviews will take place after these seminars - apart from some specially justified cases that may arise. The next stage of implementation of MAPS is the planning for the 2002 advancement and promotion exercise, for which budgetary and numerical guidelines, together with the calendar, will also be announced...

  13. Photonic-crystal fibre: Mapping the structure

    DEFF Research Database (Denmark)

    Markos, Christos

    2015-01-01

    The demonstration of real-time and non-destructive Doppler-assisted tomography of the internal structure of photonic-crystal fibres could aid the fabrication of high-quality fibres with enhanced performance.......The demonstration of real-time and non-destructive Doppler-assisted tomography of the internal structure of photonic-crystal fibres could aid the fabrication of high-quality fibres with enhanced performance....

  14. Molecular characterization and mapping of Fgf21 gene in a foodfish species asian seabass.

    Directory of Open Access Journals (Sweden)

    Le Wang

    Full Text Available Fgf21 is a newly discovered fibroblast growth factor. It is typically induced by fasting and plays important roles in the regulation of glucose and lipid metabolisms and energy balance in mammals, whereas potential functions of this gene in teleosts are still unknown. We identified the Fgf21 gene and studied its functions in Asian seabass (Lates calcarifer. The cDNA of the Fgf21 encoded a protein with 206 amino acids. Analysis of DNA and amino acid sequences of Fgf21 genes revealed that the sequences and structure of the Fgf21 genes were highly conserved in vertebrates. Real-time PCR revealed that Fgf21 was exclusively expressed in the intestine and kidney, which was different from the expression profiles of mammals. Fgf21 was down-regulated under fasting, whereas it was significantly increased during the LPS challenge. Exogenous recombinant FGF21 significantly suppressed the appetite of Asian seabass. Our data suggest that Fgf21 plays a role in energy regulation and acute phase response in Asian seabass, and may have different functions in fish and mammals. In addition, we identified one SNP in Fgf21. By using this SNP, the gene was mapped on the linkage group 23, where a suggestive QTL for growth was mapped previously. Association mapping identified significant associations between Fgf21 genotypes at the SNP and growth traits. These results not only provide important information of the functions of Fgf21, but also suggest that the SNP in this gene can be used as a marker in selecting fast-growing individuals of Asian seabass.

  15. TOPOLOGICAL STRUCTURING OF RASTER-SCANNED LINE MAP DATA.

    Science.gov (United States)

    Fegeas, Robin G.; Pearsall, Richard A.

    1984-01-01

    The U. S. Geological Survey has a requirement for the collection of large amounts of digital map data from existing graphic map separates. Prototype production techniques have been developed to capture line data from the map separates using a raster-scanning input device. After minimal editing in raster form, the data are converted to 'unstructured' vector form. In order to be processed further, the line data must be topologically structured (nodes identified and start-node, end-node, area-left, and area-right tags associated with each line-segment chain). This paper describes the techniques which have been developed at the U. S. Geological Survey to topologically structure the raster-scanned line map data.

  16. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping.

    Science.gov (United States)

    Jin, Liang; Lu, Yan; Xiao, Peng; Sun, Mei; Corke, Harold; Bao, Jinsong

    2010-08-01

    Germplasm diversity is the mainstay for crop improvement and genetic dissection of complex traits. Understanding genetic diversity, population structure, and the level and distribution of linkage disequilibrium (LD) in target populations is of great importance and a prerequisite for association mapping. In this study, 100 genome-wide simple sequence repeat (SSR) markers were used to assess genetic diversity, population structure, and LD of 416 rice accessions including landraces, cultivars and breeding lines collected mostly in China. A model-based population structure analysis divided the rice materials into seven subpopulations. 63% of the SSR pairs in these accessions were in LD, which was mostly due to an overall population structure, since the number of locus pairs in LD was reduced sharply within each subpopulation, with the SSR pairs in LD ranging from 5.9 to 22.9%. Among those SSR pairs showing significant LD, the intrachromosomal LD had an average of 25-50 cM in different subpopulations. Analysis of the phenotypic diversity of 25 traits showed that the population structure accounted for an average of 22.4% of phenotypic variation. An example association mapping for starch quality traits using both the candidate gene mapping and genome-wide mapping strategies based on the estimated population structure was conducted. Candidate gene mapping confirmed that the Wx and starch synthase IIa (SSIIa) genes could be identified as strongly associated with apparent amylose content (AAC) and pasting temperature (PT), respectively. More importantly, we revealed that the Wx gene was also strongly associated with PT. In addition to the major genes, we found five and seven SSRs were associated with AAC and PT, respectively, some of which have not been detected in previous linkage mapping studies. The results suggested that the population may be useful for the genome-wide marker-trait association mapping. This new association population has the potential to identify

  17. Identification of Pneumocystis carinii chromosomes and mapping of five genes

    DEFF Research Database (Denmark)

    Lundgren, B; Cotton, R; Lundgren, J D;

    1990-01-01

    Pulsed field gel electrophoresis was used to identify the chromosome-size DNA of Pneumocystis carinii, a major pathogen of immunocompromised patients. Thirteen chromosomes of rodent Pneumocystis carinii, ranging in size from 300 to 700 kilobases (kb), were identified. The minimum genome size for P....... carinii, estimated on the basis of the sizes of chromosomes, is 7,000 kb. Genetic heterogeneity among different P. carinii isolates was documented by demonstration of chromosomal size variability. By hybridization studies, the genes for topoisomerase I, dihydrofolate reductase, rRNA, actin......, and thymidylate synthase were mapped to single chromosomes of approximately 650, 590, 550, 460, and 350 kb, respectively. Hybridization studies further confirmed the genetic heterogeneity of P. carinii....

  18. Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models

    Directory of Open Access Journals (Sweden)

    Smith Terry J

    2004-03-01

    Full Text Available Abstract Background Many current gene prediction methods use only one model to represent protein-coding regions in a genome, and so are less likely to predict the location of genes that have an atypical sequence composition. It is likely that future improvements in gene finding will involve the development of methods that can adequately deal with intra-genomic compositional variation. Results This work explores a new approach to gene-prediction, based on the Self-Organizing Map, which has the ability to automatically identify multiple gene models within a genome. The current implementation, named RescueNet, uses relative synonymous codon usage as the indicator of protein-coding potential. Conclusions While its raw accuracy rate can be less than other methods, RescueNet consistently identifies some genes that other methods do not, and should therefore be of interest to gene-prediction software developers and genome annotation teams alike. RescueNet is recommended for use in conjunction with, or as a complement to, other gene prediction methods.

  19. The genetic population structure of northern Sweden and its implications for mapping genetic diseases.

    Science.gov (United States)

    Einarsdottir, Elisabet; Egerbladh, Inez; Beckman, Lars; Holmberg, Dan; Escher, Stefan A

    2007-11-01

    The northern Swedish population has a history of admixture of three ethnic groups and a dramatic population growth from a relatively small founder population. This has resulted in founder effects that together with unique resources for genealogical analyses provide excellent conditions for genetic mapping of monogenic diseases. Several recent examples of successful mapping of genetic factors underlying susceptibility to complex diseases have suggested that the population of northern Sweden may also be an important tool for efficient mapping of more complex phenotypes. A potential factor contributing to these effects may be population sub-isolates within the large river valleys, constituting a central geographic characteristic of this region. We here provide evidence that marriage patterns as well as the distribution of gene frequencies in a set of marker loci are compatible with this notion. The possible implications of this population structure on linkage- and association based strategies for identifying genes contributing risk to complex diseases are discussed.

  20. Functional materials discovery using energy-structure-function maps

    Science.gov (United States)

    Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

    2017-03-01

    Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

  1. Mapping the Structure of Metalloproteins with RIDME.

    Science.gov (United States)

    Astashkin, Andrei V

    2015-01-01

    Distance measurements in biological macromolecules represent a very active field of application of pulsed electron paramagnetic resonance (EPR) spectroscopy. The relatively recently introduced pulsed EPR method of relaxation-induced dipolar modulation enhancement (RIDME) is conceptually similar to the popular double electron-electron resonance (DEER), but is much more suitable for studying the structures of metalloproteins while using their native paramagnetic metal centers as structural reference points. In particular, RIDME can largely alleviate the sensitivity and orientational selectivity problems that limit the application of DEER to such systems. In this contribution, the theoretical principles, implementation, optimization, and available experimental examples of RIDME are described with the purpose of enhancing the familiarity with this technique and promoting its application.

  2. Ordered and isomorphic mapping of periodic structures in the parametrically forced logistic map

    Science.gov (United States)

    Maranhão, Dariel M.

    2016-09-01

    We investigate the periodic domains found in the parametrically forced logistic map, the classical logistic map when its control parameter changes dynamically. Phase diagrams in two-parameter spaces reveal intricate periodic structures composed of patterns of intersecting superstable orbits curves, defining the cell of a periodic window. Cells appear multifoliated and ordered, and they are isomorphically mapped when one changes the map parameters. Also, we identify the characteristics of simplest cell and apply them to other more complex, discussing how the topography on parameter space is affected. By use of the winding number as defined in periodically forced oscillators, we show that the hierarchical organization of the periodic domains is manifested in global and local scales.

  3. Memory annihilation of structured maps in bidirectional associative memories.

    Science.gov (United States)

    Kumar, S

    2000-01-01

    Structured sets comprise Boolean vectors with equal pair-wise Hamming distances, h. An external vector, if it exists at an equidistance of h/2 from each vector of the structured set, is called the centroid of the set. A structured map is a one-one onto mapping between structured sets. It is a set of associations between Boolean vectors, where both domain and range vectors are drawn from structured sets. Associations between centroids are called centroidal associations. In this paper we show that when structured maps are encoded into bidirectional associative memories using outer-product correlation encoding, the memory of these associations annihilates under certain mild conditions. When annihilation occurs, the centroidal association emerges as a stable association, and we call it an alien attractor. For the special case of maps where h=2, self-annihilation can take place when either the domain or range dimensions are greater than five. In fact, we show that for dimensions greater than eight, as few as three associations suffice for self-annihilation. As an example shows, annihilation occurs even for the case of bipolar decoding which is well known for its improved error correction capability in such associative memory models.

  4. Gene function prediction based on the Gene Ontology hierarchical structure.

    Science.gov (United States)

    Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao

    2014-01-01

    The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

  5. FeatureMap3D - a tool to map protein features and sequence conservation onto homologous structures in the PDB

    DEFF Research Database (Denmark)

    Wernersson, Rasmus; Rapacki, Krzysztof; Stærfeldt, Hans Henrik

    2006-01-01

    FeatureMap3D is a web-based tool that maps protein features onto 3D structures. The user provides sequences annotated with any feature of interest, such as post-translational modifications, protease cleavage sites or exonic structure and FeatureMap3D will then search the Protein Data Bank (PDB...... without sequence annotation, to evaluate the quality of the alignment of the input sequences to the most homologous structures in the PDB, through the sequence conservation colored 3D structure visualization tool. FeatureMap3D is available at: http://www.cbs.dtu.dk/services/FeatureMap3D/....

  6. USING OF THERMAL STRUCTURE MAPS FOR VEGETATION MAPPING (CASE OF ALTACHEYSKY WILDLIFE AREA

    Directory of Open Access Journals (Sweden)

    L. A. Abramova

    2014-01-01

    Full Text Available Thermal infrared imagery contains considerable amount of qualitative information about ground objects and landscapes. In spite of it, this type of data is often used to derive quantitative information such as land or sea surface temperatures. This paper describes the examination of Altacheysky wildlife area situated in the southern part of Buryatia Republic, Mukhorshibirsky district based on Landsat imagery and ground observations. Ground observations were led to study the vegetation cover of the area. Landsat imagery were used to make multitemporal thermal infrared image combined of 7 ETM+ scenes and to make multispectral image combined of different zones of a OLI scene. Both images were classified. The multitemporal thermal infrared classification result was used to compose thermal structure map of the wildlife area. Comparison of the map, multispectral image classification result and ground observations data reveals that thermal structure map describes better the particularities of Altacheysky wildlife area vegetation cover.

  7. Adenosine diphosphate glucose pyrophosphorylase genes in wheat: differential expression and gene mapping.

    Science.gov (United States)

    Ainsworth, C; Hosein, F; Tarvis, M; Weir, F; Burrell, M; Devos, K M; Gale, M D

    1995-01-01

    A full-length cDNA clone representing the large (shrunken-2) subunit of ADP-glucose pyrophosphorylase (AGP; EC 2.7.7.27) has been isolated from a cDNA library prepared from developing grain of hexaploid wheat (Triticum aestivum L., cv. Chinese Spring). The 2084-bp cDNA insert contains an open reading frame of 1566 nucleotides and primer-extension analysis indicated that the 5' end is 10 nucleotides shorter than the mRNA. The deduced protein contains 522 amino acids (57.8 kDa) and includes a putative transit peptide of 62 amino acids (6.5 kDa). The similarity of the deduced protein to the small subunit of AGP and to other AGP genes from plants and microorganisms is discussed. Northern hybridisation shows that the Agp1 genes (encoding the small subunit in the wheat endosperm) and the Agp2 genes (encoding the large subunit in the wheat endosperm) are differentially expressed in the wheat grain. Transcripts from both gene sets accumulate to high levels in the endosperm during grain development with the majority of the expression in the endopsperm rather than the embryo and pericarp layers. Although enzyme activity is detected in developing grains prior to 10 d post anthesis, only the Agp1 genes are active at this time (the Agp2 genes are not expressed until 10 d post anthesis). The possibility that the enzyme expressed during early grain development is a homotetramer of small subunits is discussed. The Agp1 and Agp2 genes are arranged as triplicate sets of single-copy homoeoloci in wheat. The Agp2 genes are located on the long arms of chromosomes 1A, 1B and 1D, about 80 cM from the centromere. The Agp1 genes have been mapped to a position just distal to the centromere on the long arms of chromosomes 7A, 7B and 7D.

  8. The mapping of novel genes to human chromosome 19

    Energy Technology Data Exchange (ETDEWEB)

    Buenaventura, J.M. [Sarah Lawrence College, Bronxville, NY (United States)

    1994-12-01

    The principle goal of our laboratory is the discovery of new genes on human chromosome 19. One of the strategies to achieve this goal is through the use of cDNA clones known as {open_quotes}expressed sequence tags{close_quotes} (ESTs). ESTs, short segments of sequence from a cDNA clone that correspond to the mRNA, occur as unique regions in the genome and, therefore, can be used as markers for specific positions. In collaboration with researchers from Genethon in France, fifteen cDNA clones from a normalized human infant brain cDNA library were tested and determined to map to chromosome 19. A verification procedure is then followed to confirm assignment to chromosome 19. First, primers for each cDNA clone are developed and then amplified by polymerase chain reaction from genomic DNA. Next, a {sup 32}P-radiolabeled probe is made by polymerase chain reaction for each clone and then hybridized against filters containing an LLNL chromosome 19-specific cosmid library to find putative locations on the chromosome. The location is then verified by running a polymerase chain reactions from the positive cosmids. With the Browser database at LLNL, additional information about the positive cosmids can be found. Through use of the BLAST database at the National Library of Medicine, homologous sequences to the clones can be found. Among the fifteen cDNA clones received from Genethon, all have been amplified by polymerase chain reaction. Three have turned out as repetitive elements in the genome. Ten have been mapped to specific locations on chromosome 19. Putative locations have been found for the remaining two clones and thus verification testing will proceed.

  9. Arabidopsis MAP Kinase 4 regulates gene expression via transcription factor release in the nucleus

    DEFF Research Database (Denmark)

    Qiu, Jin-Long; Fiil, Berthe Katrine; Petersen, Klaus

    2008-01-01

    Plant and animal perception of microbes through pathogen surveillance proteins leads to MAP kinase signalling and the expression of defence genes. However, little is known about how plant MAP kinases regulate specific gene expression. We report that, in the absence of pathogens, Arabidopsis MAP...... supported by the suppression of PAD3 expression in mpk4-wrky33 double mutant backgrounds. Our data establish direct links between MPK4 and innate immunity and provide an example of how a plant MAP kinase can regulate gene expression by releasing transcription factors in the nucleus upon activation....

  10. A Glimpse of the Conformal Structure of Random Planar Maps

    Science.gov (United States)

    Curien, Nicolas

    2015-02-01

    We present a way to study the conformal structure of random planar maps. The main idea is to explore the map along an SLE (Schramm-Loewner evolution) process of parameter and to combine the locality property of the SLE6 together with the spatial Markov property of the underlying lattice in order to get a non-trivial geometric information. We follow this path in the case of the conformal structure of random triangulations with a boundary. Under a reasonable assumption called (*) that we have unfortunately not been able to verify, we prove that the limit of uniformized random planar triangulations has a fractal boundary measure of Hausdorff dimension almost surely. This agrees with the physics KPZ predictions and represents a first step towards a rigorous understanding of the links between random planar maps and the Gaussian free field (GFF).

  11. Maps of random walks on complex networks reveal community structure.

    Science.gov (United States)

    Rosvall, Martin; Bergstrom, Carl T

    2008-01-29

    To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network-including physics, chemistry, molecular biology, and medicine-information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.

  12. Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes.

    Directory of Open Access Journals (Sweden)

    María José Aranzana

    2005-11-01

    Full Text Available There is currently tremendous interest in the possibility of using genome-wide association mapping to identify genes responsible for natural variation, particularly for human disease susceptibility. The model plant Arabidopsis thaliana is in many ways an ideal candidate for such studies, because it is a highly selfing hermaphrodite. As a result, the species largely exists as a collection of naturally occurring inbred lines, or accessions, which can be genotyped once and phenotyped repeatedly. Furthermore, linkage disequilibrium in such a species will be much more extensive than in a comparable outcrossing species. We tested the feasibility of genome-wide association mapping in A. thaliana by searching for associations with flowering time and pathogen resistance in a sample of 95 accessions for which genome-wide polymorphism data were available. In spite of an extremely high rate of false positives due to population structure, we were able to identify known major genes for all phenotypes tested, thus demonstrating the potential of genome-wide association mapping in A. thaliana and other species with similar patterns of variation. The rate of false positives differed strongly between traits, with more clinal traits showing the highest rate. However, the false positive rates were always substantial regardless of the trait, highlighting the necessity of an appropriate genomic control in association studies.

  13. Getting Started with GeneRecon — An Introduction to the Association Mapping Tool GeneRecon

    DEFF Research Database (Denmark)

    Mailund, T; Schauser, Leif

    2006-01-01

    GeneRecon is a software package for linkage disequilibrium mapping using coalescent theory. It is based on Bayesian Markov-chain Monte Carlo (MCMC) method for fine-scale linkage-disequilibrium gene mapping using high-density marker maps. GeneRecon explicitly models the genealogy of a sample...... of the case chromosomes in the vicinity of a disease locus. Given case and control data in the form of genotype or haplotype information, it estimates a number of parameters, most importantly, the disease position....

  14. Integrated Transcriptome Map Highlights Structural and Functional Aspects of the Normal Human Heart.

    Science.gov (United States)

    Caracausi, Maria; Piovesan, Allison; Vitale, Lorenza; Pelleri, Maria Chiara

    2017-04-01

    A systematic meta-analysis of the available gene expression profiling datasets for the whole normal human heart generated a quantitative transcriptome reference map of this organ. Transcriptome Mapper (TRAM) software integrated 32 gene expression profile datasets from different sources returning a reference value of expression for each of the 43,360 known, mapped transcripts assayed by any of the experimental platforms used in this regard. Main findings include the visualization at the gene and chromosomal levels of the classical description of the basic histology and physiology of the heart, the identification of suitable housekeeping reference genes, the analysis of stoichiometry of gene products, and the focusing on chromosome 21 genes, which are present in one excess copy in Down syndrome subjects, presenting cardiovascular defects in 30-40% of cases. Independent in vitro validation showed an excellent correlation coefficient (r = 0.98) with the in silico data. Remarkably, heart/non-cardiac tissue expression ratio may also be used to anticipate that effects of mutations will most probably affect or not the heart. The quantitative reference global portrait of gene expression in the whole normal human heart illustrates the structural and functional aspects of the whole organ and is a general model to understand the mechanisms underlying heart pathophysiology. J. Cell. Physiol. 232: 759-770, 2017. © 2016 Wiley Periodicals, Inc.

  15. Simulating the large-scale structure of HI intensity maps

    Science.gov (United States)

    Seehars, Sebastian; Paranjape, Aseem; Witzemann, Amadeus; Refregier, Alexandre; Amara, Adam; Akeret, Joel

    2016-03-01

    Intensity mapping of neutral hydrogen (HI) is a promising observational probe of cosmology and large-scale structure. We present wide field simulations of HI intensity maps based on N-body simulations of a 2.6 Gpc / h box with 20483 particles (particle mass 1.6 × 1011 Msolar / h). Using a conditional mass function to populate the simulated dark matter density field with halos below the mass resolution of the simulation (108 Msolar / h assign HI to those halos according to a phenomenological halo to HI mass relation. The simulations span a redshift range of 0.35 lesssim z lesssim 0.9 in redshift bins of width Δ z ≈ 0.05 and cover a quarter of the sky at an angular resolution of about 7'. We use the simulated intensity maps to study the impact of non-linear effects and redshift space distortions on the angular clustering of HI. Focusing on the autocorrelations of the maps, we apply and compare several estimators for the angular power spectrum and its covariance. We verify that these estimators agree with analytic predictions on large scales and study the validity of approximations based on Gaussian random fields, particularly in the context of the covariance. We discuss how our results and the simulated maps can be useful for planning and interpreting future HI intensity mapping surveys.

  16. Fractal structures in a generalized square map with exponential terms

    Institute of Scientific and Technical Information of China (English)

    Li Xian-Feng; Chu Yan-Dong; Zhang Hui

    2012-01-01

    Fractal structures in a generalized squared map with exponential terms are expanded in this paper.We describe how complex behaviors can arise as the parameters change.The appearances of different kinds of fractal structures,in both the attractive and the divergent regions,and most interestingly,on small regular islands embedded in the chaotic region,are manifested to have a variety of extraordinary geometries in the parameter plane.

  17. A Novel Phytophthora sojae Resistance Rps12 Gene Mapped to a Genomic Region That Contains Several Rps Genes

    Science.gov (United States)

    Sahoo, Dipak K.; Abeysekara, Nilwala S.; Cianzio, Silvia R.; Robertson, Alison E.

    2017-01-01

    Phytophthora sojae Kaufmann and Gerdemann, which causes Phytophthora root rot, is a widespread pathogen that limits soybean production worldwide. Development of Phytophthora resistant cultivars carrying Phytophthora resistance Rps genes is a cost-effective approach in controlling this disease. For this mapping study of a novel Rps gene, 290 recombinant inbred lines (RILs) (F7 families) were developed by crossing the P. sojae resistant cultivar PI399036 with the P. sojae susceptible AR2 line, and were phenotyped for responses to a mixture of three P. sojae isolates that overcome most of the known Rps genes. Of these 290 RILs, 130 were homozygous resistant, 12 heterzygous and segregating for Phytophthora resistance, and 148 were recessive homozygous and susceptible. From this population, 59 RILs homozygous for Phytophthora sojae resistance and 61 susceptible to a mixture of P. sojae isolates R17 and Val12-11 or P7074 that overcome resistance encoded by known Rps genes mapped to Chromosome 18 were selected for mapping novel Rps gene. A single gene accounted for the 1:1 segregation of resistance and susceptibility among the RILs. The gene encoding the Phytophthora resistance mapped to a 5.8 cM interval between the SSR markers BARCSOYSSR_18_1840 and Sat_064 located in the lower arm of Chromosome 18. The gene is mapped 2.2 cM proximal to the NBSRps4/6-like sequence that was reported to co-segregate with the Phytophthora resistance genes Rps4 and Rps6. The gene is mapped to a highly recombinogenic, gene-rich genomic region carrying several nucleotide binding site-leucine rich repeat (NBS-LRR)-like genes. We named this novel gene as Rps12, which is expected to be an invaluable resource in breeding soybeans for Phytophthora resistance. PMID:28081566

  18. Accurate and unambiguous tag-to-gene mapping in serial analysis of gene expression

    Directory of Open Access Journals (Sweden)

    Melo Francisco

    2006-11-01

    Full Text Available Abstract Background In this study, we present a robust and reliable computational method for tag-to-gene assignment in serial analysis of gene expression (SAGE. The method relies on current genome information and annotation, incorporation of several new features, and key improvements over alternative methods, all of which are important to determine gene expression levels more accurately. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. Results We applied this method to the Saccharomyces cerevisiae genome, producing the most thorough and accurate annotation of potential virtual SAGE tags that is available today for this organism. The usefulness of this method is exemplified by the significant reduction of ambiguous cases in existing experimental SAGE data. In addition, we report new insights from the analysis of existing SAGE data. First, we found that experimental SAGE tags mapping onto introns, intron-exon boundaries, and non-coding RNA elements are observed in all available SAGE data. Second, a significant fraction of experimental SAGE tags was found to map onto genomic regions currently annotated as intergenic. Third, a significant number of existing experimental SAGE tags for yeast has been derived from truncated cDNAs, which are synthesized through oligo-d(T priming to internal poly-(A regions during reverse transcription. Conclusion We conclude that an accurate and unambiguous tag mapping process is essential to increase the quality and the amount of information that can be extracted from SAGE experiments. This is supported by the results obtained here and also by the large impact that the erroneous interpretation of these data could have on downstream applications.

  19. One-dimensional map lattices: Synchronization, bifurcations, and chaotic structures

    DEFF Research Database (Denmark)

    Belykh, Vladimir N.; Mosekilde, Erik

    1996-01-01

    The paper presents a qualitative analysis of coupled map lattices (CMLs) for the case of arbitrary nonlinearity of the local map and with space-shift as well as diffusion coupling. The effect of synchronization where, independently of the initial conditions, all elements of a CML acquire uniform...... dynamics is investigated and stable chaotic time behaviors, steady structures, and traveling waves are described. Finally, the bifurcations occurring under the transition from spatiotemporal chaos to chaotic synchronization and the peculiarities of CMLs with specific symmetries are discussed....

  20. Global analysis of candidate genes important for fitness in a competitive biofilm using DNA-array-based transposon mapping.

    Science.gov (United States)

    Junker, Lauren M; Peters, Joseph E; Hay, Anthony G

    2006-08-01

    Escherichia coli strain PHL628 was subjected to saturating Tn5 transposon mutagenesis and then grown under competitive planktonic or biofilm conditions. The locations of transposon insertions from the remaining cells were then mapped on a gene array. The results from the array mapping indicated that 4.5 % of the E. coli genome was important under these conditions. Specifically, 114 genes were identified as important for the biofilm lifestyle, whereas 80 genes were important for the planktonic lifestyle. Four broad functional categories were identified as biofilm-important. These included genes encoding cell structures, small-molecule transport, energy metabolism and regulatory functions. For one of these genes, arcA, an insertion mutant was generated and its biofilm-related phenotype was examined. Results from both the transposon array and insertion mutagenesis indicated that arcA, which is known to be a negative response regulator of genes in aerobic pathways, was important for competitiveness in E. coli PHL628 biofilms. This work also demonstrated that ligation-mediated PCR, coupled with array-based transposon mapping, was an effective tool for identifying a large variety of candidate genes that are important for biofilm fitness.

  1. Cognitive structure of occupational risks represented by a perceptual map.

    Science.gov (United States)

    Cardoso-Junior, M M; Scarpel, R A

    2012-01-01

    The main focus of risk management is technical and rational analysis about the operational risks and by those imposed by the occupational environment. In this work one seeks to contribute to the risk perception study and to better comprehend how a group of occupational safety students assesses a set of activities and environmental agents. In this way it was used theory sustained by psychometric paradigm and multivariate analysis tools, mainly multidimensional scaling, generalized Procrustes analysis and facets theory, in order to construct the perceptual map of occupational risks. The results obtained showed that the essential characteristics of risks, which were initially splited in 4 facets were detected and maintained in the perceptual map. It was not possible to reveal the cognitive structure of the group, because the variability of the students was too high. Differences among the risks analyzed could not be detected as well in the perceptual map of the group.

  2. Computer technology of genogeographic analysis of a gene pool: II. Statistical transformation of maps

    Energy Technology Data Exchange (ETDEWEB)

    Balanovskaya, E.V.; Nurbaev, S.D.; Rychkov, Yu.G. [Vavilov Institute of General Genetics, Moscow (Russian Federation)

    1994-11-01

    Transformations of computer maps of geographic distribution of gene frequencies using basic mathematical statistical procedures are considered. These transformations are designated as statistical transformation of maps. Two transformation groups are considered: of one map separately and of a group of maps. Transformations possess a value beyond their use as intermediate stages of more complicated cartographical analysis: the resulting maps carry entirely new information on the geography of genes or a gene pool. This article considers three examples of obtaining new genetic profiles using statistical transformation algorithms. These profiles are of: (1) heterozygosity (of HLA-A, B, C loci in northeastern Eurasia); (2) disease risk (Rh-incompatibility of mother and child with simultaneous registration of Rh and ABO blood groups in Eastern Europe); (3) genetic distances (from own mean ethnic values for Belarus and from mean Russian values for the gene pool of Eastern Europe). 15 refs., 9 figs., 1 tab.

  3. Geophysical mapping of complex glaciogenic large-scale structures

    DEFF Research Database (Denmark)

    Høyer, Anne-Sophie

    2013-01-01

    is required to understand the structures. In practice, however, also the applicability and costs of the methods are crucial. The SkyTEM method is very cost-effective in providing dense data sets, and it is therefore recommendable to use this method initially in mapping campaigns. For more detailed structural...... by periglacial and postglacial erosion that formed the present-day terrain. Paleoglaciological calculations based on the observed thrust structures show that the deformation was caused by a very thick ice sheet with a steep ice profile, resting on permafrost....

  4. Mapping the magnetic and crystal structure in cobalt nanowires

    Energy Technology Data Exchange (ETDEWEB)

    Cantu-Valle, Jesus; Betancourt, Israel; Sanchez, John E.; Ruiz-Zepeda, Francisco; Mendoza-Santoyo, Fernando; Ponce, Arturo, E-mail: arturo.ponce@utsa.edu [Department of Physics and Astronomy, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249 (United States); Maqableh, Mazin M.; Stadler, Bethanie J. H. [Electrical and Computer Engineering, University of Minnesota, 4-174 EE/CSci Bldg., 200 Union St. SE, Minneapolis, Minnesota 55455 (United States)

    2015-07-14

    Using off-axis electron holography under Lorentz microscopy conditions to experimentally determine the magnetization distribution in individual cobalt (Co) nanowires, and scanning precession-electron diffraction to obtain their crystalline orientation phase map, allowed us to directly visualize with high accuracy the effect of crystallographic texture on the magnetization of nanowires. The influence of grain boundaries and disorientations on the magnetic structure is correlated on the basis of micromagnetic analysis in order to establish the detailed relationship between magnetic and crystalline structure. This approach demonstrates the applicability of the method employed and provides further understanding on the effect of crystalline structure on magnetic properties at the nanometric scale.

  5. Reference Map Technique for Incompressible Fluid-Structure Interaction Problems

    Science.gov (United States)

    Rycroft, Chris; Wu, Chen-Hung; Yu, Yue; Kamrin, Ken

    2016-11-01

    We present a fully Eulerian approach to simulate soft structures immersed in an incompressible fluid. The flow is simulated on a fixed grid using a second order projection method to solve the incompressible Navier-Stokes equations, and the fluid-structure interfaces are modeled using the level set method. By introducing a reference map variable to model finite-deformation constitutive relations in the structure on the same grid as the fluid, the interfacial coupling is highly simplified. This fully Eulerian approach provides a computationally efficient alternative to moving mesh approaches. Example simulations featuring many-body contacts and flexible swimmers will be presented.

  6. Simulating the Large-Scale Structure of HI Intensity Maps

    CERN Document Server

    Seehars, Sebastian; Witzemann, Amadeus; Refregier, Alexandre; Amara, Adam; Akeret, Joel

    2015-01-01

    Intensity mapping of neutral hydrogen (HI) is a promising observational probe of cosmology and large-scale structure. We present wide field simulations of HI intensity maps based on N-body simulations, the halo model, and a phenomenological prescription for assigning HI mass to halos. The simulations span a redshift range of 0.35 < z < 0.9 in redshift bins of width $\\Delta z \\approx 0.05$ and cover a quarter of the sky at an angular resolution of about 7'. We use the simulated intensity maps to study the impact of non-linear effects on the angular clustering of HI. We apply and compare several estimators for the angular power spectrum and its covariance. We verify that they agree with analytic predictions on large scales and study the validity of approximations based on Gaussian random fields, particularly in the context of the covariance. We discuss how our results and the simulated maps can be useful for planning and interpreting future HI intensity mapping surveys.

  7. Gene therapy in glaucoma-part 2: Genetic etiology and gene mapping.

    Science.gov (United States)

    Mahdy, Mohamed Abdel-Monem Soliman

    2010-05-01

    Glaucoma diagnosis, identification of people at risk, initiation of treatment and timing of surgical intervention remains a problem. Despite new and improving diagnostic and therapeutic options for glaucoma, blindness from glaucoma is increasing and glaucoma remains a major public health problem. The role of heredity in ocular disease is attracting greater attention as the knowledge and recent advances of Human Genome Project and the HapMap Project have made genetic analysis of many human disorders possible.Glaucoma offers a variety of potential targets for gene therapy. All risk factors for glaucoma and their underlying causes are potentially susceptible to modulation by gene transfer.The discovery of genes responsible for glaucoma has led to the development of new methods of Deoxyribonucleic acid (DNA)-based diagnosis and treatment. As genetic defects responsible for glaucoma are identified and the biochemical mechanisms underlying the disease are recognized, new methods of therapy can be developed. It is of utmost importance for the ophthalmologists and glaucoma specialists to be familiar with and understand the basic molecular mechanisms, genes responsible for glaucoma and the ways of genetic treatment. METHOD OF LITERATURE SEARCH: The literature was searched on the Medline database, using the PubMed interface.

  8. Construction of microsatellite-based linkage map and mapping of nectarilessness and hairiness genes in Gossypium tomentosum

    Indian Academy of Sciences (India)

    Meiying Hou; Caiping Cai; Shuwen Zhang; Wangzhen Guo; Tianzhen Zhang; Baoliang Zhou

    2013-12-01

    Gossypium tomentosum, a wild tetraploid cotton species with AD genomes, possesses genes conferring strong fibers and high heat tolerance. To effectively transfer these genes into Gossypium hirsutum, an entire microsatellite (simple sequence repeat, SSR)-based genetic map was constructed using the interspecific cross of G. hirsutum × G. tomentosum (HT). We detected 1800 loci from 1347 pairs of polymorphic primers. Of these, 1204 loci were grouped into 35 linkage groups at LOD ≥4. The map covers 3320.8 cM, with a mean density of 2.76 cM per locus. We detected 420 common loci (186 in the At subgenome and 234 in Dt) between the HT map and the map of TM-1 (G. hirsutum) and Hai 7124 (G. barbadense; HB map). The linkage groups were assigned chromosome numbers based on location of common loci and the HB map as reference. A comparison of common markers revealed that no significant chromosomal rearrangement exist between G. tomentosum and G. barbadense. Interestingly, however, we detected numerous (33.7%) segregation loci deviating from 3:1 ratio ($P \\lt 0.05$) in HT, mostly clustering on eight chromosomes in the Dt subgenome, with some on three chromosomes in At. Two morphological traits, leaf hairiness and leaf nectarilessness were mapped on chromosomes 6 (A6) and 26 (D12), respectively. The SSR-based map constructed in this study will be useful for further genetic studies on cotton breeding, including mapping loci controlling quantitative traits associated with fiber quality, stress tolerance and developing chromosome segment specific introgression lines from G. tomentosum into G. hirsutum using marker-assisted selection.

  9. iSLIM: a comprehensive approach to mapping and characterizing gene regulatory networks.

    Science.gov (United States)

    Rockel, Sylvie; Geertz, Marcel; Hens, Korneel; Deplancke, Bart; Maerkl, Sebastian J

    2013-02-01

    Mapping gene regulatory networks is a significant challenge in systems biology, yet only a few methods are currently capable of systems-level identification of transcription factors (TFs) that bind a specific regulatory element. We developed a microfluidic method for integrated systems-level interaction mapping of TF-DNA interactions, generating and interrogating an array of 423 full-length Drosophila TFs. With integrated systems-level interaction mapping, it is now possible to rapidly and quantitatively map gene regulatory networks of higher eukaryotes.

  10. Chicken rRNA Gene Cluster Structure.

    Directory of Open Access Journals (Sweden)

    Alexander G Dyomin

    Full Text Available Ribosomal RNA (rRNA genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5'ETS (1836 bp, 18S rRNA gene (1823 bp, ITS1 (2530 bp, 5.8S rRNA gene (157 bp, ITS2 (733 bp, 28S rRNA gene (4441 bp and 3'ETS (343 bp. The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through in situ fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against de novo assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region. The results have confirmed the chicken rRNA gene cluster validity.

  11. Predicting the size of the progeny mapping population required to positionally clone a gene.

    Science.gov (United States)

    Dinka, Stephen J; Campbell, Matthew A; Demers, Tyler; Raizada, Manish N

    2007-08-01

    A key frustration during positional gene cloning (map-based cloning) is that the size of the progeny mapping population is difficult to predict, because the meiotic recombination frequency varies along chromosomes. We describe a detailed methodology to improve this prediction using rice (Oryza sativa L.) as a model system. We derived and/or validated, then fine-tuned, equations that estimate the mapping population size by comparing these theoretical estimates to 41 successful positional cloning attempts. We then used each validated equation to test whether neighborhood meiotic recombination frequencies extracted from a reference RFLP map can help researchers predict the mapping population size. We developed a meiotic recombination frequency map (MRFM) for approximately 1400 marker intervals in rice and anchored each published allele onto an interval on this map. We show that neighborhood recombination frequencies (R-map, >280-kb segments) extracted from the MRFM, in conjunction with the validated formulas, better predicted the mapping population size than the genome-wide average recombination frequency (R-avg), with improved results whether the recombination frequency was calculated as genes/cM or kb/cM. Our results offer a detailed road map for better predicting mapping population size in diverse eukaryotes, but useful predictions will require robust recombination frequency maps based on sampling more progeny.

  12. Bifurcation of learning and structure formation in neuronal maps

    DEFF Research Database (Denmark)

    Marschler, Christian; Faust-Ellsässer, Carmen; Starke, Jens

    2014-01-01

    Most learning processes in neuronal networks happen on a much longer time scale than that of the underlying neuronal dynamics. It is therefore useful to analyze slowly varying macroscopic order parameters to explore a network's learning ability. We study the synaptic learning process giving rise...... to map formation in the laminar nucleus of the barn owl's auditory system. Using equation-free methods, we perform a bifurcation analysis of spatio-temporal structure formation in the associated synaptic-weight matrix. This enables us to analyze learning as a bifurcation process and follow the unstable...... states as well. A simple time translation of the learning window function shifts the bifurcation point of structure formation and goes along with traveling waves in the map, without changing the animal's sound localization performance....

  13. Topographic hub maps of the human structural neocortical network.

    Directory of Open Access Journals (Sweden)

    Emil H J Nijhuis

    Full Text Available Hubs within the neocortical structural network determined by graph theoretical analysis play a crucial role in brain function. We mapped neocortical hubs topographically, using a sample population of 63 young adults. Subjects were imaged with high resolution structural and diffusion weighted magnetic resonance imaging techniques. Multiple network configurations were then constructed per subject, using random parcellations to define the nodes and using fibre tractography to determine the connectivity between the nodes. The networks were analysed with graph theoretical measures. Our results give reference maps of hub distribution measured with betweenness centrality and node degree. The loci of the hubs correspond with key areas from known overlapping cognitive networks. Several hubs were asymmetrically organized across hemispheres. Furthermore, females have hubs with higher betweenness centrality and males have hubs with higher node degree. Female networks have higher small-world indices.

  14. Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci

    Directory of Open Access Journals (Sweden)

    Sehgal Deepmala

    2012-01-01

    -based markers represent an important resource for identification of candidate genes for other mapped abiotic stress QTLs in pearl millet. They also provide a resource for initiating association studies using candidate genes and also for comparing the structure and function of distantly related plant genomes such as other Poaceae members.

  15. Mapping regulatory genes as candidates for cold and drought stress tolerance in barley.

    Science.gov (United States)

    Tondelli, A; Francia, E; Barabaschi, D; Aprile, A; Skinner, J S; Stockinger, E J; Stanca, A M; Pecchioni, N

    2006-02-01

    Cereal crop yield is greatly affected in many growing areas by abiotic stresses, mainly low temperature and drought. In order to find candidates for the tolerance genes for these stresses, 13 genes encoding for transcription factors and upstream regulators were screened by amplification and SSCP on six parental genotypes of three barley mapping populations ('Nure' x 'Tremois', 'Proctor' x 'Nudinka', and 'Steptoe' x 'Morex'), and mapped as newly developed STS, SNP, and SSCP markers. A new consensus function map was then drawn using the three maps above, including 16 regulatory candidate genes (CGs). The positions of barley cold and drought tolerance quantitative trait loci (QTLs) presently described in the literature were added to the consensus map to find positional candidates from among the mapped genes. A cluster of six HvCBF genes co-mapped with the Fr-H2 cold tolerance QTL, while no QTLs for the same trait were positioned on chromosome 7H, where two putative barley regulators of CBF expression, ICE1 and FRY1, found by homology search, were mapped in this work. These observations suggest that CBF gene(s) themselves, rather than their two regulators, are at present the best candidates for cold tolerance. Four out of 12 drought tolerance QTLs of the consensus map are associated with regulatory CGs, on chromosomes 2H, 5H, and 7H, and two QTLs with effector genes, on chromosomes 5H and 6H. The results obtained could be used to guide MAS applications, allowing introduction into an ideal genotype of favourable alleles of tolerance QTLs.

  16. Fine mapping of the Ht2 (Helminthosporium turcicum resistance 2) gene in maize

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Fine mapping of Helminthosporium turcicum resistance gene Ht2 is extremely valuable for map-based cloning of the Ht2 gene, gaining a better knowledge of the distribution of resistance genes in maize genome and marker-assisted selection in maize breeding. An F2 mapping population was developed from a cross between a resistant inbred line 77Ht2 and a susceptible inbred line Huobai. With the aid of RFLP marker analyses, the Ht2 gene was mapped between the RFLP markers UMC89 and BNL2.369 on chromosome 8, with a genetic distance of 0.9 cM to BNL2.369. There was a linkage between SSR markers UMC1202, BNLG1152, UMC1149 and the Ht2 gene by SSR assay. Among the SSR markers, the genetic distance between UMC1149 and the Ht2 gene was 7.2 cM. By bulked segregant analysis 7 RAPD-amplified products which were probably linked to the Ht2 gene were selected after screening 450 RAPD primers and converted the single-copy ones into SCAR markers. Linkage analysis showed that the genetic distance between the SCAR marker SD-06633 and the Ht2 gene was 0.4 cM. From these results, a part of linkage map around the Ht2 gene was constructed.

  17. Modeling adsorption properties of structurally deformed metal-organic frameworks using structure-property map.

    Science.gov (United States)

    Jeong, WooSeok; Lim, Dae-Woon; Kim, Sungjune; Harale, Aadesh; Yoon, Minyoung; Suh, Myunghyun Paik; Kim, Jihan

    2017-07-25

    Structural deformation and collapse in metal-organic frameworks (MOFs) can lead to loss of long-range order, making it a challenge to model these amorphous materials using conventional computational methods. In this work, we show that a structure-property map consisting of simulated data for crystalline MOFs can be used to indirectly obtain adsorption properties of structurally deformed MOFs. The structure-property map (with dimensions such as Henry coefficient, heat of adsorption, and pore volume) was constructed using a large data set of over 12000 crystalline MOFs from molecular simulations. By mapping the experimental data points of deformed SNU-200, MOF-5, and Ni-MOF-74 onto this structure-property map, we show that the experimentally deformed MOFs share similar adsorption properties with their nearest neighbor crystalline structures. Once the nearest neighbor crystalline MOFs for a deformed MOF are selected from a structure-property map at a specific condition, then the adsorption properties of these MOFs can be successfully transformed onto the degraded MOFs, leading to a new way to obtain properties of materials whose structural information is lost.

  18. MODELING METHOD FOR PRODUCT STRUCTURE MAPPING BASED ON REVERSE SOLVING OF LOCUS AND MOTION

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shuyou; YI Guodong; XU Xiaofeng

    2007-01-01

    Aiming at the problem of structure design in reverse-design of mechanism, a structure mapping method based on reverse solving of locus and motion (RSLM) is presented. The mechanism scheme meeting the requirements of geometric and structural features is obtained through RSLM. The element instance subsets related to component are established based on the element type mapping, pair structure type mapping and design knowledge mapping between components and elements layer by layer. The assembly position mapping of elements is established based on the topological structure information of mechanism scheme, and the product modeling of structure mapping is realized. The algorithm program and prototype system of product structure mapping based on RSLM are developed. Application samples show that the method implements the integration of scheme design, assembly design and structure design, and modeling for product structure mapping based on RSLM. The feasibility of assembly is analyzed in scheme design that contributes to reducing the design error, and raising the design efficiency and quality.

  19. The bovine 5' AMPK gene family: mapping and single nucleotide polymorphism detection.

    Science.gov (United States)

    McKay, Stephanie D; White, Stephen N; Kata, Srinivas R; Loan, Raymond; Womack, James E

    2003-12-01

    The 5'-AMP-activated protein kinase (AMPK) family is an ancient stress response system whose primary function is regulation of cellular ATP. Activation of AMPK, which is instigated by environmental and nutritional stresses, initiates energy-conserving measures that protect the cell by inhibition and phosphorylation of key enzymes in energy-consuming biochemical pathways. The seven genes that comprise the bovine AMPK family were mapped in cattle by using a radiation hybrid panel. The seven genes mapped to six different cattle chromosomes, each with a LOD score greater than 10.0. PRKAA1 mapped to BTA 20, PRKAA2 and PRKAB2 to BTA 3, PRKAB1 to BTA 17, PRKAG1 to BTA 5, PRKAG2 to BTA 4, and PRKAG3 to BTA 2. Five of the seven genes mapped to regions expected from human/cattle comparative maps. PRKAB2 and PRKAG3, however, have not been mapped in humans. We predict these genes to be located on HSA 1 and 2, respectively. Additionally, one synonymous and one non-synonymous single nucleotide polymorphism (SNP) were detected in PRKAG3 in Bos taurus cattle. In an effort to determine ancestral origins, various herds of mixed breed cattle as well as other ruminant species were characterized for sequence variation in this region of PRKAG3. Owing to the physiological importance of this gene family, we believe that its individual genes are candidate genes for conferring resistance to diseases in cattle.

  20. 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.

  1. QTL mapping in white spruce: gene maps and genomic regions underlying adaptive traits across pedigrees, years and environments

    Directory of Open Access Journals (Sweden)

    Meirmans Patrick G

    2011-03-01

    Full Text Available Abstract Background The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments. Results Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth. Conclusions This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic

  2. GIS-Based Data Structure for Geological Mapping of Ceres — One Global Map Composed of 15 Map Sheets

    Science.gov (United States)

    Naß, A.; Dawn Mapping Team

    2017-06-01

    Deriving valid statements out of interpretative geological mapping is very time intensive. Another challenge is generating one map composed of several map sheets which presents a geologically-consistent and geometrical/visual comparable content.

  3. Mapping gene associations in human mitochondria using clinical disease phenotypes.

    Directory of Open Access Journals (Sweden)

    Curt Scharfe

    2009-04-01

    Full Text Available Nuclear genes encode most mitochondrial proteins, and their mutations cause diverse and debilitating clinical disorders. To date, 1,200 of these mitochondrial genes have been recorded, while no standardized catalog exists of the associated clinical phenotypes. Such a catalog would be useful to develop methods to analyze human phenotypic data, to determine genotype-phenotype relations among many genes and diseases, and to support the clinical diagnosis of mitochondrial disorders. Here we establish a clinical phenotype catalog of 174 mitochondrial disease genes and study associations of diseases and genes. Phenotypic features such as clinical signs and symptoms were manually annotated from full-text medical articles and classified based on the hierarchical MeSH ontology. This classification of phenotypic features of each gene allowed for the comparison of diseases between different genes. In turn, we were then able to measure the phenotypic associations of disease genes for which we calculated a quantitative value that is based on their shared phenotypic features. The results showed that genes sharing more similar phenotypes have a stronger tendency for functional interactions, proving the usefulness of phenotype similarity values in disease gene network analysis. We then constructed a functional network of mitochondrial genes and discovered a higher connectivity for non-disease than for disease genes, and a tendency of disease genes to interact with each other. Utilizing these differences, we propose 168 candidate genes that resemble the characteristic interaction patterns of mitochondrial disease genes. Through their network associations, the candidates are further prioritized for the study of specific disorders such as optic neuropathies and Parkinson disease. Most mitochondrial disease phenotypes involve several clinical categories including neurologic, metabolic, and gastrointestinal disorders, which might indicate the effects of gene defects

  4. A robust linkage map of the porcine autosome based on gene-associated SNPs

    DEFF Research Database (Denmark)

    Vingborg, Rikke K K; Gregersen, Vivi R; Zhan, Bujie;

    2009-01-01

    Background Genetic linkage maps are necessary for mapping of mendelian traits and quantitative trait loci (QTLs). To identify the actual genes, which control these traits, a map based on gene-associated single nucleotide polymorphism (SNP) markers is highly valuable. In this study, the SNPs were...... genotyped in a large family material comprising more than 5,000 piglets derived from 12 Duroc boars crossed with 236 Danish Landrace/Danish Large White sows. The SNPs were identified in sequence alignments of 4,600 different amplicons obtained from the 12 boars and containing coding regions of genes derived...... from expressed sequence tags (ESTs) and genomic shotgun sequences. Results Linkage maps of all 18 porcine autosomes were constructed based on 456 gene-associated and six porcine EST-based SNPs. The total length of the averaged-sex whole porcine autosome was estimated to 1,711.8 cM resulting...

  5. Evolutionary optimization of biopolymers and sequence structure maps

    Energy Technology Data Exchange (ETDEWEB)

    Reidys, C.M.; Kopp, S.; Schuster, P. [Institut fuer Molekulare Biotechnologie, Jena (Germany)

    1996-06-01

    Searching for biopolymers having a predefined function is a core problem of biotechnology, biochemistry and pharmacy. On the level of RNA sequences and their corresponding secondary structures we show that this problem can be analyzed mathematically. The strategy will be to study the properties of the RNA sequence to secondary structure mapping that is essential for the understanding of the search process. We show that to each secondary structure s there exists a neutral network consisting of all sequences folding into s. This network can be modeled as a random graph and has the following generic properties: it is dense and has a giant component within the graph of compatible sequences. The neutral network percolates sequence space and any two neutral nets come close in terms of Hamming distance. We investigate the distribution of the orders of neutral nets and show that above a certain threshold the topology of neutral nets allows to find practically all frequent secondary structures.

  6. Structure, expression and functions of MTA genes.

    Science.gov (United States)

    Kumar, Rakesh; Wang, Rui-An

    2016-05-15

    Metastatic associated proteins (MTA) are integrators of upstream regulatory signals with the ability to act as master coregulators for modifying gene transcriptional activity. The MTA family includes three genes and multiple alternatively spliced variants. The MTA proteins neither have their own enzymatic activity nor have been shown to directly interact with DNA. However, MTA proteins interact with a variety of chromatin remodeling factors and complexes with enzymatic activities for modulating the plasticity of nucleosomes, leading to the repression or derepression of target genes or other extra-nuclear and nucleosome remodeling and histone deacetylase (NuRD)-complex independent activities. The functions of MTA family members are driven by the steady state levels and subcellular localization of MTA proteins, the dynamic nature of modifying signals and enzymes, the structural features and post-translational modification of protein domains, interactions with binding proteins, and the nature of the engaged and resulting features of nucleosomes in the proximity of target genes. In general, MTA1 and MTA2 are the most upregulated genes in human cancer and correlate well with aggressive phenotypes, therapeutic resistance, poor prognosis and ultimately, unfavorable survival of cancer patients. Here we will discuss the structure, expression and functions of the MTA family of genes in the context of cancer cells.

  7. Further mapping of the properdin deficiency gene in a Tunisian Jewish family--evidence for genetic homogeneity.

    Science.gov (United States)

    Ash, S; Johnson, C; Shohat, M; Shohat, T; Schlesinger, M

    1994-08-01

    The properdin deficiency gene has been localized to Xp21.1-Xcen; however, it is not clear whether the mutation responsible for the disease co-maps exactly with the structural properdin gene. Based on a recent study on a total of six families, the gene was found linked to DXS255 (theta = 0.00). As only a few families have been studied, it is not known whether the same gene is responsible for the disease in all families. In order to better localize the disease gene in Israel, we studied a Tunisian Jewish family with properdin deficiency for linkage with various X-markers. A maximum lod score of 1.93 at theta = 0.00 was calculated with the DXS7 probe while there was one recombination with DXS255. This study helps to better localize the properdin deficiency gene to Xp11.3-p21.1 proximal to DXS255 locus and confirms that there is no indication of genetic heterogeneity. Whether the properdin structural gene (PFC) and properdin deficiency locus are one and the same await demonstration of mutations in the structural gene in patients with properdin deficiency.

  8. GeneRecon—A coalescent based tool for fine-scale association mapping

    DEFF Research Database (Denmark)

    Mailund, Thomas; Schierup, Mikkel Heide; Pedersen, Christian Nørgaard Storm

    2006-01-01

    GeneRecon is a tool for fine-scale association mapping using a coalescence model. GeneRecon takes as input case-control data from phased or unphased SNP and micro-satellite genotypes. The posterior distribution of disease locus position is obtained by Metropolis Hastings sampling in the state space...... of genealogies. Input format, search strategy, and the sampled statistics can be configured through the Guile Scheme programming language embedded in GeneRecon, making GeneRecon highly configurable....

  9. Mapping of QTL for resistance to powdery mildew and resistance gene analogues in perennial ryegrass

    DEFF Research Database (Denmark)

    Schejbel, B; Jensen, L B; Asp, T;

    2008-01-01

    The objective of this study was to map resistance gene analogues (RGA) and quantitative trait loci (QTL) for powdery mildew resistance in perennial ryegrass (Lolium perenne L.). The mapping population consisted of 184 F2 genotypes produced from a cross between one genotype of a synthetic perennial...

  10. Genetic Alterations in Familial Breast Cancer: Mapping and Cloning Genes Other Than BRCAl

    Science.gov (United States)

    1997-09-01

    predispose to breast cancer . These mutations are always in the context of Cowden’s Syndrome, and do not appear in families with brest cancer in the...AD AWARD NUMBER DAMD17-94-J-4307 TITLE: Genetic Alterations in Familial Breast Cancer : Mapping and Cloning Genes Other Than BRCA1 PRINCIPAL...Aug97-) Genetic Alterations in Familial Breast Cancer : Mapping and Cloning Genes Other than BRCA1 6. AUTHOR{S) Mary-Clair King, Ph.D. 7

  11. Admixture mapping as a tool in gene discovery.

    Science.gov (United States)

    Seldin, Michael F

    2007-06-01

    Admixture mapping is a rapidly developing method to map susceptibility alleles in complex genetic disease associated with continental ancestry. Theoretically, when admixture between continental populations has occurred relatively recently, the chromosomal segments derived from the parental populations can be deduced from the differences in genotype allele frequencies. Progress in computational algorithms, in identification of ancestry informative single nucleotide polymorphisms, and in recent studies applying these tools suggests that this approach will complement other strategies for identifying the variation that underlies many complex diseases.

  12. Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

    Science.gov (United States)

    González-Prendes, Rayner; Quintanilla, Raquel; Cánovas, Angela; Manunza, Arianna; Figueiredo Cardoso, Tainã; Jordana, Jordi; Noguera, José Luis; Pena, Ramona N.; Amills, Marcel

    2017-01-01

    Meat quality traits have an increasing importance in the pig industry because of their strong impact on consumer acceptance. Herewith, we have combined phenotypic and microarray expression data to map loci with potential effects on five meat quality traits recorded in the longissimus dorsi (LD) and gluteus medius (GM) muscles of 350 Duroc pigs, i.e. pH at 24 hours post-mortem (pH24), electric conductivity (CE) and muscle redness (a*), lightness (L*) and yellowness (b*). We have found significant genome-wide associations for CE of LD on SSC4 (~104 Mb), SSC5 (~15 Mb) and SSC13 (~137 Mb), while several additional regions were significantly associated with meat quality traits at the chromosome-wide level. There was a low positional concordance between the associations found for LD and GM traits, a feature that reflects the existence of differences in the genetic determinism of meat quality phenotypes in these two muscles. The performance of an eQTL search for SNPs mapping to the regions associated with meat quality traits demonstrated that the GM a* SSC3 and pH24 SSC17 QTL display positional concordance with cis-eQTL regulating the expression of several genes with a potential role on muscle metabolism. PMID:28054563

  13. Tridimensional Regression for Comparing and Mapping 3D Anatomical Structures

    Directory of Open Access Journals (Sweden)

    Kendra K. Schmid

    2012-01-01

    Full Text Available Shape analysis is useful for a wide variety of disciplines and has many applications. There are many approaches to shape analysis, one of which focuses on the analysis of shapes that are represented by the coordinates of predefined landmarks on the object. This paper discusses Tridimensional Regression, a technique that can be used for mapping images and shapes that are represented by sets of three-dimensional landmark coordinates, for comparing and mapping 3D anatomical structures. The degree of similarity between shapes can be quantified using the tridimensional coefficient of determination (2. An experiment was conducted to evaluate the effectiveness of this technique to correctly match the image of a face with another image of the same face. These results were compared to the 2 values obtained when only two dimensions are used and show that using three dimensions increases the ability to correctly match and discriminate between faces.

  14. Using structure restoration maps to comprehensively identify potential faults and fractures in compressional structures

    Institute of Scientific and Technical Information of China (English)

    OU Cheng-hua; CHEN Wei; LI Chao-chun

    2016-01-01

    Faults and fractures of multiple scales are frequently induced and generated in compressional structural system. Comprehensive identification of these potential faults and fractures that cannot be distinguished directly from seismic profile of the complex structures is still an unanswered problem. Based on the compressional structural geometry and kinematics theories as well as the structural interpretation from seismic data, a set of techniques is established for the identification of potential faults and fractures in compressional structures. Firstly, three-dimensional (3D) patterns and characteristics of the faults directly interpreted from seismic profile were illustrated by 3D structural model. Then, the unfolding index maps, the principal structural curvature maps, and tectonic stress field maps were obtained from structural restoration. Moreover, potential faults and fractures in compressional structures were quantitatively identified relying on comprehensive analysis of these three maps. Successful identification of the potential faults and fractures in Mishrif limestone formation and in Asmari dolomite formation of Buzurgan anticline in Iraq demonstrates the applicability and reliability of these techniques.

  15. An Arabidopsis example of association mapping in structured samples.

    Directory of Open Access Journals (Sweden)

    Keyan Zhao

    2007-01-01

    Full Text Available A potentially serious disadvantage of association mapping is the fact that marker-trait associations may arise from confounding population structure as well as from linkage to causative polymorphisms. Using genome-wide marker data, we have previously demonstrated that the problem can be severe in a global sample of 95 Arabidopsis thaliana accessions, and that established methods for controlling for population structure are generally insufficient. Here, we use the same sample together with a number of flowering-related phenotypes and data-perturbation simulations to evaluate a wider range of methods for controlling for population structure. We find that, in terms of reducing the false-positive rate while maintaining statistical power, a recently introduced mixed-model approach that takes genome-wide differences in relatedness into account via estimated pairwise kinship coefficients generally performs best. By combining the association results with results from linkage mapping in F2 crosses, we identify one previously known true positive and several promising new associations, but also demonstrate the existence of both false positives and false negatives. Our results illustrate the potential of genome-wide association scans as a tool for dissecting the genetics of natural variation, while at the same time highlighting the pitfalls. The importance of study design is clear; our study is severely under-powered both in terms of sample size and marker density. Our results also provide a striking demonstration of confounding by population structure. While statistical methods can be used to ameliorate this problem, they cannot always be effective and are certainly not a substitute for independent evidence, such as that obtained via crosses or transgenic experiments. Ultimately, association mapping is a powerful tool for identifying a list of candidates that is short enough to permit further genetic study.

  16. 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.

  17. Mapping of gene expression reveals CYP27A1 as a susceptibility gene for sporadic ALS.

    Directory of Open Access Journals (Sweden)

    Frank P Diekstra

    Full Text Available Amyotrophic lateral sclerosis (ALS is a progressive, neurodegenerative disease characterized by loss of upper and lower motor neurons. ALS is considered to be a complex trait and genome-wide association studies (GWAS have implicated a few susceptibility loci. However, many more causal loci remain to be discovered. Since it has been shown that genetic variants associated with complex traits are more likely to be eQTLs than frequency-matched variants from GWAS platforms, we conducted a two-stage genome-wide screening for eQTLs associated with ALS. In addition, we applied an eQTL analysis to finemap association loci. Expression profiles using peripheral blood of 323 sporadic ALS patients and 413 controls were mapped to genome-wide genotyping data. Subsequently, data from a two-stage GWAS (3,568 patients and 10,163 controls were used to prioritize eQTLs identified in the first stage (162 ALS, 207 controls. These prioritized eQTLs were carried forward to the second sample with both gene-expression and genotyping data (161 ALS, 206 controls. Replicated eQTL SNPs were then tested for association in the second-stage GWAS data to find SNPs associated with disease, that survived correction for multiple testing. We thus identified twelve cis eQTLs with nominally significant associations in the second-stage GWAS data. Eight SNP-transcript pairs of highest significance (lowest p = 1.27 × 10(-51 withstood multiple-testing correction in the second stage and modulated CYP27A1 gene expression. Additionally, we show that C9orf72 appears to be the only gene in the 9p21.2 locus that is regulated in cis, showing the potential of this approach in identifying causative genes in association loci in ALS. This study has identified candidate genes for sporadic ALS, most notably CYP27A1. Mutations in CYP27A1 are causal to cerebrotendinous xanthomatosis which can present as a clinical mimic of ALS with progressive upper motor neuron loss, making it a plausible

  18. Mapping of Defense Response Gene Homologs and Their Association with Resistance Loci in Maize

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Defense response genes in higher plant species are involved in a variety of signal tranaduction pathways and biochemical reactions to counterattack invading pathogens. In this study, a total of 366 non-redundant defense response gene homologs (DRHs), Including 124 unigenes/expressed sequence tags, 226 tentative consensuses, and 16 DRH contigs have been identified by mining the Maize Genetics and Genomics and The Institute for Genomic Research maize databases using 35 essential defense response genes. Of 366 DRHs, 202 are mapped to 152 loci across ten maize chromosomes via both the genetic and in silico mapping approaches. The mapped DRHs seem to cluster together rather than be evenly distributed along the maize genome. Approximately half of these DHRs are located in regions harboring either major resistance genes or quantitative trait loci(QTL). Therefore, this comprehensive DRH linkage map will provide reference sequences to Identify either positional candidate genes for resistance genes and/or QTLs or to develop makers for fine-mapping and marker-assisted selection of resistance genes and/or QTLs.

  19. Mapping of Candidate Genes Involved in Bud Dormancy and Flowering Time in Sweet Cherry (Prunus avium).

    Science.gov (United States)

    Castède, Sophie; Campoy, José Antonio; Le Dantec, Loïck; Quero-García, José; Barreneche, Teresa; Wenden, Bénédicte; Dirlewanger, Elisabeth

    2015-01-01

    The timing of flowering in perennial plants is crucial for their survival in temperate climates and is regulated by the duration of bud dormancy. Bud dormancy release and bud break depend on the perception of cumulative chilling during endodormancy and heat during the bud development. The objectives of this work were to identify candidate genes involved in dormancy and flowering processes in sweet cherry, their mapping in two mapping progenies 'Regina' × 'Garnet' and 'Regina' × 'Lapins', and to select those candidate genes which co-localized with quantitative trait loci (QTLs) associated with temperature requirements for bud dormancy release and flowering. Based on available data on flowering processes in various species, a list of 79 candidate genes was established. The peach and sweet cherry orthologs were identified and primers were designed to amplify sweet cherry candidate gene fragments. Based on the amplified sequences of the three parents of the mapping progenies, SNPs segregations in the progenies were identified. Thirty five candidate genes were genetically mapped in at least one of the two progenies and all were in silico mapped. Co-localization between candidate genes and QTLs associated with temperature requirements and flowering date were identified for the first time in sweet cherry. The allelic composition of the candidate genes located in the major QTL for heat requirements and flowering date located on linkage group 4 have a significant effect on these two traits indicating their potential use for breeding programs in sweet cherry to select new varieties adapted to putative future climatic conditions.

  20. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.

    Science.gov (United States)

    Talukder, Zahirul I; Gong, Li; Hulke, Brent S; Pegadaraju, Venkatramana; Song, Qijian; Schultz, Quentin; Qi, Lili

    2014-01-01

    A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.

  1. Mapping the stellar structure of the Milky Way

    CERN Document Server

    de Jong, Jelte T A; Rix, Hans-Walter; Dolphin, Andrew E; Martin, Nicolas F; Beers, Timothy C

    2009-01-01

    We map the stellar structure of the Galaxy by applying color-magnitude diagram (CMD) fitting to photometric data from the SEGUE survey allowing, for the first time, a comprehensive analysis of Milky Way structure at both high and low latitudes using uniform SDSS photometry. The advantage of CMD fitting is that it incorporates photometry of all relevant stars simultaneously, bypassing the need to choose single tracer populations. Using three template stellar populations we obtain a sparse 3-D map of the stellar mass distribution. Fitting a smooth Milky Way model, comprised of exponential thin and thick disks and an axisymmetric power-law halo, allows us to constrain the structural parameters of the thick disk and halo. The thick disk scale height and length of such models are well constrained at 0.75+-0.07 kpc and 4.1+-0.4 kpc, respectively. We find a stellar halo flattening within ~25 kpc of c/a=0.88+-0.03 and a power-law index of 2.75+-0.07. The model fits yield densities at the solar location of rho_{thick,...

  2. Gene organization, evolution and expression of the microtubule-associated protein ASAP (MAP9

    Directory of Open Access Journals (Sweden)

    Giorgi Dominique

    2008-09-01

    Full Text Available Abstract Background ASAP is a newly characterized microtubule-associated protein (MAP essential for proper cell-cycling. We have previously shown that expression deregulation of human ASAP results in profound defects in mitotic spindle formation and mitotic progression leading to aneuploidy, cytokinesis defects and/or cell death. In the present work we analyze the structure and evolution of the ASAP gene, as well as the domain composition of the encoded protein. Mouse and Xenopus cDNAs were cloned, the tissue expression characterized and the overexpression profile analyzed. Results Bona fide ASAP orthologs are found in vertebrates with more distantly related potential orthologs in invertebrates. This single-copy gene is conserved in mammals where it maps to syntenic chromosomal regions, but is also clearly identified in bird, fish and frog. The human gene is strongly expressed in brain and testis as a 2.6 Kb transcript encoding a ~110 KDa protein. The protein contains MAP, MIT-like and THY domains in the C-terminal part indicative of microtubule interaction, while the N-terminal part is more divergent. ASAP is composed of ~42% alpha helical structures, and two main coiled-coil regions have been identified. Different sequence features may suggest a role in DNA damage response. As with human ASAP, the mouse and Xenopus proteins localize to the microtubule network in interphase and to the mitotic spindle during mitosis. Overexpression of the mouse protein induces mitotic defects similar to those observed in human. In situ hybridization in testis localized ASAP to the germ cells, whereas in culture neurons ASAP localized to the cell body and growing neurites. Conclusion The conservation of ASAP indicated in our results reflects an essential function in vertebrates. We have cloned the ASAP orthologs in mouse and Xenopus, two valuable models to study the function of ASAP. Tissue expression of ASAP revealed a high expression in brain and testis, two

  3. Amplification and characterization of eukaryotic structural genes.

    Science.gov (United States)

    Maniatis, T; Efstratiadis, A; Sim, G K; Kafatos, F

    1978-05-01

    An approach to the study of eukaryotic structural genes which are differentially expressed during development is described. This approach involves the isolation and amplification of mRNA sequences by in vitro conversion of mRNA to double-stranded cDNA followed by molecular cloning in bacterial plasmids. This procedure provides highly specific hybridization probes that can be used to identify genes and their contiguous DNA sequences in genomic DNA, and to detect specific RNA transcripts during development. The nature of the method allows the isolation of individual mRNA sequences from a complex population of molecules at different stages of development.

  4. Mapping human whole-brain structural networks with diffusion MRI.

    Directory of Open Access Journals (Sweden)

    Patric Hagmann

    Full Text Available Understanding the large-scale structural network formed by neurons is a major challenge in system neuroscience. A detailed connectivity map covering the entire brain would therefore be of great value. Based on diffusion MRI, we propose an efficient methodology to generate large, comprehensive and individual white matter connectional datasets of the living or dead, human or animal brain. This non-invasive tool enables us to study the basic and potentially complex network properties of the entire brain. For two human subjects we find that their individual brain networks have an exponential node degree distribution and that their global organization is in the form of a small world.

  5. [Recent progress in gene mapping through high-throughput sequencing technology and forward genetic approaches].

    Science.gov (United States)

    Lu, Cairui; Zou, Changsong; Song, Guoli

    2015-08-01

    Traditional gene mapping using forward genetic approaches is conducted primarily through construction of a genetic linkage map, the process of which is tedious and time-consuming, and often results in low accuracy of mapping and large mapping intervals. With the rapid development of high-throughput sequencing technology and decreasing cost of sequencing, a variety of simple and quick methods of gene mapping through sequencing have been developed, including direct sequencing of the mutant genome, sequencing of selective mutant DNA pooling, genetic map construction through sequencing of individuals in population, as well as sequencing of transcriptome and partial genome. These methods can be used to identify mutations at the nucleotide level and has been applied in complex genetic background. Recent reports have shown that sequencing mapping could be even done without the reference of genome sequence, hybridization, and genetic linkage information, which made it possible to perform forward genetic study in many non-model species. In this review, we summarized these new technologies and their application in gene mapping.

  6. Soft Topographic Maps for Clustering and Classifying Bacteria Using Housekeeping Genes

    Directory of Open Access Journals (Sweden)

    Massimo La Rosa

    2011-01-01

    Full Text Available The Self-Organizing Map (SOM algorithm is widely used for building topographic maps of data represented in a vectorial space, but it does not operate with dissimilarity data. Soft Topographic Map (STM algorithm is an extension of SOM to arbitrary distance measures, and it creates a map using a set of units, organized in a rectangular lattice, defining data neighbourhood relationships. In the last years, a new standard for identifying bacteria using genotypic information began to be developed. In this new approach, phylogenetic relationships of bacteria could be determined by comparing a stable part of the bacteria genetic code, the so-called “housekeeping genes.” The goal of this work is to build a topographic representation of bacteria clusters, by means of self-organizing maps, starting from genotypic features regarding housekeeping genes.

  7. Genetic mapping and characteristics of genes specifically or preferentially expressed during fiber development in cotton.

    Directory of Open Access Journals (Sweden)

    Ximei Li

    Full Text Available Cotton fiber is an ideal model to study cell elongation and cell wall construction in plants. During fiber development, some genes and proteins have been reported to be specifically or preferentially expressed. Mapping of them will reveal the genomic distribution of these genes, and will facilitate selection in cotton breeding. Based on previous reports, we designed 331 gene primers and 164 protein primers, and used single-strand conformation polymorphism (SSCP to map and integrate them into our interspecific BC(1 linkage map. This resulted in the mapping of 57 loci representing 51 genes or proteins on 22 chromosomes. For those three markers which were tightly linked with quantitative trait loci (QTLs, the QTL functions obtained in this study and gene functions reported in previous reports were consistent. Reverse transcription-polymerase chain reaction (RT-PCR analysis of 52 polymorphic functional primers showed that 21 gene primers and 17 protein primers had differential expression between Emian22 (Gossypium hirsutum and 3-79 (G. barbadense. Both RT-PCR and quantitative real-time PCR (qRT-PCR analyses of the three markers tightly linked with QTLs were consistent with QTL analysis and field experiments. Gene Ontology (GO categorization revealed that almost all 51 mapped genes belonged to multiple categories that contribute to fiber development, indicating that fiber development is a complex process regulated by various genes. These 51 genes were all specifically or preferentially expressed during fiber cell elongation and secondary wall biosynthesis. Therefore, these functional gene-related markers would be beneficial for the genetic improvement of cotton fiber length and strength.

  8. 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.

  9. Mapping of polyketide biosynthesis pathways in Aspergillus nidulans using a genome wide PKS gene deletion library

    DEFF Research Database (Denmark)

    Larsen, Thomas Ostenfeld; Rank, Christian; Klejnstrup, Marie Louise;

    In order to map new links between PKS genes and their products in Aspergillus nidulans we have systematically deleted all thirty-two individual genes predicted to encode polyketide synthases in this model organism. This number greatly exceeds the number of currently known PKs calling for new...

  10. GeneRecon—A coalescent based tool for fine-scale association mapping

    DEFF Research Database (Denmark)

    Mailund, Thomas; Schierup, Mikkel Heide; Pedersen, Christian Nørgaard Storm

    2006-01-01

    GeneRecon is a tool for fine-scale association mapping using a coalescence model. GeneRecon takes as input case-control data from phased or unphased SNP and micro-satellite genotypes. The posterior distribution of disease locus position is obtained by Metropolis Hastings sampling in the state space...

  11. Radiation hybrid mapping of cataract genes in the dog

    NARCIS (Netherlands)

    Hunter, L; Sidjanin, D; Johnson, J; Zangerl, B; Galibert, F; Andre, C; Kirkness, E; Talamas, E; Acland, G; Aguirre, G

    2006-01-01

    Purpose: To facilitate the molecular characterization of naturally occurring cataracts in dogs by providing the radiation hybrid location of 21 cataract-associated genes along with their closely associated polymorphic markers. These can be used for segregation testing of the candidate genes in canin

  12. Microstructure of polycrystalline PBTTT films: domain mapping and structure formation.

    Science.gov (United States)

    Schuettfort, Torben; Watts, Benjamin; Thomsen, Lars; Lee, Mijung; Sirringhaus, Henning; McNeill, Christopher R

    2012-02-28

    We utilize near-edge X-ray absorption fine structure (NEXAFS) spectroscopy and scanning transmission X-ray microscopy (STXM) to study the microstructure and domain structure of polycrystalline films of the semiconducting polymer poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). Total electron yield NEXAFS spectroscopy is used to examine the surface structure of the first 1-2 molecular layers, while bulk-sensitive STXM is used to produce maps of domain orientation and order sampled through the entire film thickness. We study different phases of PBTTT including as-cast, terraced and nanoribbon morphologies produced via spin-coating as well as aligned films of as-cast and nanoribbon morphologies produced by zone-casting. For the terraced morphology, domains are observed that are larger than the size of the terraced surface features, and the calculated degree of order is reduced compared to the nanoribbon morphology. For zone-cast films, we find that, although little optical anisotropy is observed in the bulk of as-cast films, a high degree of surface structural anisotropy is observed with NEXAFS spectroscopy, similar to what is observed in annealed nanoribbon films. This observation indicates that the aligned surface structure in unannealed zone-cast films templates the bulk ordering of the aligned nanoribbon phase. STXM domain mapping of aligned nanoribbon films reveals elongated, micrometer-wide domains with each domain misoriented with respect to its neighbor by up to 45°, but with broad domain boundaries. Within each nanoribbon domain, a high degree of X-ray dichroism is observed, indicating correlated ordering throughout the bulk of the film.

  13. Independent continuous mapping for topological optimization of frame structures

    Institute of Scientific and Technical Information of China (English)

    Yunkang Sui; Jiazheng Du; Yingqiao Guo

    2006-01-01

    Based on the Independent Continuous Mapping method (ICM),a topological optimization model with continuous topological variables is built by introducing three filter functions for element weight,element allowable stress and element stiffness,which transform the 0-1 type discrete topological variables into continuous topological variables between 0 and 1.Two methods for the filter functions are adopted to avoid the structural singularity and recover falsely deleted elements: the weak material element method and the tiny section element method.Three criteria (no structural singularity,no violated constraints and no change of structural weight) are introduced to judge iteration convergence.These criteria allow finding an appropriate threshold by adjusting a discount factor in the iteration procedure.To improve the efficiency,the original optimization model is transformed into a dual problem according to the dual theory and solved in its dual space.By using MSC/Nastran as the structural solver and MSC/Patran as the developing platform.A topological optimization software of frame structures is accomplished.Numerical examples show that the ICM method is very efficient for the topological optimization of frame structures.

  14. Systems mapping of metabolic genes through control theory.

    Science.gov (United States)

    Liu, Guodong; Kong, Lan; Wang, Zhong; Wang, Chenguang; Wu, Rongling

    2013-06-30

    The formation of any complex phenotype involves a web of metabolic pathways in which one chemical is transformed through the catalysis of enzymes into another. Traditional approaches for mapping quantitative trait loci (QTLs) are based on a direct association analysis between DNA marker genotypes and end-point phenotypes, neglecting the mechanistic processes of how a phenotype is formed biochemically. Here, we propose a new dynamic framework for mapping metabolic QTLs (mQTLs) responsible for phenotypic formation. By treating metabolic pathways as a biological system, robust differential equations have proven to be a powerful means of studying and predicting the dynamic behavior of biochemical reactions that cause a high-order phenotype. The new framework integrates these differential equations into a statistical mixture model for QTL mapping. Since the mathematical parameters that define the emergent properties of the metabolic system can be estimated and tested for different mQTL genotypes, the framework allows the dynamic pattern of genetic effects to be quantified on metabolic capacity and efficacy across a time-space scale. Based on a recent study of glycolysis in Saccharomyces cerevisiae, we design and perform a series of simulation studies to investigate the statistical properties of the framework and validate its usefulness and utilization in practice. This framework can be generalized to mapping QTLs for any other dynamic systems and may stimulate pharmacogenetic research toward personalized drug and treatment intervention.

  15. Human bZIP transcription factor gene NRL: structure, genomic sequence, and fine linkage mapping at 14q11.2 and negative mutation analysis in patients with retinal degeneration.

    Science.gov (United States)

    Farjo, Q; Jackson, A; Pieke-Dahl, S; Scott, K; Kimberling, W J; Sieving, P A; Richards, J E; Swaroop, A

    1997-10-15

    The NRL gene encodes an evolutionarily conserved basic motif-leucine zipper transcription factor that is implicated in regulating the expression of the photoreceptor-specific gene rhodopsin. NRL is expressed in postmitotic neuronal cells and in lens during embryonic development, but exhibits a retina-specific pattern of expression in the adult. To understand regulation of NRL expression and to investigate its possible involvement in retinopathies, we have determined the complete sequence of the human NRL gene, identified a polymorphic (CA)n repeat (identical to D14S64) within the NRL-containing cosmid, and refined its location by linkage analysis. Since a locus for autosomal recessive retinitis pigmentosa (arRP) has been linked to markers at 14q11 and since mutations in rhodopsin can lead to RP, we sequenced genomic PCR products of the NRL gene and of the rhodopsin-Nrl response element from a panel of patients representing independent families with inherited retinal degeneration. The analysis did not reveal any causative mutations in this group of patients. These investigations provide the basis for delineating the DNA sequence elements that regulate NRL expression in distinct neuronal cell types and should assist in the analysis of NRL as a candidate gene for inherited diseases/syndromes affecting visual function. Copyright 1997 Academic Press.

  16. Structurally controlled hazard mapping of Southern Leyte, Philippines

    Science.gov (United States)

    Luzon, P. K.; Montalbo, K. P.; Galang, J. A. M.; Sabado, J. M.; Escape, C. M.; Felix, R. P.; Lagmay, A. M. F.

    2015-10-01

    The 2006 Guinsaugon landslide in St. Bernard, Southern Leyte is one of the largest known landslides in the Philippines in recent history. It consists of a 15-20 million m3 rockslide-debris avalanche from an approximately 675 m high mountain weakened by continuous movement of the Philippine fault. The catastrophic Guinsaugon landslide killed 1221 people and displaced 19 000 residents over its 4.5 km path. To investigate the present day morphology of the scar and potential failure that may occur, analysis of a 5 m resolution IfSAR-derived Digital Elevation Model was conducted using Coltop3D and Matterocking software, leading to the generation of a landslide hazard map for the province of Southern Leyte in Central Philippines. The dip and dip-direction of discontinuity sets that contribute to gravitational failure in mountainous areas of the province were identified and measured using a lower Schmidt-Lambert color scheme. After measurement of the morpho-structural orientations, potential sites of failure were analyzed. Conefall was then utilized to compute the extent of rock mass runout. Results of the analysis show instability in the scarp area of the 2006 Guinsaugon landslide and in adjacent slopes because of the presence of steep discontinuities that range from 45-60°. Apart from the 2006 Guinsaugon landslide site, runout models simulated farther rock mass extent in its adjacent slopes, revealing a high potential for fatal landslides to happen in the municipality of St. Bernard. Concerned agencies may use maps produced in the same manner as this study to identify possible sites where structurally-controlled landslides can occur. In a country like the Philippines, where fractures and faults are common, this type of simulated hazard maps would be useful for disaster prevention and facilitate disaster risk reduction efforts for landslide-susceptible areas.

  17. Synteny mapping of five human chromosome 7 genes on bovine chromosomes 4 and 21.

    Science.gov (United States)

    Antoniou, E; Womack, J E; Grosz, M D

    1999-01-01

    Five genes on human chromosome 7 (HSA 7) were assigned to bovine chromosome 21 (BTA 21) and 4 (BTA 4) using a bovine-rodent somatic hybrid cell panel. These five genes were alpha-I subunit of adenylate cyclase-inhibiting G-protein (GNAI1), alpha/beta preprotachykinin (TAC1), reelin (RELN), c-AMP dependant protein kinase type II beta regulatory chain (PRKAR2B) and apolipoprotein A1 regulatory protein 1 (TFCOUP2). Four genes mapped to BTA 4 (GNAI1, TAC1, RELN, PRKAR2B) while one gene mapped to BTA 21 (TFCOUP2). This study confirms the synteny conservation between HSA 7 and BTA 4, finely maps the breakpoints of conserved synteny on HSA 7 and defines a new synteny conservation between HSA 7 and BTA 21.

  18. Mapping of a liver phosphorylase kinase [alpha]-subunit gene on the mouse x chromosome

    Energy Technology Data Exchange (ETDEWEB)

    Geng, Yan; Derry, J.M.J.; Barnard, P.J. (MRC Molecular Neurobiology Unit, Cambridge (United Kingdom)); Hendrickx, J.; Coucke, P.; Willems, P.R. (Univ. of Antwerp (Belgium))

    1993-01-01

    Phosphorylase kinase (PHK) is a regulatory enzyme of the glycogenolytic pathway composed of a complex of four subunits. We recently mapped the muscle [alpha]-subunit gene (Phka) to the mouse X chromosome in a region syntenic with the proximal long arm of the human X chromosome and containing the human homologue of this gene, PHKA. We now report the mapping of the liver [alpha]-subunit gene to the telomeric end of the mouse X chromosome. This mapping position would suggest a location for the human liver [alpha]-subunit gene on the proximal short arm of the X chromosome, a region recently implicated in X-linked liver glycogenosis (XLG). 20 refs., 2 figs.

  19. Comparative mapping of the actin-binding protein 280 genes in human and mouse

    Energy Technology Data Exchange (ETDEWEB)

    Gariboldi, M.; Canzian, F.; Manenti, G.; De Gregorio, L. (Istituto Nazionale Tumori, Milan (Italy)); Maestrini, E.; Rivella, S. (Istituto di Genetica Biochimica ed Evoluzionistica, Pavia (Italy)); Chatterjee, A.; Herman, G.E. (Universita di Bari (Italy)); Archidiacono, N.; Antonacci, R. (Institute for Molecular Genetics, Houston, TX (United States)) (and others)

    1994-05-15

    Two genes encode actin-binding protein 280 isoforms. ABP-280 or filamin (FLN1) is present in the cytoskeleton of many cell types, whereas expression of FLN2 is limited to skeletal muscle and heart. FLN1 maps to human chromosome Xq28, and, by physical mapping in YAC clones, the authors have mapped the homologous murine locus (Fln1) to mouse chromosome X, in a region of syntenic homology with human chromosome X. They mapped FLN2 to human chromosome 7q32-q35 by analysis of somatic cell hybrids containing portions of chromosome 7, and, by using a mapping panel from an interspecific murine cross, they mapped the corresponding murine locus (Fln2) to murine chromosome 6 in a region homologous to human chromosome 7. 21 refs., 1 fig., 1 tab.

  20. Comparative mapping of the actin-binding protein 280 genes in human and mouse.

    Science.gov (United States)

    Gariboldi, M; Maestrini, E; Canzian, F; Manenti, G; De Gregorio, L; Rivella, S; Chatterjee, A; Herman, G E; Archidiacono, N; Antonacci, R

    1994-05-15

    Two genes encode actin-binding protein 280 isoforms. ABP-280 or filamin (FLN1) is present in the cytoskeleton of many cell types, whereas expression of FLN2 is limited to skeletal muscle and heart. FLN1 maps to human chromosome Xq28, and, by physical mapping in YAC clones, we have mapped the homologous murine locus (Fln1) to mouse chromosome X, in a region of syntenic homology with human chromosome X. We mapped FLN2 to human chromosome 7q32-q35 by analysis of somatic cell hybrids containing portions of chromosome 7, and, by using a mapping panel from an interspecific murine cross, we mapped the corresponding murine locus (Fln2) to murine chromosome 6 in a region homologous to human chromosome 7.

  1. An integrated linkage map reveals candidate genes underlying adaptive variation in Chinook salmon (Oncorhynchus tshawytscha)

    DEFF Research Database (Denmark)

    Mckinney, G. J.; Seeb, L. W.; Larson, W. A.

    2016-01-01

    Salmonids are an important cultural and ecological resource exhibiting near worldwide distribution between their native and introduced range. Previous research has generated linkage maps and genomic resources for several species as well as genome assemblies for two species. We first leveraged...... improvements in mapping and genotyping methods to create a dense linkage map for Chinook salmon Oncorhynchus tshawytscha by assembling family data from different sources. We successfully mapped 14 620 SNP loci including 2336 paralogs in subtelomeric regions. This improved map was then used as a foundation...... to integrate genomic resources for gene annotation and population genomic analyses. We anchored a total of 286 scaffolds from the Atlantic salmon genome to the linkage map to provide a framework for the placement 11 728 Chinook salmon ESTs. Previously identified thermotolerance QTL were found to colocalize...

  2. Mapping of Wbph6(t)—a new gene resistant to whitebacked planthopper

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Whitebacked planthopper (WBPH, Sogatella furcifera Horvath) is one of the most destructive insects for rice. The utilization of WBPH resistance genes is always an efficient solution to this problem. Besides five WBPH resistance genes registered, Wbph1, Wbph2, Wbph3, wbph4, and Wbph5, classical segregation analysis and allelism test showed that several rice landraces from Yunan Province, China, carried a new dominant resistance gene Wbph6(t). We herein reported the mapping of Wbph6(t) by using DNA markers.

  3. A multilevel pan-cancer map links gene mutations tocancer hallmarks

    Institute of Scientific and Technical Information of China (English)

    TheoAKnijnenburg; TychoBismeijer; LodewykFAWessels; IlyaShmulevich

    2015-01-01

    Background:A central challenge in cancer research is to create models that bridge the gap between the molecular level on which interventions can be designed and the cellular and tissue levels on which the disease phenotypes are manifested. This study was undertaken to construct such a model from functional annotations and explore its use when integrated with large-scale cancer genomics data. Methods:We created a map that connects genes to cancer hallmarks via signaling pathways. We projected gene mutation and focal copy number data from various cancer types onto this map. We performed statistical analyses to uncover mutually exclusive and co-occurring oncogenic aberrations within this topology. Results:Our analysis showed that although the genetic ifngerprint of tumor types could be very different, there were less variations at the level of hallmarks, consistent with the idea that different genetic alterations have similar functional outcomes. Additionally, we showed how the multilevel map could help to clarify the role of infrequently mutated genes, and we demonstrated that mutually exclusive gene mutations were more prevalent in pathways, whereas many co-occurring gene mutations were associated with hallmark characteristics. Conclusions:Overlaying this map with gene mutation and focal copy number data from various cancer types makes it possible to investigate the similarities and differences between tumor samples systematically at the levels of not only genes but also pathways and hallmarks.

  4. Structural mapping: how to study the genetic architecture of a phenotypic trait through its formation mechanism.

    Science.gov (United States)

    Tong, Chunfa; Shen, Lianying; Lv, Yafei; Wang, Zhong; Wang, Xiaoling; Feng, Sisi; Li, Xin; Sui, Yihan; Pang, Xiaoming; Wu, Rongling

    2014-01-01

    Traditional approaches for genetic mapping are to simply associate the genotypes of a quantitative trait locus (QTL) with the phenotypic variation of a complex trait. A more mechanistic strategy has emerged to dissect the trait phenotype into its structural components and map specific QTLs that control the mechanistic and structural formation of a complex trait. We describe and assess such a strategy, called structural mapping, by integrating the internal structural basis of trait formation into a QTL mapping framework. Electrical impedance spectroscopy (EIS) has been instrumental for describing the structural components of a phenotypic trait and their interactions. By building robust mathematical models on circuit EIS data and embedding these models within a mixture model-based likelihood for QTL mapping, structural mapping implements the EM algorithm to obtain maximum likelihood estimates of QTL genotype-specific EIS parameters. The uniqueness of structural mapping is to make it possible to test a number of hypotheses about the pattern of the genetic control of structural components. We validated structural mapping by analyzing an EIS data collected for QTL mapping of frost hardiness in a controlled cross of jujube trees. The statistical properties of parameter estimates were examined by simulation studies. Structural mapping can be a powerful alternative for genetic mapping of complex traits by taking account into the biological and physical mechanisms underlying their formation.

  5. Concept Map Structure, Gender and Teaching Methods: An Investigation of Students' Science Learning

    Science.gov (United States)

    Gerstner, Sabine; Bogner, Franz X.

    2009-01-01

    Background: This study deals with the application of concept mapping to the teaching and learning of a science topic with secondary school students in Germany. Purpose: The main research questions were: (1) Do different teaching approaches affect concept map structure or students' learning success? (2) Is the structure of concept maps influenced…

  6. Mapping the genetic architecture of gene expression in human liver.

    Directory of Open Access Journals (Sweden)

    Eric E Schadt

    2008-05-01

    Full Text Available Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order disease traits. Therefore, identifying the molecular phenotypes that vary in response to changes in DNA and that also associate with changes in disease traits has the potential to provide the functional information required to not only identify and validate the susceptibility genes that are directly affected by changes in DNA, but also to understand the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. Toward that end, we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases. The utility of these data for elucidating the causes of common human diseases is demonstrated by integrating them with genotypic and expression data from other human and mouse populations. This provides much-needed functional support for the candidate susceptibility genes being identified at a growing number of genetic loci that have been identified as key drivers of disease from genome-wide association studies of disease. By using an integrative genomics approach, we highlight how the gene RPS26 and not ERBB3 is supported by our data as the most likely susceptibility gene for a novel type 1 diabetes locus recently identified in a large

  7. Double-bottom chaotic map particle swarm optimization based on chi-square test to determine gene-gene interactions.

    Science.gov (United States)

    Yang, Cheng-Hong; Lin, Yu-Da; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2014-01-01

    Gene-gene interaction studies focus on the investigation of the association between the single nucleotide polymorphisms (SNPs) of genes for disease susceptibility. Statistical methods are widely used to search for a good model of gene-gene interaction for disease analysis, and the previously determined models have successfully explained the effects between SNPs and diseases. However, the huge numbers of potential combinations of SNP genotypes limit the use of statistical methods for analysing high-order interaction, and finding an available high-order model of gene-gene interaction remains a challenge. In this study, an improved particle swarm optimization with double-bottom chaotic maps (DBM-PSO) was applied to assist statistical methods in the analysis of associated variations to disease susceptibility. A big data set was simulated using the published genotype frequencies of 26 SNPs amongst eight genes for breast cancer. Results showed that the proposed DBM-PSO successfully determined two- to six-order models of gene-gene interaction for the risk association with breast cancer (odds ratio > 1.0; P value <0.05). Analysis results supported that the proposed DBM-PSO can identify good models and provide higher chi-square values than conventional PSO. This study indicates that DBM-PSO is a robust and precise algorithm for determination of gene-gene interaction models for breast cancer.

  8. Double-Bottom Chaotic Map Particle Swarm Optimization Based on Chi-Square Test to Determine Gene-Gene Interactions

    Directory of Open Access Journals (Sweden)

    Cheng-Hong Yang

    2014-01-01

    Full Text Available Gene-gene interaction studies focus on the investigation of the association between the single nucleotide polymorphisms (SNPs of genes for disease susceptibility. Statistical methods are widely used to search for a good model of gene-gene interaction for disease analysis, and the previously determined models have successfully explained the effects between SNPs and diseases. However, the huge numbers of potential combinations of SNP genotypes limit the use of statistical methods for analysing high-order interaction, and finding an available high-order model of gene-gene interaction remains a challenge. In this study, an improved particle swarm optimization with double-bottom chaotic maps (DBM-PSO was applied to assist statistical methods in the analysis of associated variations to disease susceptibility. A big data set was simulated using the published genotype frequencies of 26 SNPs amongst eight genes for breast cancer. Results showed that the proposed DBM-PSO successfully determined two- to six-order models of gene-gene interaction for the risk association with breast cancer (odds ratio > 1.0; P value <0.05. Analysis results supported that the proposed DBM-PSO can identify good models and provide higher chi-square values than conventional PSO. This study indicates that DBM-PSO is a robust and precise algorithm for determination of gene-gene interaction models for breast cancer.

  9. Mapping of the Sca1 and pcd genes on mouse chromosome 13 provides evidence that they are different genes

    Energy Technology Data Exchange (ETDEWEB)

    Servadio, A.; McCall, A.; Zoghbi, H. [Baylor College of Medicine, Houston, TX (United States); Eicher, E.M. [Jackson Laboratory, Bar Harbor, ME (United States)

    1995-10-10

    It is well established that large chromosomal segments have remained intact during the evolution of different mammalian species. Thus, mapping information for a gene in mammalian species facilitates mapping the same gene in another mammalian species. In addition, phenotypically similar diseases that map to linkage conserved regions in two species may be caused by mutations in the same gene. Spinocerebellar ataxia type 1 (SCA1) is a dominantly inherited human disorder characterized by progressive ataxia, dysarthria, and dysmetria. SCA1 maps to the short arm of human chromosome (Chr) 6 in the 6p23-p22 region. SCA1 is caused by the expansion of an unstable CAG repeat located within the coding region of a novel protein, ataxin-1, Purkinje cell degeneration (pcd) is a recessively inherited mouse disorder characterized by a moderate ataxia, usually noted by 3-4 weeks of age. Progressive degeneration of Purkinje cells is the underlying pathogenesis in this disorder. The pcd gene was assigned to mouse Chr 13 because it showed linkage to extra toes (Xt) and pearl (pe). Some doubt about this assignment existed, however, because the calculated genetic distance between pcd and Xt was 32 cM and that between pcd and pe was 18 cM. If pcd is located in Chr 13, its placement relative to Xt and pe suggests that it would be located in the region that shares linkage homology with the region that shares linkage homology with the region of human Chr 6 that contains SCA1. Here, we present data that confirm the assignment of pcd to Chr 13, map the mouse Sca1 gene to Chr 13, and eliminate Sca1 as a candidate gene for pcd. 11 refs., 1 tab.

  10. Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology.

    Science.gov (United States)

    Hallingbäck, Henrik R; Fogelqvist, Johan; Powers, Stephen J; Turrion-Gomez, Juan; Rossiter, Rachel; Amey, Joanna; Martin, Tom; Weih, Martin; Gyllenstrand, Niclas; Karp, Angela; Lagercrantz, Ulf; Hanley, Steven J; Berlin, Sofia; Rönnberg-Wästljung, Ann-Christin

    2016-05-01

    Willow species (Salix) are important as short-rotation biomass crops for bioenergy, which creates a demand for faster genetic improvement and breeding through deployment of molecular marker-assisted selection (MAS). To find markers associated with important adaptive traits, such as growth and phenology, for use in MAS, we genetically dissected the trait variation of a Salix viminalis (L.) population of 323 accessions. The accessions were sampled throughout northern Europe and were established at two field sites in Pustnäs, Sweden, and at Woburn, UK, offering the opportunity to assess the impact of genotype-by-environment interactions (G × E) on trait-marker associations. Field measurements were recorded for growth and phenology traits. The accessions were genotyped using 1536 SNP markers developed from phenology candidate genes and from genes previously observed to be differentially expressed in contrasting environments. Association mapping between 1233 of these SNPs and the measured traits was performed taking into account population structure and threshold selection bias. At a false discovery rate (FDR) of 0.2, 29 SNPs were associated with bud burst, leaf senescence, number of shoots or shoot diameter. The percentage of accession variation (Radj2) explained by these associations ranged from 0.3% to 4.4%, suggesting that the studied traits are controlled by many loci of limited individual impact. Despite this, a SNP in the EARLY FLOWERING 3 gene was repeatedly associated (FDR < 0.2) with bud burst. The rare homozygous genotype exhibited 0.4-1.0 lower bud burst scores than the other genotype classes on a five-grade scale. Consequently, this marker could be promising for use in MAS and the gene deserves further study. Otherwise, associations were less consistent across sites, likely due to their small Radj2 estimates and to considerable G × E interactions indicated by multivariate association analyses and modest trait accession correlations across sites (0.32-0.61).

  11. Localizing F(ST) outliers on a QTL map reveals evidence for large genomic regions of reduced gene exchange during speciation-with-gene-flow.

    Science.gov (United States)

    Via, Sara; Conte, Gina; Mason-Foley, Casey; Mills, Kelly

    2012-11-01

    Populations that maintain phenotypic divergence in sympatry typically show a mosaic pattern of genomic divergence, requiring a corresponding mosaic of genomic isolation (reduced gene flow). However, mechanisms that could produce the genomic isolation required for divergence-with-gene-flow have barely been explored, apart from the traditional localized effects of selection and reduced recombination near centromeres or inversions. By localizing F(ST) outliers from a genome scan of wild pea aphid host races on a Quantitative Trait Locus (QTL) map of key traits, we test the hypothesis that between-population recombination and gene exchange are reduced over large 'divergence hitchhiking' (DH) regions. As expected under divergence hitchhiking, our map confirms that QTL and divergent markers cluster together in multiple large genomic regions. Under divergence hitchhiking, the nonoutlier markers within these regions should show signs of reduced gene exchange relative to nonoutlier markers in genomic regions where ongoing gene flow is expected. We use this predicted difference among nonoutliers to perform a critical test of divergence hitchhiking. Results show that nonoutlier markers within clusters of F(ST) outliers and QTL resolve the genetic population structure of the two host races nearly as well as the outliers themselves, while nonoutliers outside DH regions reveal no population structure, as expected if they experience more gene flow. These results provide clear evidence for divergence hitchhiking, a mechanism that may dramatically facilitate the process of speciation-with-gene-flow. They also show the power of integrating genome scans with genetic analyses of the phenotypic traits involved in local adaptation and population divergence. © 2012 Blackwell Publishing Ltd.

  12. Physical mapping of the retinoid X receptor B gene in mouse and human

    Energy Technology Data Exchange (ETDEWEB)

    Nagata, T.; Kitagawa, K.; Taketo, M. [Banyu Tsukuba Research Institute, Tsukuba (Japan); Weiss, E.H. [Ludwig-Maximilians-Univ., Munich (Germany); Abe, K. [Kumamoto Univ. School of Medicine, Kumamoto (Japan); Ando, A.; Yara-Kikuti, Y.; Inoko, H. [Tokai Univ. School of Medicine, Isehara (Japan); Seldin, M.F. [Duke Univ. Medical Center, Durham, NC (United States); Ozato, K. [National Institutes of Health, Bethesda, MD (United States)

    1995-01-11

    Retinoid X receptors (RXRs) are zinc finger-containing nuclear transcription factors. They belong to the nuclear receptor superfamily that contains retinoid receptors, vitamin D receptors, thyroid hormone receptors, and steroid hormone receptors as well as the so-called orphan receptors. We previously mapped all three RXR genes on mouse chromosomes, using a panel of Mus spretus-Mus musculus interspecific backcross mice: namely, the RXRA-gene (Rxra) on Chr 2 near the centromere, the RXRB gene (Rxrb) on Chr 17 in the H2 region, and the RXRG gene (Rxrg) on distal Chr 1. Using cosmid clones that cover the major histocompatibility complex (MHC) region, we determined the precise physical map positions of the gene encoding mouse and human RXRB, respectively. The mouse gene (Rxrb) maps between H2-Ke4 and H2-Ke5: namely, immediately telomeric to H2-Ke4 which encodes a histidine-rich transmembrane protein, and 12 kilobases centromeric to H2-Ke5 which is expressed in lymphoid tissues, Rxrb and H2-Ke4 are transcribed into opposite directions from a CpG-rich promoter of about 250 base pairs. This gene organization is well conserved also in the human genome at the HLA-DP subregion of Chr 6p, underscoring the strong conservation of the gene organization in the MHC region between the two mammals. 54 refs., 4 figs.

  13. A systematic approach to mapping recessive disease genes in individuals from outbred populations.

    Directory of Open Access Journals (Sweden)

    Friedhelm Hildebrandt

    2009-01-01

    Full Text Available The identification of recessive disease-causing genes by homozygosity mapping is often restricted by lack of suitable consanguineous families. To overcome these limitations, we apply homozygosity mapping to single affected individuals from outbred populations. In 72 individuals of 54 kindred ascertained worldwide with known homozygous mutations in 13 different recessive disease genes, we performed total genome homozygosity mapping using 250,000 SNP arrays. Likelihood ratio Z-scores (ZLR were plotted across the genome to detect ZLR peaks that reflect segments of homozygosity by descent, which may harbor the mutated gene. In 93% of cases, the causative gene was positioned within a consistent ZLR peak of homozygosity. The number of peaks reflected the degree of inbreeding. We demonstrate that disease-causing homozygous mutations can be detected in single cases from outbred populations within a single ZLR peak of homozygosity as short as 2 Mb, containing an average of only 16 candidate genes. As many specialty clinics have access to cohorts of individuals from outbred populations, and as our approach will result in smaller genetic candidate regions, the new strategy of homozygosity mapping in single outbred individuals will strongly accelerate the discovery of novel recessive disease genes.

  14. Evaluation of phenoxybenzamine in the CFA model of pain following gene expression studies and connectivity mapping.

    Science.gov (United States)

    Chang, Meiping; Smith, Sarah; Thorpe, Andrew; Barratt, Michael J; Karim, Farzana

    2010-09-16

    We have previously used the rat 4 day Complete Freund's Adjuvant (CFA) model to screen compounds with potential to reduce osteoarthritic pain. The aim of this study was to identify genes altered in this model of osteoarthritic pain and use this information to infer analgesic potential of compounds based on their own gene expression profiles using the Connectivity Map approach. Using microarrays, we identified differentially expressed genes in L4 and L5 dorsal root ganglia (DRG) from rats that had received intraplantar CFA for 4 days compared to matched, untreated control animals. Analysis of these data indicated that the two groups were distinguishable by differences in genes important in immune responses, nerve growth and regeneration. This list of differentially expressed genes defined a "CFA signature". We used the Connectivity Map approach to identify pharmacologic agents in the Broad Institute Build02 database that had gene expression signatures that were inversely related ('negatively connected') with our CFA signature. To test the predictive nature of the Connectivity Map methodology, we tested phenoxybenzamine (an alpha adrenergic receptor antagonist) - one of the most negatively connected compounds identified in this database - for analgesic activity in the CFA model. Our results indicate that at 10 mg/kg, phenoxybenzamine demonstrated analgesia comparable to that of Naproxen in this model. Evaluation of phenoxybenzamine-induced analgesia in the current study lends support to the utility of the Connectivity Map approach for identifying compounds with analgesic properties in the CFA model.

  15. On the Structure of Infinity-Harmonic Maps

    CERN Document Server

    Katzourakis, Nikolaos I

    2012-01-01

    In this paper we primarily study 2-dimensional $\\infty$-Harmonic maps $u : \\Om \\sub \\R^2 \\longrightarrow \\R^N$, $N\\geq 2$, that is solutions to \\[\\label{1} \\Delta_\\infty u \\ :=\\ \\Big(Du \\otimes Du \\, +\\, |Du|^2 [Du]^\\bot \\otimes I \\Big) : D^2 u\\ = \\ 0. \\tag{1}\\] PDE \\eqref{1} and the Aronsson system with respect to general Hamiltonians were derived in recent work \\cite{K3}. By establishing a general Rigidity Theorem for Rank-One Lipschitz Maps of independent interest, we analyse the structure of phase separation of solutions and of their interfaces whereon the coefficients of \\eqref{1} become discontinuous. As a corollary, we extend the Aronsson-Evans-Yu theorem on the non-existence of zeros of $|Du|$ for solutions to \\eqref{1} to all $N \\geq 2$ and establish a Maximum Principle (Convex Hull Property) for N=2. We further classify all Hamiltonians $H \\in C^2(\\R^N \\ot \\R^n)$ which lead to elliptic Aronsson systems: they are the "geometric" ones, which depend on $Du$ via the Riemannian metric $Du^\\top Du$. We fi...

  16. Infinite loop space structure(s) on the stable mapping class group

    DEFF Research Database (Denmark)

    Wahl, Nathalie

    2004-01-01

    Tillmann introduced two infinite loop space structures on the plus construction of the classifying space of the stable mapping class group, each with different computational advantages. The first one uses disjoint union on a suitable cobordism category, whereas the second uses an operad which...

  17. A new CGMW map: The structural map of the Indian Ocean: An attempt at ocean cartography

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    The Commission for the Geological Map of the World (CGMW), an IUGS affiliated body, has just issued the first edition of the Structural Map of the Indian Ocean which was presented during the 32nd IGC (Florence). During the 1980's, the Commission published the Geological Atlas of the World, which included the maps of the 5 oceans of the globe. Two decades have elapsed and the knowledge of the sea-floor experienced very significant progress; therefore some 5 years ago, the Commission decided to launch a new type of ocean mapping. The Structural Map of the Indian Ocean is the first of this new series of maps.

  18. Structured scale dependence in the Lyapunov exponent of a Boolean chaotic map.

    Science.gov (United States)

    Cohen, Seth D

    2015-04-01

    We report on structures in a scale-dependent Lyapunov exponent of an experimental chaotic map that arise due to discontinuities in the map. The chaos is realized in an autonomous Boolean network, which is constructed using asynchronous logic gates to form a map operator that outputs an unclocked pulse-train of varying widths. The map operator executes pulse-width stretching and folding and the operator's output is fed back to its input to continuously iterate the map. Using a simple model, we show that the structured scale-dependence in the system's Lyapunov exponent is the result of the discrete logic elements in the map operator's stretching function.

  19. Mapping the AAV capsid host antibody response towards the development of second generation gene delivery vectors

    Directory of Open Access Journals (Sweden)

    Yu-Shan eTseng

    2014-01-01

    Full Text Available The recombinant Adeno-associated virus (rAAV gene delivery system is entering a crucial and exciting phase with the promise of more than 20 years of intense research now realized in a number of successful human clinical trials. However, as a natural host to AAV infection, anti-AAV antibodies are prevalent in the human population. For example, ~70% of human sera samples are positive for AAV serotype 2 (AAV2. Furthermore, low levels of pre-existing neutralizing antibodies in the circulation are detrimental to the efficacy of corrective therapeutic AAV gene delivery. A key component to overcoming this obstacle is the identification of regions of the AAV capsid that participate in interactions with host immunity, especially neutralizing antibodies, to be modified for neutralization escape. Three main approaches have been utilized to map antigenic epitopes on AAV capsids. The first is directed evolution in which AAV variants are selected in the presence of monoclonal antibodies or pooled human sera. This results in AAV variants with mutations on important neutralizing epitopes. The second is epitope searching, achieved by peptide scanning, peptide insertion or site-directed mutagenesis. The third, a structure biology-based approach, utilizes cryo-electron microscopy and image reconstruction of AAV capsids complexed to fragment antibodies, which are generated from monoclonal antibodies, to directly visualize the epitopes. In this review, the contribution of these three approaches to the current knowledge of AAV epitopes and success in their use to create second generation vectors will be discussed.

  20. Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes.

    Science.gov (United States)

    Carpenter, Margaret A; Shaw, Martin; Cooper, Rebecca D; Frew, Tonya J; Butler, Ruth C; Murray, Sarah R; Moya, Leire; Coyne, Clarice J; Timmerman-Vaughan, Gail M

    2017-08-01

    Although starch consists of large macromolecules composed of glucose units linked by α-1,4-glycosidic linkages with α-1,6-glycosidic branchpoints, variation in starch structural and functional properties is found both within and between species. Interest in starch genetics is based on the importance of starch in food and industrial processes, with the potential of genetics to provide novel starches. The starch metabolic pathway is complex but has been characterized in diverse plant species, including pea. To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. Variation in the percent amylose composition of extracted seed starch and (amylopectin) chain length distribution, one measure of starch structure, were characterized for these lines. Association mapping was undertaken to identify polymorphisms associated with the variation in starch chain length distribution and percent amylose, using a mixed linear model that incorporated population structure and kinship. Associations were found for polymorphisms in seven candidate genes plus Mendel's r locus (which conditions the round versus wrinkled seed phenotype). The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding.

  1. Exclusive gene mapping of congenital microphthalmia in a Chinese family

    Institute of Scientific and Technical Information of China (English)

    YIN Yanan; LI Hui; YU Ping; ZHOU Qiang; ZHAO Luhang; ZHANG Ya-Ping

    2006-01-01

    Congenital microphthalmia is a developmental ocular disorder and might be caused by the mutations in the genes involved in eye development.To uncover the genetic cause in a six-generation Chinese pedigree with autosomal dominant congenital microphthalmia, we performed genescan and linkage analysis in this family. Fourteen microsatellite markers on chromosomes 3, 11, 14 and 15 were selected as genetic markers according to the five previously reported loci associated with microphthalmia (MITF, SOX2, PAX6, MCOP and NN02). The genomic DNA of each member in the pedigree was amplified with 14 pairs of fluorescence labeled primers. Genome screening and genotyping were conducted on ABI377 DNA sequencer and linkage analysis was performed with Linkage software package. All two-point LOD scores of linkage analysis between the suggested disease genes and microsatellite markers were <-2, which indicated that none of the five genes were responsible for microphthalmia in this Chinese family. Microphthalmia in this family may be caused by mutation in a new gene which is essential in eye development.

  2. Structure map including off-stoichiometric and ternary sp-d-valent compounds

    Science.gov (United States)

    Hammerschmidt, T.; Bialon, A. F.; Drautz, R.

    2017-10-01

    Structure maps predict the crystal structure of a compound from the knowledge of constituent elements and chemical composition. We recently developed a highly predictive, three-dimensional structure map for stoichiometric binary sp- d-valent compounds. Here we show that the descriptors of this structure map are transferable to off-stoichiometric compounds with similar predictive power. We furthermore demonstrate that the descriptors are suitable for ternary prototypes. In particular, we construct a three-dimensional structure map for 129 prototypical crystal structures for ternary compounds. The crystal structure is predicted correctly with a probability of 78%. With a confidence of 95% the correct crystal structure is among the three most likely crystal structures predicted by the structure map.

  3. Multilocus analysis for gene-centromere mapping using first polar bodies and secondary oocytes

    Energy Technology Data Exchange (ETDEWEB)

    Da, Y.; Jarrell, V.L.; Wang, T.; Fernando, R.L.; Wheeler, M.B.; Lewin, H.A. [Univ. of Illinois, Urbana, IL (United States)

    1995-02-01

    Polar body and oocyte typing is a new technique for gene-centromere mapping and for generating female linkage maps. A maximum likelihood approach is presented for ordering multiple markers relative to the centromere and for estimating recombination frequencies between markers and between the centromere and marker loci. Three marker-centromere orders are possible for each pair of markers: two orders when the centromere flanks the two markers and one order when the centromere is flanked by the two markers. For each possible order, the likelihood was expressed as a function of recombination frequencies for two adjacent intervals. LOD score for recombination frequency between markers or between the centromere and a marker locus was derived based on the likelihood for each gene-centromere order. The methods developed herein provide a general solution to the problem of multilocus gene-centromere mapping that involves all theoretical crossover possibilities, including four-strand double crossovers. 24 refs., 2 figs., 2 tabs.

  4. A New Advanced Backcross Tomato Population Enables High Resolution Leaf QTL Mapping and Gene Identification

    Directory of Open Access Journals (Sweden)

    Daniel Fulop

    2016-10-01

    Full Text Available Quantitative Trait Loci (QTL mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum and its more distant interfertile relatives typically follow a near isogenic line (NIL design, such as the S. pennellii Introgression Line (IL population, with a single wild introgression per line in an otherwise domesticated genetic background. Here, we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar and S. pennellii. This so-called Backcrossed Inbred Line (BIL population is comprised of a mix of BC2 and BC3 lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existing S. pennellii IL population, with which it shares parents. Using the BILs, we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous hidden Markov model for genotyping the lines, and by using state-of-the-art sparse regression techniques for QTL mapping.

  5. Electrical mapping of microtubular structures by surface potential microscopy

    Science.gov (United States)

    Zhang, Peng; Cantiello, Horacio F.

    2009-09-01

    Microtubules (MTs) are important cytoskeletal polymers that play an essential role in cell division and transport in all eukaryotes and information processing in neurons. MTs are highly charged polyelectrolytes, composed of hollow cylindrical arrangements of αβ-tubulin dimers. To date, there is little information about electrical properties of MTs. Here, we deposited and dried MTs onto a gold-plated surface to image their topology by atomic force microscopy (AFM), and determined their electrical mapping with surface potential microscopy (SPM). We found a strong linear correlation between the magnitude of relative surface potential and MT parameters, including diameter and height. AFM images confirmed the cylindrical topology of microtubular structures, and the presence of topological discontinuities along their surface, which may contribute to their unique electrical properties.

  6. Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii.

    OpenAIRE

    Jacobson, M R; Brigle, K E; Bennett, L T; Setterquist, R A; Wilson, M. S.; Cash, V L; Beynon, J.; Newton, W.E.; Dean, D R

    1989-01-01

    Determination of a 28,793-base-pair DNA sequence of a region from the Azotobacter vinelandii genome that includes and flanks the nitrogenase structural gene region was completed. This information was used to revise the previously proposed organization of the major nif cluster. The major nif cluster from A. vinelandii encodes 15 nif-specific genes whose products bear significant structural identity to the corresponding nif-specific gene products from Klebsiella pneumoniae. These genes include ...

  7. Physical and genetic map of the major nif gene cluster from Azotobacter vinelandii.

    OpenAIRE

    Jacobson, M. R.; Brigle, K E; Bennett, L T; Setterquist, R. A.; Wilson, M S; Cash, V L; Beynon, J; Newton, W E; Dean, D. R.

    1989-01-01

    Determination of a 28,793-base-pair DNA sequence of a region from the Azotobacter vinelandii genome that includes and flanks the nitrogenase structural gene region was completed. This information was used to revise the previously proposed organization of the major nif cluster. The major nif cluster from A. vinelandii encodes 15 nif-specific genes whose products bear significant structural identity to the corresponding nif-specific gene products from Klebsiella pneumoniae. These genes include ...

  8. Flexible mapping of homology onto structure with Homolmapper

    Directory of Open Access Journals (Sweden)

    Lagarias J Clark

    2007-04-01

    Full Text Available Abstract Background Over the past decade, a number of tools have emerged for the examination of homology relationships among protein sequences in a structural context. Most recent software implementations for such analysis are tied to specific molecular viewing programs, which can be problematic for collaborations involving multiple viewing environments. Incorporation into larger packages also adds complications for users interested in adding their own scoring schemes or in analyzing proteins incorporating unusual amino acid residues such as selenocysteine. Results We describe homolmapper, a command-line application for mapping information from a multiple protein sequence alignment onto a protein structure for analysis in the viewing software of the user's choice. Homolmapper is small (under 250 K for the application itself and is written in Python to ensure portability. It is released for non-commercial use under a modified University of California BSD license. Homolmapper permits facile import of additional scoring schemes and can incorporate arbitrary additional amino acids to allow handling of residues such as selenocysteine or pyrrolysine. Homolmapper also provides tools for defining and analyzing subfamilies relative to a larger alignment, for mutual information analysis, and for rapidly visualizing the locations of mutations and multi-residue motifs. Conclusion Homolmapper is a useful tool for analysis of homology relationships among proteins in a structural context. There is also extensive, example-driven documentation available. More information about homolmapper is available at http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm.

  9. Topographic mapping of oral structures - problems and applications in prosthodontics

    Science.gov (United States)

    Young, John M.; Altschuler, Bruce R.

    1981-10-01

    The diagnosis and treatment of malocclusion, and the proper design of restorations and prostheses, requires the determination of surface topography of the teeth and related oral structures. Surface contour measurements involve not only affected teeth, but adjacent and opposing surface contours composing a complexly interacting occlusal system. No a priori knowledge is predictable as dental structures are largely asymmetrical, non-repetitive, and non-uniform curvatures in 3-D space. Present diagnosis, treatment planning, and fabrication relies entirely on the generation of physical replicas during each stage of treatment. Fabrication is limited to materials that lend themselves to casting or coating, and to hand fitting and finishing. Inspection is primarily by vision and patient perceptual feedback. Production methods are time-consuming. Prostheses are entirely custom designed by manual methods, require costly skilled technical labor, and do not lend themselves to centralization. The potential improvement in diagnostic techniques, improved patient care, increased productivity, and cost-savings in material and man-hours that could result, if rapid and accurate remote measurement and numerical (automated) fabrication methods were devised, would be significant. The unique problems of mapping oral structures, and specific limitations in materials and methods, are reviewed.

  10. Utilization of Gene Mapping and Candidate Gene Mutation Screening for Diagnosing Clinically Equivocal Conditions:A Norrie Disease Case Study

    Institute of Scientific and Technical Information of China (English)

    Vasiliki Chini; Danai Stambouli; Florina Mihaela Nedelea; George Alexandru Filipescu; Diana Mina; Marios Kambouris; Hatem El-Shanti

    2014-01-01

    Prenatal diagnosis was requested for an undiagnosed eye disease showing X-linked inheritance in a family. No medical records existed for the affected family members..Mapping of the X chromosome and candidate gene mutation screening i-dentified a c.C267A[p.F89L] mutation in NPD previously de-scribed as possibly causing Norrie disease..The detection of the c.C267A[p.F89L] variant in another unrelated family con-firms the pathogenic nature of the mutation for the Norrie dis-ease phenotype. Gene mapping, haplotype analysis, and can-didate gene screening have been previously utilized in research applications but were applied here in a diagnostic setting due to the scarcity of available clinical information..The clinical diagnosis and mutation identification were critical for provid-ing proper genetic counseling and prenatal diagnosis for this family.

  11. Fine Mapping and Candidate Gene Analysis of Resistance Gene RSC3Q to Soybean mosaic virus in Qihuang 1

    Institute of Scientific and Technical Information of China (English)

    Zheng gui-jie; Yang Yong-qing; Ma Ying; Yang Xiao-feng; Chen Shan-yu; Ren Rui; Wang Da-gang; Yang Zhong-lu; ZhI hai-jian

    2014-01-01

    Soybean mosaic virus (SMV) disease is one of the most destructive viral diseases in soybean (Glycine max (L.) Merr.). SMV strain SC3 is the major prevalent strain in huang-huai and Yangtze valleys, China. The soybean cultivar Qihuang 1 is of a rich resistance spectrum and has a wide range of application in breeding programs in China. In this study, F1, F2 and F2:3 from Qihuang 1×nannong 1138-2 were used to study inheritance and linkage mapping of the SC3 resistance gene in Qihuang 1. The secondary F2 population and near isogenic lines (nILs) derived from residual heterozygous lines (RhLs) of Qihuang 1×nannong 1138-2 were separatively used in the ifne mapping and candidate gene analysis of the resistance gene. Results indicated that a single dominant gene (designated RSC3Q) controls resistance, which was located on chromosome 13. Two genomic-simple sequence repeat (SSR) markers BARCSOYSSR_13_1114 and BARCSOYSSR_13_1136 were found lfanking the two sides of the RSC3Q. The interval between the two markers was 651 kb. Quantitative real-time PCR analysis of the candidate genes showed that ifve genes (Glyma13g25730, 25750, 25950, 25970 and 26000) were likely involved in soybean SMV resistance. These results would have utility in cloning of RSC3Q resistance candidate gene and marker-assisted selection (MaS) in resistance breeding to SMV.

  12. Mapping the genetic architecture of gene regulation in whole blood.

    Directory of Open Access Journals (Sweden)

    Katharina Schramm

    Full Text Available BACKGROUND: We aimed to assess whether whole blood expression quantitative trait loci (eQTLs with effects in cis and trans are robust and can be used to identify regulatory pathways affecting disease susceptibility. MATERIALS AND METHODS: We performed whole-genome eQTL analyses in 890 participants of the KORA F4 study and in two independent replication samples (SHIP-TREND, N = 976 and EGCUT, N = 842 using linear regression models and Bonferroni correction. RESULTS: In the KORA F4 study, 4,116 cis-eQTLs (defined as SNP-probe pairs where the SNP is located within a 500 kb window around the transcription unit and 94 trans-eQTLs reached genome-wide significance and overall 91% (92% of cis-, 84% of trans-eQTLs were confirmed in at least one of the two replication studies. Different study designs including distinct laboratory reagents (PAXgene™ vs. Tempus™ tubes did not affect reproducibility (separate overall replication overlap: 78% and 82%. Immune response pathways were enriched in cis- and trans-eQTLs and significant cis-eQTLs were partly coexistent in other tissues (cross-tissue similarity 40-70%. Furthermore, four chromosomal regions displayed simultaneous impact on multiple gene expression levels in trans, and 746 eQTL-SNPs have been previously reported to have clinical relevance. We demonstrated cross-associations between eQTL-SNPs, gene expression levels in trans, and clinical phenotypes as well as a link between eQTLs and human metabolic traits via modification of gene regulation in cis. CONCLUSIONS: Our data suggest that whole blood is a robust tissue for eQTL analysis and may be used both for biomarker studies and to enhance our understanding of molecular mechanisms underlying gene-disease associations.

  13. Analysis of rice blast resistance genes by QTL mapping

    Institute of Scientific and Technical Information of China (English)

    XU Jichen; WANG Jiulin; LING Zhongzhuan; ZHU Lihuang

    2004-01-01

    Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several minor genes. Its complexity and the mutable characteristic of rice blast isolates both hinder the development of the blast resistance research. The article here tried to explore the resistance gene distribution on rice chromosomes and the way of function. Totally 124 QTLs have been identified against 20 isolates using Cartographer software with a ZYQ8/JX17 DH population, which separately are at 100 loci of 72 marker intervals on 12 rice chromosomes. Of them, 16 QTLs were determined by the isolate HB-97-36-1. 82 QTLs (66.13%) are from the resistant parent alleles, ZYQ8, while 42 QTLs (33.87%) are from the susceptible parent alleles, JX17. In comparison of their positions on chromosome, most QTLs are clustered together and distributed nearby the major genes especially the regions on chromosomes 1, 2, 8, 10 and 12. Each QTL could account for the resistance variation between 3.52%-68.64%. And, a positional QTL might display the resistance to several different isolates with different contributions.

  14. Quantitative trait locus (QTL mapping reveals a role for unstudied genes in Aspergillus virulence.

    Directory of Open Access Journals (Sweden)

    Julian K Christians

    Full Text Available Infections caused by the fungus Aspergillus are a major cause of morbidity and mortality in immunocompromised populations. To identify genes required for virulence that could be used as targets for novel treatments, we mapped quantitative trait loci (QTL affecting virulence in the progeny of a cross between two strains of A. nidulans (FGSC strains A4 and A91. We genotyped 61 progeny at 739 single nucleotide polymorphisms (SNP spread throughout the genome, and constructed a linkage map that was largely consistent with the genomic sequence, with the exception of one potential inversion of ∼527 kb on Chromosome V. The estimated genome size was 3705 cM and the average intermarker spacing was 5.0 cM. The average ratio of physical distance to genetic distance was 8.1 kb/cM, which is similar to previous estimates, and variation in recombination rate was significantly positively correlated with GC content, a pattern seen in other taxa. To map QTL affecting virulence, we measured the ability of each progeny strain to kill model hosts, larvae of the wax moth Galleria mellonella. We detected three QTL affecting in vivo virulence that were distinct from QTL affecting in vitro growth, and mapped the virulence QTL to regions containing 7-24 genes, excluding genes with no sequence variation between the parental strains and genes with only synonymous SNPs. None of the genes in our QTL target regions have been previously associated with virulence in Aspergillus, and almost half of these genes are currently annotated as "hypothetical". This study is the first to map QTL affecting the virulence of a fungal pathogen in an animal host, and our results illustrate the power of this approach to identify a short list of unknown genes for further investigation.

  15. Mapping of Candidate Genes Involved in Bud Dormancy and Flowering Time in Sweet Cherry (Prunus avium.

    Directory of Open Access Journals (Sweden)

    Sophie Castède

    Full Text Available The timing of flowering in perennial plants is crucial for their survival in temperate climates and is regulated by the duration of bud dormancy. Bud dormancy release and bud break depend on the perception of cumulative chilling during endodormancy and heat during the bud development. The objectives of this work were to identify candidate genes involved in dormancy and flowering processes in sweet cherry, their mapping in two mapping progenies 'Regina' × 'Garnet' and 'Regina' × 'Lapins', and to select those candidate genes which co-localized with quantitative trait loci (QTLs associated with temperature requirements for bud dormancy release and flowering. Based on available data on flowering processes in various species, a list of 79 candidate genes was established. The peach and sweet cherry orthologs were identified and primers were designed to amplify sweet cherry candidate gene fragments. Based on the amplified sequences of the three parents of the mapping progenies, SNPs segregations in the progenies were identified. Thirty five candidate genes were genetically mapped in at least one of the two progenies and all were in silico mapped. Co-localization between candidate genes and QTLs associated with temperature requirements and flowering date were identified for the first time in sweet cherry. The allelic composition of the candidate genes located in the major QTL for heat requirements and flowering date located on linkage group 4 have a significant effect on these two traits indicating their potential use for breeding programs in sweet cherry to select new varieties adapted to putative future climatic conditions.

  16. The Mycoplasma hominis vaa gene displays a mosaic gene structure

    DEFF Research Database (Denmark)

    Boesen, Thomas; Emmersen, Jeppe M. G.; Jensen, Lise T.;

    1998-01-01

    Mycoplasma hominis contains a variable adherence-associated (vaa) gene. To classify variants of the vaa genes, we examined 42 M. hominis isolated by PCR, DNA sequencing and immunoblotting. This uncovered the existence of five gene categories. Comparison of the gene types revealed a modular compos...

  17. Generalized gamut mapping using image derivative structures for color constancy

    NARCIS (Netherlands)

    Gijsenij, A.; Gevers, T.; van de Weijer, J.

    2010-01-01

    The gamut mapping algorithm is one of the most promising methods to achieve computational color constancy. However, so far, gamut mapping algorithms are restricted to the use of pixel values to estimate the illuminant. Therefore, in this paper, gamut mapping is extended to incorporate the statistica

  18. SNPs and Hox gene mapping in Ciona intestinalis

    Directory of Open Access Journals (Sweden)

    Biffali Elio

    2008-01-01

    Full Text Available Abstract Background The tunicate Ciona intestinalis (Enterogona, Ascidiacea, a major model system for evolutionary and developmental genetics of chordates, harbours two cryptic species. To assess the degree of intra- and inter-specific genetic variability, we report the identification and analysis of C. intestinalis SNP (Single Nucleotide Polymorphism markers. A SNP subset was used to determine the genetic distance between Hox-5 and -10 genes. Results DNA fragments were amplified from 12 regions of C. intestinalis sp. A. In total, 128 SNPs and 32 one bp indels have been identified within 8 Kb DNA. SNPs in coding regions cause 4 synonymous and 12 non-synonymous substitutions. The highest SNP frequency was detected in the Hox5 and Hox10 intragenic regions. In C. intestinalis, these two genes have lost their archetypal topology within the cluster, such that Hox10 is located between Hox4 and Hox5. A subset of the above primers was used to perform successful amplification in C. intestinalis sp. B. In this cryptic species, 62 SNPs were identified within 3614 bp: 41 in non-coding and 21 in coding regions. The genetic distance of the Hox-5 and -10 loci, computed combining a classical backcross approach with the application of SNP markers, was found to be 8.4 cM (Haldane's function. Based on the physical distance, 1 cM corresponds to 39.5 Kb. Linkage disequilibrium between the aforementioned loci was calculated in the backcross generation. Conclusion SNPs here described allow analysis and comparisons within and between C. intestinalis cryptic species. We provide the first reliable computation of genetic distance in this important model chordate. This latter result represents an important platform for future studies on Hox genes showing deviations from the archetypal topology.

  19. Physical and genetic mapping of the muscle phosphofructokinase gene (PFKM): Reassignment to human chromosome 12q

    Energy Technology Data Exchange (ETDEWEB)

    Howard, T.D.; Akots, G.; Bowden, D.W. [Bowman Gray School of Medicine of Wake Forest Univ., Winston-Salem, NC (United States)

    1996-05-15

    Phosphofructokinase (PFK) is a key rate-limiting enzyme in glycolysis and represents a major control point in the metabolism of glucose. There are at least three known isoforms of PFK in humans, referred to as the muscle, platelet, and liver forms, each of which is differentially expressed in various tissues. The gene for muscle phosphofructokinase, PFKM, is mutated in Tarui disease and conceivably contributes to non-insulin-dependent diabetes mellitus (NIDDM). Based on physical and genetic mapping, we have found that the gene for PFKM does not map to chromosome 1 as previously described, but instead maps to chromosome 12. PCR analysis with a somatic cell hybrid mapping panel using primers derived from intron 6 and exon 18 of the PFKM gene showed consistent amplification of cell lines containing chromosome 12 (concordance, 100%). Fluorescence in situ hybridization analysis with CEPH YAC 762G4, isolated with exon 18 primers, indicated that this clone maps to 12q13, centromeric to the diacylglycerol kinase gene (DAGK) at 12q13.3. A highly informative genetic marker isolated from YAC 762G4 was used to map PFKM genetically between the CHLC framework markers D12S1090 and D12S390. This placement for 762G4 was significantly proximal to the recently reported locus for a third gene for maturity onset diabetes of the young (MODY). The PFKM-associated microsatellite will be a valuable tool in the evaluation of PFKM in diabetic populations as well as in linkage analysis in families with Tarui disease. 23 refs., 3 figs., 2 tabs.

  20. Mapping cardiac surface mechanics with structured light imaging.

    Science.gov (United States)

    Laughner, Jacob I; Zhang, Song; Li, Hao; Shao, Connie C; Efimov, Igor R

    2012-09-15

    Cardiovascular disease often manifests as a combination of pathological electrical and structural heart remodeling. The relationship between mechanics and electrophysiology is crucial to our understanding of mechanisms of cardiac arrhythmias and the treatment of cardiac disease. While several technologies exist for describing whole heart electrophysiology, studies of cardiac mechanics are often limited to rhythmic patterns or small sections of tissue. Here, we present a comprehensive system based on ultrafast three-dimensional (3-D) structured light imaging to map surface dynamics of whole heart cardiac motion. Additionally, we introduce a novel nonrigid motion-tracking algorithm based on an isometry-maximizing optimization framework that forms correspondences between consecutive 3-D frames without the use of any fiducial markers. By combining our 3-D imaging system with nonrigid surface registration, we are able to measure cardiac surface mechanics at unprecedented spatial and temporal resolution. In conclusion, we demonstrate accurate cardiac deformation at over 200,000 surface points of a rabbit heart recorded at 200 frames/s and validate our results on highly contrasting heart motions during normal sinus rhythm, ventricular pacing, and ventricular fibrillation.

  1. Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes.

    Science.gov (United States)

    Khaja, Razi; MacDonald, Jeffrey R; Zhang, Junjun; Scherer, Stephen W

    2006-01-01

    The aim of this chapter is to provide instruction for analyzing and mapping recent segmental and gene duplications in eukaryotic genomes. We describe a bioinformatics-based approach utilizing computational tools to manage eukaryotic genome sequences to characterize and understand the evolutionary fates and trajectories of duplicated genes. An introduction to bioinformatics tools and programs such as BLAST, Perl, BioPerl, and the GFF specification provides the necessary background to complete this analysis for any eukaryotic genome of interest.

  2. Fine mapping of susceptibility genes by Lewontin's linkage disequilibrium measure with application to Alzheimer's disease

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Objectives To formulate an equation for fine mapping of disease loci under complex conditions and determine the marker-disease distance in a specific case using this equation. Methods Lewontin's linkage disequilibrium (LD) measure D' was used to formulate an equation for mapping disease genes in the presence of phenocopies, locus heterogeneity, gene-gene and gene-environment interactions, incomplete penetrance, uncertain liability and threshold, incomplete initial LD, natural selection, recurrent mutation, high disease allele frequency and unknown mode of inheritance. This equation was then used to determine the distance between a marker (ε4 within the apolipoprotein E gene, APOE) and Alzheimer's disease (AD) loci using published data.Results An equation was formulated for mapping disease genes under the above conditions. If these conditions are present but ignored, then recombination fraction θ between marker and disease loci will be either overestimated or estimated with little bias. Therefore, an upper limit of θ can be obtained. AD has been found to be associated with the marker allele ε4 in Africans, Asians, and Caucasians. This suggests that the AD-ε4 allelic LD predates the divergence of peoples occurring 100·!000 years ago. With the age of AD-ε4 allelic LD so estimated, the maximal distance was calculated to be 23.2 kb (mean 5.8 kb).Conclusions (1) A method is developed for LD mapping of susceptibility genes. (2) A mutation within the APOE gene itself, among others, is responsible for the susceptibility to AD, which is supported by recent evidence from studies using transgenic mice.

  3. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12.

    Directory of Open Access Journals (Sweden)

    Zahirul I Talukder

    Full Text Available A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468. The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.

  4. Mapping and identification of a Cicer arietinum NSP2 gene involved in nodulation pathway.

    Science.gov (United States)

    Ali, L; Madrid, E; Varshney, R K; Azam, S; Millan, T; Rubio, J; Gil, J

    2014-02-01

    For the first time the putative NSP2 gene in chickpea has been identified using pairs of NILs differing for the Rn1 / rn1 nodulation gene that was located in LG5 of chickpea genetic map. An intraspecific cross between the mutant non-nodulating genotype PM233, carrying the recessive gene rn1, and the wild-type CA2139 was used to develop two pairs of near-isogenic lines (NILs) for nodulation in chickpea. These pairs of NILs were characterized using sequence tagged microsatellite site (STMS) markers distributed across different linkage groups (LGs) of the chickpea genetic map leading to the detection of polymorphic markers located in LG5. Using this information, together with the genome annotation in Medicago truncatula, a candidate gene (NSP2) known to be involved in nodulation pathway was selected for mapping in chickpea. The full length sequence obtained in chickpea wild-type (CaNSP2) was 1,503 bp. Linkage analysis in an F3 population of 118 plants derived from the cross between the pair of NILS NIL7-2A (nod) × NIL7-2B (non-nod) revealed a co-localization between CaNSP2 and Rn1 gene. These data implicate the CaNSP2 gene as a candidate for identity to Rn1, and suggest that it could act in the nodulation signaling transduction pathway similarly to that in other legumes species.

  5. A special kind of local structure in the CMB intensity maps: duel peak structure

    Institute of Scientific and Technical Information of China (English)

    Hao Liu; Ti-Pei Li

    2009-01-01

    We study the local structure of Cosmic Microwave Background (CMB) tem-perature maps released by the Wilkinson Microwave Anisotropy Probe (WMAP) team, and find a new kind of structure, which can be described as follows: a peak (or valley) of average temperature is often followed by a peak of temperature fluctuation that is 4° away. This structure is important for the following reasons: both the well known cold spot detected by Cruz et al. and the hot spot detected by Vielva et al. with the same technology (the third spot in their article) have such structure; more spots that are similar to them can be found on CMB maps and they also tend to be significant cold/hot spots; if we change the 4° characteristic into an artificial one, such as 3° or 5°, there will be less "similar spots", and the temperature peaks or valleys will be less significant. The presented "sim-ilar spots" have passed a strict consistency test which requires them to be significant on at least three different CMB temperature maps. We hope that this article could arouse some interest in the relationship of average temperature with temperature fluctuation in local areas; meanwhile, we are also trying to find an explanation for it which might be important to CMB observation and theory.

  6. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX autosol wizard

    Energy Technology Data Exchange (ETDEWEB)

    Terwilliger, Thomas C [Los Alamos National Laboratory; Adams, Paul D [LBNL; Read, Randy J [UNIV OF CAMBRIDGE; Mccoy, Airlie J [UNIV OF CAMBRIDGE

    2008-01-01

    Ten measures of experimental electron-density-map quality are examined and the skewness of electron density is found to be the best indicator of actual map quality. A Bayesian approach to estimating map quality is developed and used in the PHENIX AutoSol wizard to make decisions during automated structure solution.

  7. Radiation hybrid mapping of a cytokine gene cluster located in the proximal region of 5q

    Energy Technology Data Exchange (ETDEWEB)

    Segal, A.L.; McPherson, J.D.; Wasmuth, J.J. [Univ. of California, Irvine (United States)

    1994-09-01

    The long (q) arm of chromosome 5 has been shown to contain a large number of genes encoding growth factors, growth factor receptors, hormone receptors and neurotransmitter receptors. IL-3, IL-4, IL-5, IL-9, IL-13, GM-CSF and IRF-1 are located in the 5q22-31.1 interval, while three GABA receptors map to 5q33-34. A number of receptors, including the prolactin and growth hormone receptors, the IL-7 receptor and the leukemia inhibitory factor receptor, map to proximal 5p. Genes encoding three of the complement components, C6, C7 and C9, are also located in the same region. YAC data indicates that C6 and C7 lie within 170 kb of each other. We have used a panel of 180 Chinese hamster-human radiation hybrids possessing fragments of human chromosome 5 to construct a physical map of this region of 5q. Two-point and multi-point analyses were done on the data and significant LOD scores (from 3 to 30) were observed. LIFR, PRLR, GHR, IL-7R, C6, C7, C9, TARS, and a number of CEPH-Genethon dinucleotide repeat markers were ordered and mapped. Yeast artificial chromosomes and cosmids have been isolated and inter-Alu PCR products from them are being used to construct a contig and to improve the physical map. The long term goal of this work is to identify and characterize new genes in the region.

  8. Mapping of two new brown planthopper resistance genes from wild rice

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A brown planthopper (BPH) resistance line, B5, derived its resistance genes from the wild rice Oryza officinalis Wall exwatt, was hybridized with Taichung Native 1, a cultivar highly susceptible to BPH. A mapping population composed of randomly selected 167 F2 individuals was used for determining the BPH resistance genes by the restriction fragment length polymorphism analysis (RFLP). Bulked segregant analysis was conducted to identify RFLP makers linked to the BPH resistance genes in B5. The results indicat-ed that the markers linked to BPH resistance are located at two genomic regions on the long arm of chromosome 3 and the short arm of chromosome 4, respectively. The existence of the two loci was further assessed by the quantitative trait locus (QTL) analysis. We located the two loci at a 3.2 cM interval between G1318 and R1925 on chromosome 3 and a 1.2 cM interval between C820 and S11182 on chromosome 4. Comparison with the BPH genes that have been reported indicated that the BPH resistance genes in B5 are novel. These two genes may be useful BPH resistance resource for rice breeding. Furthermore, the mapping of the two genes is useful for cloning the BPH resistance genes.

  9. Rate of decay in admixture linkage disequilibrium and its implication in gene mapping

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Modeling linkage disequilibria (LD) between genes usually observed in admixed natural populations has been shown an effective approach in high-resolution mapping of disease genes in humans. A prerequisite to obtain accurate estimation of recombination fraction between genes at a marker locus and the disease locus using the approach is a reliable prediction of the proportion of the admixture populations. The present study suggested the use of gene frequencies to predict the estimate of the admixture propor-tion based on the observation that the gene frequencies are much more stable quantities than the haplotype frequencies over evolution of the population. In this paper, we advanced the theory and methods by which the decay rate of nonlinear term of LD in admixed population may be used to estimate the recombination fraction between the genes. Theoretical analysis and simulation study indicate that, the larger the difference of gene frequencies between parental populations and the more closely the admixture proportion approaches 0.5, the more important the nonlinear term of the LD in the admixed population, and hence the more informative such admixed populations in the high-resolution gene mapping practice.

  10. Use of linkage disequilibrium approaches to map genes for bipolar disorder in the Costa Rican population

    NARCIS (Netherlands)

    Escamilla, MA; Spesny, M; Reus, [No Value; Gallegos, A; Meza, L; Molina, J; Sandkuijl, LA; Fournier, E; Leon, PE; Smith, LB; Freimer, NB

    1996-01-01

    Linkage disequilibrium (LD) analysis provides a powerful means for screening the genome to map the location of disease genes, such as those for bipolar disorder (BP), As described in this paper, the population of the Central Valley of Costa Rica, which is descended from a small number of founders, s

  11. The Morquio A syndrome (mucopolysaccharidosis IVA) gene maps to 16q24. 3

    Energy Technology Data Exchange (ETDEWEB)

    Baker, E.; Xiaohui Guo; Orsborn, A.M.; Sutherland, G.R.; Callen, D.F.; Hopwood, J.J.; Morris, C.P. (Adelaide Children' s Hospital, North Adelaide (Australia))

    1993-01-01

    The gene for N-acetylgalactosamine-6-sulfatase, the deficiency of which results in Morquio A syndrome (mucopolysaccharidosis type IVA), was assigned to chromosome 16 at band q24.3 by fluorescence in situ hybridization. Localization to this band was confirmed by PCR analysis of a somatic cell hybrid panel used for fine mapping of chromosome 16. 12 refs., 1 fig., 1 tab.

  12. Fine genetic mapping of target leaf spot resistance gene cca-3 in cucumber, Cucumis sativus L

    Science.gov (United States)

    The target leaf spot (TLS) is a very important fungal disease in cucumber. In this study, we conducted fine genetic mapping of a recessively inherited resistance gene, cca-2 against TLS with 1,083 F2 plants derived from the resistant cucumber inbred line D31 and the susceptible line D5. Initial mapp...

  13. Fine-scaling mapping of the gene responsible for multiple endocrine neoplasia type I (MEN1)

    Energy Technology Data Exchange (ETDEWEB)

    Fujimori, Minoru; Nakamura, Yusuke (Cancer Institute, Tokyo (Japan)); Wells, S.A. (Washington University School of Medicine, St. Louis (United States))

    1992-02-01

    The authors have constructed a high-resolution genetic linkage map in the vicinity of the gene responsible for multiple endocrine neoplasia type 1 (MEN1). The mutation causing this disease, inherited as an autosomal dominant, predisposes carriers to development of neoplastic tumors in the parathyroid, the endocrine pancreas, and the anterior lobe of the pituitary. The 12 markers on the genetic linkage map reported here span nearly 20 cM, and linkage analysis of MEN1 pedigrees has placed the MEN1 locus within the 8-cM region between D11S480 and D11S546. The markers on this map will be useful for prenatal or presymptomatic diagnosis of individuals in families that segregate a mutant allele of the MEN1 gene.

  14. Fine mapping of a semidwarf gene sd-g in indica rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    LIANG Guohua; CAO Xiaoying; SUI Jiongming; ZHAO Xiangqiang; YAN Changjie; YI Chuandeng; GU Minghong

    2004-01-01

    The semidwarf gene sd-g which has been used in indica rice breeding in southern China is a new one, nonallelic to sd-1. To map sd-g, an F2 population derived from the cross between Xinguiaishuangai and 02428 was constructed. The sd-g was roughly mapped between two microsatellite markers RM440 and RM163, with genetic distances of 0.5 and 2.5 cM, respectively. Then nine new polymorphic microsatellite markers were developed in this region. The sd-g was further mapped between two microsatellite markers SSR5-1 and SSR5-51, with genetic distances of 0.1 and 0.3 cM, respectively, while cosegregated with SSR418. A BAC contig was found to span the sd-g locus, the region being delimited to 85 kb. This result was very useful for cloning of the sd-g gene.

  15. USGS National Map Corps VGI Structures Acquisition Plan Objectives for FY17 from The National Map - National Geospatial Data Asset (NGDA) USGS National Structures Dataset

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — U.S. Geological Survey, Department of the Interior - The annual National Map Corps Volunteered Geographic Information (VGI) structures acquisition plan is to add new...

  16. Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis.

    Directory of Open Access Journals (Sweden)

    Pablo Cordero

    2015-11-01

    Full Text Available Landscapes exhibiting multiple secondary structures arise in natural RNA molecules that modulate gene expression, protein synthesis, and viral infection [corrected]. We report herein that high-throughput chemical experiments can isolate an RNA's multiple alternative secondary structures as they are stabilized by systematic mutagenesis (mutate-and-map, M2 and that a computational algorithm, REEFFIT, enables unbiased reconstruction of these states' structures and populations. In an in silico benchmark on non-coding RNAs with complex landscapes, M2-REEFFIT recovers 95% of RNA helices present with at least 25% population while maintaining a low false discovery rate (10% and conservative error estimates. In experimental benchmarks, M2-REEFFIT recovers the structure landscapes of a 35-nt MedLoop hairpin, a 110-nt 16S rRNA four-way junction with an excited state, a 25-nt bistable hairpin, and a 112-nt three-state adenine riboswitch with its expression platform, molecules whose characterization previously required expert mutational analysis and specialized NMR or chemical mapping experiments. With this validation, M2-REEFFIT enabled tests of whether artificial RNA sequences might exhibit complex landscapes in the absence of explicit design. An artificial flavin mononucleotide riboswitch and a randomly generated RNA sequence are found to interconvert between three or more states, including structures for which there was no design, but that could be stabilized through mutations. These results highlight the likely pervasiveness of rich landscapes with multiple secondary structures in both natural and artificial RNAs and demonstrate an automated chemical/computational route for their empirical characterization.

  17. Mapping and characterization of two relevance networks from SNP and gene levels

    Institute of Scientific and Technical Information of China (English)

    Wei Jiang; Lijie Zhang; Bo Na; Lihong Wang; Jiankai Xu; Xia Li; Yadong Wang; Shaoqi Rao

    2009-01-01

    Variations of gene expression and DNA sequence are genetically associated.The goal of this study was to build genetic networks to map from SNPs to gene expressions and to characterize the two different kinds of networks.We employed mutual information to evaluate the strength of SNP-SNP and gene-gene associations based on SNPs identity by descent (IBD) data and differences of gene expressions.We applied the approach to one dataset of Genetics of Gene Expression in Humans,and discovered that both the SNP relevance network and the gene relevance network approximated the scale-free topology.We also found that 12.09% of SNP-SNP interactions matched 24.49% of gene-gene interactions,which was consistent with that of the previous studies.Finally,we identified 49 hub SNPs and 115 hub genes in their relevance networks,in which 27 hub SNPs were associated with 25 hub genes.(C) 2009 National Natural Science Foundation of China and Chinese Academy of Sciences.Published by Elsevier Limited and Science in China Press.All rights reserved.

  18. New algorithm improves fine structure of the barley consensus SNP map

    Directory of Open Access Journals (Sweden)

    Endelman Jeffrey B

    2011-08-01

    Full Text Available Abstract Background The need to integrate information from multiple linkage maps is a long-standing problem in genetics. One way to visualize the complex ordinal relationships is with a directed graph, where each vertex in the graph is a bin of markers. When there are no ordering conflicts between the linkage maps, the result is a directed acyclic graph, or DAG, which can then be linearized to produce a consensus map. Results New algorithms for the simplification and linearization of consensus graphs have been implemented as a package for the R computing environment called DAGGER. The simplified consensus graphs produced by DAGGER exactly capture the ordinal relationships present in a series of linkage maps. Using either linear or quadratic programming, DAGGER generates a consensus map with minimum error relative to the linkage maps while remaining ordinally consistent with them. Both linearization methods produce consensus maps that are compressed relative to the mean of the linkage maps. After rescaling, however, the consensus maps had higher accuracy (and higher marker density than the individual linkage maps in genetic simulations. When applied to four barley linkage maps genotyped at nearly 3000 SNP markers, DAGGER produced a consensus map with improved fine structure compared to the existing barley consensus SNP map. The root-mean-squared error between the linkage maps and the DAGGER map was 0.82 cM per marker interval compared to 2.28 cM for the existing consensus map. Examination of the barley hardness locus at the 5HS telomere, for which there is a physical map, confirmed that the DAGGER output was more accurate for fine structure analysis. Conclusions The R package DAGGER is an effective, freely available resource for integrating the information from a set of consistent linkage maps.

  19. Mapping our genes: The genome projects: How big, how fast

    Energy Technology Data Exchange (ETDEWEB)

    none,

    1988-04-01

    For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for /open quotes/writing the rules/close quotes/ of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. OTA prepared this report with the assistance of several hundred experts throughout the world. 342 refs., 26 figs., 11 tabs.

  20. Mapping Our Genes: The Genome Projects: How Big, How Fast

    Science.gov (United States)

    1988-04-01

    For the past 2 years, scientific and technical journals in biology and medicine have extensively covered a debate about whether and how to determine the function and order of human genes on human chromosomes and when to determine the sequence of molecular building blocks that comprise DNA in those chromosomes. In 1987, these issues rose to become part of the public agenda. The debate involves science, technology, and politics. Congress is responsible for �writing the rules� of what various federal agencies do and for funding their work. This report surveys the points made so far in the debate, focusing on those that most directly influence the policy options facing the US Congress. Congressional interest focused on how to assess the rationales for conducting human genome projects, how to fund human genome projects (at what level and through which mechanisms), how to coordinate the scientific and technical programs of the several federal agencies and private interests already supporting various genome projects, and how to strike a balance regarding the impact of genome projects on international scientific cooperation and international economic competition in biotechnology. The Office of Technology Assessment (OTA) prepared this report with the assistance of several hundred experts throughout the world.

  1. Lesion Mapping the Four-Factor Structure of Emotional Intelligence

    Directory of Open Access Journals (Sweden)

    Joachim Thomas Operskalski

    2015-12-01

    Full Text Available Emotional intelligence refers to an individual’s ability to process and respond to emotions, including recognizing the expression of emotions in others, using emotions to enhance thought and decision making, and regulating emotions to drive effective behaviors. Despite their importance for goal-directed social behavior, little is known about the neural mechanisms underlying specific facets of emotional intelligence. Here, we report findings from a study investigating the neural bases of these specific components for emotional intelligence in a sample of 130 combat veterans with penetrating traumatic brain injury. We examined the neural mechanisms underlying experiential (perceiving and using emotional information and strategic (understanding and managing emotions facets of emotional intelligence. Factor scores were submitted to voxel-based lesion symptom mapping to elucidate their neural substrates. The results indicate that two facets of emotional intelligence (perceiving and managing emotions engage common and distinctive neural systems, with shared dependence on the social knowledge network, and selective engagement of the orbitofrontal and parietal cortex for strategic aspects of emotional information processing. The observed pattern of findings suggests that sub-facets of experiential and strategic emotional intelligence can be characterized as separable but related processes that depend upon a core network of brain structures within frontal, temporal and parietal cortex.

  2. Lesion Mapping the Four-Factor Structure of Emotional Intelligence

    Science.gov (United States)

    Operskalski, Joachim T.; Paul, Erick J.; Colom, Roberto; Barbey, Aron K.; Grafman, Jordan

    2015-01-01

    Emotional intelligence (EI) refers to an individual’s ability to process and respond to emotions, including recognizing the expression of emotions in others, using emotions to enhance thought and decision making, and regulating emotions to drive effective behaviors. Despite their importance for goal-directed social behavior, little is known about the neural mechanisms underlying specific facets of EI. Here, we report findings from a study investigating the neural bases of these specific components for EI in a sample of 130 combat veterans with penetrating traumatic brain injury. We examined the neural mechanisms underlying experiential (perceiving and using emotional information) and strategic (understanding and managing emotions) facets of EI. Factor scores were submitted to voxel-based lesion symptom mapping to elucidate their neural substrates. The results indicate that two facets of EI (perceiving and managing emotions) engage common and distinctive neural systems, with shared dependence on the social knowledge network, and selective engagement of the orbitofrontal and parietal cortex for strategic aspects of emotional information processing. The observed pattern of findings suggests that sub-facets of experiential and strategic EI can be characterized as separable but related processes that depend upon a core network of brain structures within frontal, temporal and parietal cortex. PMID:26858627

  3. Lesion Mapping the Four-Factor Structure of Emotional Intelligence.

    Science.gov (United States)

    Operskalski, Joachim T; Paul, Erick J; Colom, Roberto; Barbey, Aron K; Grafman, Jordan

    2015-01-01

    Emotional intelligence (EI) refers to an individual's ability to process and respond to emotions, including recognizing the expression of emotions in others, using emotions to enhance thought and decision making, and regulating emotions to drive effective behaviors. Despite their importance for goal-directed social behavior, little is known about the neural mechanisms underlying specific facets of EI. Here, we report findings from a study investigating the neural bases of these specific components for EI in a sample of 130 combat veterans with penetrating traumatic brain injury. We examined the neural mechanisms underlying experiential (perceiving and using emotional information) and strategic (understanding and managing emotions) facets of EI. Factor scores were submitted to voxel-based lesion symptom mapping to elucidate their neural substrates. The results indicate that two facets of EI (perceiving and managing emotions) engage common and distinctive neural systems, with shared dependence on the social knowledge network, and selective engagement of the orbitofrontal and parietal cortex for strategic aspects of emotional information processing. The observed pattern of findings suggests that sub-facets of experiential and strategic EI can be characterized as separable but related processes that depend upon a core network of brain structures within frontal, temporal and parietal cortex.

  4. Genetic Analysis and Molecular Mapping of a Novel Chlorophyll-Deficit Mutant Gene in Rice

    Institute of Scientific and Technical Information of China (English)

    HUANG Xiao-qun; WANG Ping-rong; ZHAO Hai-xin; DENG Xiao-jian

    2008-01-01

    A rice etiolation mutant 824ys featured with chlorophyll deficiency was identified from a normal green rice variety 824B.It showed whole green-yellow plant from the seedling stage,reduced number of tillers and longer growth duration.The contents of chlorophyll,chlorophyll a,chlorophyll b and net photosynthetic rate in leaves of the mutant obviously decreased,as well as the number of spikelets per panicle,seed setting rate and 1000-grain weight compared with its wild-type parent.Genetic analyses on F1 and F2 generetions of 824ys crossed with three normal green varieties showed that the chlorophyll-deficit mutant character was controlled by a pair of recessive nuclear gene.Genetic mapping of the mutant gene was conducted by using microsatellite markers and F2 mapping population of 495R/824ys,and the mutant gene of 824ys was mapped on the shon arm of rice chromosome 3.The genetic distances from the target gene to the markers RM218,RM282 and RM6959 were 25.6 cM,5.2 cM and 21.8 cM,respectively.It was considered to be a now chlorophyll-deficit mutant gene and tentatively named as chl11(t).

  5. Sequencing and mapping hemoglobin gene clusters in the australian model dasyurid marsupial sminthopsis macroura

    Energy Technology Data Exchange (ETDEWEB)

    De Leo, A.A.; Wheeler, D.; Lefevre, C.; Cheng, Jan-Fang; Hope, R.; Kuliwaba, J.; Nicholas, K.R.; Westermanc, M.; Graves, J.A.M.

    2004-07-26

    Comparing globin genes and their flanking sequences across many species has allowed globin gene evolution to be reconstructed in great detail. Marsupial globin sequences have proved to be of exceptional significance. A previous finding of a beta-like omega gene in the alpha cluster in the tammar wallaby suggested that the alpha and beta cluster evolved via genome duplication and loss rather than tandem duplication. To confirm and extend this important finding we isolated and sequenced BACs containing the alpha and beta loci from the distantly related Australian marsupial Sminthopsis macroura. We report that the alpha gene lies in the same BAC as the beta-like omega gene, implying that the alpha-omega juxtaposition is likely to be conserved in all marsupials. The LUC7L gene was found 3' of the S. macroura alpha locus, a gene order shared with humans but not mouse, chicken or fugu. Sequencing a BAC contig that contained the S. macroura beta globin and epsilon globin loci showed that the globin cluster is flanked by olfactory genes, demonstrating a gene arrangement conserved for over 180 MY. Analysis of the region 5' to the S. macroura epsilon globin gene revealed a region similar to the eutherian LCR, containing sequences and potential transcription factor binding sites with homology to eutherian hypersensitive sites 1 to 5. FISH mapping of BACs containing S. macroura alpha and beta globin genes located the beta globin cluster on chromosome 3q and the alpha locus close to the centromere on 1q, resolving contradictory map locations obtained by previous radioactive in situ hybridization.

  6. Mapping the structural and dynamical features of kinesin motor domains.

    Directory of Open Access Journals (Sweden)

    Guido Scarabelli

    Full Text Available Kinesin motor proteins drive intracellular transport by coupling ATP hydrolysis to conformational changes that mediate directed movement along microtubules. Characterizing these distinct conformations and their interconversion mechanism is essential to determining an atomic-level model of kinesin action. Here we report a comprehensive principal component analysis of 114 experimental structures along with the results of conventional and accelerated molecular dynamics simulations that together map the structural dynamics of the kinesin motor domain. All experimental structures were found to reside in one of three distinct conformational clusters (ATP-like, ADP-like and Eg5 inhibitor-bound. These groups differ in the orientation of key functional elements, most notably the microtubule binding α4-α5, loop8 subdomain and α2b-β4-β6-β7 motor domain tip. Group membership was found not to correlate with the nature of the bound nucleotide in a given structure. However, groupings were coincident with distinct neck-linker orientations. Accelerated molecular dynamics simulations of ATP, ADP and nucleotide free Eg5 indicate that all three nucleotide states could sample the major crystallographically observed conformations. Differences in the dynamic coupling of distal sites were also evident. In multiple ATP bound simulations, the neck-linker, loop8 and the α4-α5 subdomain display correlated motions that are absent in ADP bound simulations. Further dissection of these couplings provides evidence for a network of dynamic communication between the active site, microtubule-binding interface and neck-linker via loop7 and loop13. Additional simulations indicate that the mutations G325A and G326A in loop13 reduce the flexibility of these regions and disrupt their couplings. Our combined results indicate that the reported ATP and ADP-like conformations of kinesin are intrinsically accessible regardless of nucleotide state and support a model where neck

  7. A 4.5-megabase YAC contig and physical map over the hemochromatosis gene region

    Energy Technology Data Exchange (ETDEWEB)

    Burt, M.J.; Smit, D.J.; Pyper, W.R.; Powell, L.W.; Jazwinska, E.C. [Univ. of Queensland, Brisbane (Australia)

    1996-04-15

    We have constructed a yeast artificial chromosome (YAC) contig over the candidate hemochromatosis gene region. This contig comprises hemochromatosis gene region. This contig comprises 16 YACs from the CEPH, Washington University, and ICI YAC libraries and covers 4.5 Mb at 6p21.3-6p22. The complete contig has been restriction mapped, enabling the precise relationship between the YACs to be determined and the mapping of a total of 12 STSs. Nine of these are highly polymorphic STSs that are closely linked to hemochromatosis; this series includes D6S265 and D6S1260, which comprise the most proximal and distal markers linked to HC. This is the first YAC contig that spans the hemochromatosis candidate region, and it provides valuable resource material for the cloning of this and other genes in the region distal to the MHC class I complex. 33 refs., 1 fig., 1 tab.

  8. Mapping a gene for adult-onset primary open-angle glaucoma to chromosome 3q

    Energy Technology Data Exchange (ETDEWEB)

    Wirtz, M.K.; Samples, J.R.; Kramer, P.L. [Oregon Health Sciences Univ., Portland, OR (United States)] [and others

    1997-02-01

    Glaucoma is the third-leading cause of blindness in the world, affecting >13.5 million people. Adult-on-set primary open-angle glaucoma (POAG) is the most common form of glaucoma in the United States. We present a family in which adult-onset POAG is inherited as an autosomal dominant trait. Twelve affected family members were identified from 44 at-risk individuals. The disease-causing gene was mapped to chromosome 3q21-24, with analysis of recombinant haplotypes suggesting a total inclusion region of 11.1 cM between markers D3S3637 and D3S1744. This is the first report of mapping of an adult-onset POAG gene to chromosome 3q, gene symbol GLC1C. 57 refs., 3 figs., 3 tabs.

  9. SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation.

    Science.gov (United States)

    Norambuena, Tomás; Malig, Rodrigo; Melo, Francisco

    2007-07-01

    We describe a web server for the accurate mapping of experimental tags in serial analysis of gene expression (SAGE). The core of the server relies on a database of genomic virtual tags built by a recently described method that attempts to reduce the amount of ambiguous assignments for those tags that are not unique in the genome. The method provides a complete annotation of potential virtual SAGE tags within a genome, along with an estimation of their confidence for experimental observation that ranks tags that present multiple matches in the genome. The output of the server consists of a table in HTML format that contains links to a graphic representation of the results and to some external servers and databases, facilitating the tasks of analysis of gene expression and gene discovery. Also, a table in tab delimited text format is produced, allowing the user to export the results into custom databases and software for further analysis. The current server version provides the most accurate and complete SAGE tag mapping source that is available for the yeast organism. In the near future, this server will also allow the accurate mapping of experimental SAGE-tags from other model organisms such as human, mouse, frog and fly. The server is freely available on the web at: http://dna.bio.puc.cl/SAGExplore.html.

  10. Mapping a candidate gene (MdMYB10 for red flesh and foliage colour in apple

    Directory of Open Access Journals (Sweden)

    Allan Andrew C

    2007-07-01

    Full Text Available Abstract Background Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes. Results We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs and Single Nucleotide Polymorphisms (SNPs in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG 09 of the apple genome. Conclusion We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species.

  11. Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple

    Science.gov (United States)

    Chagné, David; Carlisle, Charmaine M; Blond, Céline; Volz, Richard K; Whitworth, Claire J; Oraguzie, Nnadozie C; Crowhurst, Ross N; Allan, Andrew C; Espley, Richard V; Hellens, Roger P; Gardiner, Susan E

    2007-01-01

    Background Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes. Results We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG) 09 of the apple genome. Conclusion We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species. PMID:17608951

  12. Resistance to Colletotrichum lindemuthianum in Phaseolus vulgaris: a case study for mapping two independent genes.

    Science.gov (United States)

    Geffroy, Valérie; Sévignac, Mireille; Billant, Paul; Dron, Michel; Langin, Thierry

    2008-02-01

    Anthracnose, caused by the hemibiotrophic fungal pathogen Colletotrichum lindemuthianum is a devastating disease of common bean. Resistant cultivars are economical means for defense against this pathogen. In the present study, we mapped resistance specificities against 7 C. lindemuthianum strains of various geographical origins revealing differential reactions on BAT93 and JaloEEP558, two parents of a recombinant inbred lines (RILs) population, of Meso-american and Andean origin, respectively. Six strains revealed the segregation of two independent resistance genes. A specific numerical code calculating the LOD score in the case of two independent segregating genes (i.e. genes with duplicate effects) in a RILs population was developed in order to provide a recombination value (r) between each of the two resistance genes and the tested marker. We mapped two closely linked Andean resistance genes (Co-x, Co-w) at the end of linkage group (LG) B1 and mapped one Meso-american resistance genes (Co-u) at the end of LG B2. We also confirmed the complexity of the previously identified B4 resistance gene cluster, because four of the seven tested strains revealed a resistance specificity near Co-y from JaloEEP558 and two strains identified a resistance specificity near Co-9 from BAT93. Resistance genes found within the same cluster confer resistance to different strains of a single pathogen such as the two anthracnose specificities Co-x and Co-w clustered at the end of LG B1. Clustering of resistance specificities to multiple pathogens such as fungi (Co-u) and viruses (I) was also observed at the end of LG B2.

  13. Mapping of a rice thermosensitive genic male sterility gene from a TGMS mutant line

    Energy Technology Data Exchange (ETDEWEB)

    Vu Duc Quang; Nguyen Van Dong; Pham Ngoc Luong; Tran Duy Quy [Argicultural Genetics Institute, Hanoi (Viet Nam); Nguyen, Henry T. [Texas Tech Univ., Department of Plant and Soil Science, Lubbock TX (United States)

    2001-03-01

    At the Agricultural Genetics Institute (AGI), Hanoi, Vietnam, a number of thermo-sensitive genic male sterility (TGMS) homozygous rice lines have been developed by means of experimental mutagenesis followed by anther culture techniques. One of them (TGMS-1 indica mutant line) was used in this research. The critical temperature (at the period from pollen mother cell formation to the beginning of meiotic division) for TGMS-1 sterility was 24-25degC, below which the plants were fertile and above which the plants became sterile. Segregation analysis showed that the TGMS trait of the TGMS-1 mutant line was controlled by a single recessive gene. An F{sub 2} mapping population from a cross between TGMS-1 mutant line and CH1 (a fertile indica line) was developed for tagging and mapping the TGMS gene. From survey of 200 AFLP primer combinations in a bulked segregant analysis, 4 AFLP markers (E2/M5-200, E3/M16-400, E5/M12-600 and E5/M12-200) linked to TGMS-1 gene were identified and cloned. All except E2/M5-200 were found to be low-copy number sequences. The marker E5/M12-600 showed polymorphism in RFLP analysis and was closely linked to the TGMS gene at a distance of 3.3cM. This marker was subsequently mapped on chromosome 2 using doubled-haploid mapping populations derived from the crosses IR64xAzucena and CT9993xIR62666. Linkage of microsatellite marker RM27 with the TGMS gene further confirmed its location on chromosome 2. The closest marker, E5/M12-600, was sequenced so that a PCR marker can be developed for the use in marker-assisted breeding. The application of TGMS genes to the commercial two-line hybrid rice breeding system was discussed. (author)

  14. Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean

    Directory of Open Access Journals (Sweden)

    Sujan Mamidi

    2016-07-01

    Full Text Available White mold, caused by the necrotrophic fungus (Lib. de Bary, is a major disease of common bean ( L.. WM7.1 and WM8.3 are two quantitative trait loci (QTL with major effects on tolerance to the pathogen. Advanced backcross populations segregating individually for either of the two QTL, and a recombinant inbred (RI population segregating for both QTL were used to fine map and confirm the genetic location of the QTL. The QTL intervals were physically mapped using the reference common bean genome sequence, and the physical intervals for each QTL were further confirmed by sequence-based introgression mapping. Using whole-genome sequence data from susceptible and tolerant DNA pools, introgressed regions were identified as those with significantly higher numbers of single-nucleotide polymorphisms (SNPs relative to the whole genome. By combining the QTL and SNP data, WM7.1 was located to a 660-kb region that contained 41 gene models on the proximal end of chromosome Pv07, while the WM8.3 introgression was narrowed to a 1.36-Mb region containing 70 gene models. The most polymorphic candidate gene in the WM7.1 region encodes a BEACH-domain protein associated with apoptosis. Within the WM8.3 interval, a receptor-like protein with the potential to recognize pathogen effectors was the most polymorphic gene. The use of gene and sequence-based mapping identified two candidate genes whose putative functions are consistent with the current model of pathogenicity.

  15. A transcription map of the 6p22.3 reading disability locus identifying candidate genes

    Directory of Open Access Journals (Sweden)

    Gruen Jeffrey R

    2003-06-01

    Full Text Available Abstract Background Reading disability (RD is a common syndrome with a large genetic component. Chromosome 6 has been identified in several linkage studies as playing a significant role. A more recent study identified a peak of transmission disequilibrium to marker JA04 (G72384 on chromosome 6p22.3, suggesting that a gene is located near this marker. Results In silico cloning was used to identify possible candidate genes located near the JA04 marker. The 2 million base pairs of sequence surrounding JA04 was downloaded and searched against the dbEST database to identify ESTs. In total, 623 ESTs from 80 different tissues were identified and assembled into 153 putative coding regions from 19 genes and 2 pseudogenes encoded near JA04. The identified genes were tested for their tissue specific expression by RT-PCR. Conclusions In total, five possible candidate genes for RD and other diseases mapping to this region were identified.

  16. Genetic analysis and gene mapping of a narrow leaf mutant in rice (Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    WANG DeKai; LIU HeQin; LI KeLei; LI SuJuan; TAO YueZhi

    2009-01-01

    A narrow leaf mutant was obtained after T-DNA transformation conducted on a rice variety Zhonghua 11. Several abnormal morphological characteristics, including semi-dwarf, delayed flowering time, narrow and inward rolling leaves, and lower seed-setting, were observed. The rate of net photosynthesis (un-der saturate light) of flag leaves in the mutant was significantly lower than that of the wild type. More-over, the leaf transpiration rate and stomatal conductance in the mutant flag leaf were lower than those of the wild type at the grain filling stage. It was found that the mutant phenotype was not caused by the T-DNA insertion. Genetic analysis showed that the mutant was controlled by a single recessive gene,designated as nal3(t). A genetic linkage map was constructed using a large F2 mapping population de-rived from a cross between nal3(t) and an indica variety Longtefu B with 6 polymorphic markers on chromosome 12 identified from 366 SSR markers by the BAS method. Gene nal3(t) was mapped be-tween the markers RM7018 and RM3331. Fine mapping of nal3(t) locus was conducted with 22 newly developed STS markers based on the sequence diversity around the region harboring nal3(t) between Nipponbare and 93-11, and nal3(f) was finally mapped to a 136-kb region between the STS markers NS10 and RH12-8.

  17. Development of specific chromosomal DNA pool for rice field eel and their application to gene mapping

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The chromosomes 1, 3, 5, 6, 7, 10 and 12 of rice field eel (Monopterus albus Zuiew) have been microdissected successfully from meiosis I diakinesis spreads by using glass microneedle under an inverted microscope. And the DOP-PCR products of the single chromosome dotted on the nylon membrane as "specific chromosomal DNA pool", have been hybridized with 6 probes to map these genes. The mapping results show that Zfa has been mapped to chromosome 1, rDNA to chromosomes 3 and 7, both Gh and Pdeg to chromosome 10, Hsl to chromosome 5 and Hox genes have been detected on chromosomes 1, 3, 6 and 10 meantime. It has initiatively been suggested that chromosome 10 of rice field eel might possess the commom conserved synteny to that on chromosome 17 of human, chromosome 11 of mouse,chromosome 12 of pig and chromosome 19 of bovine. And so chromosome 3 of rice field eel might also contain the commom conserved synteny to that on chromosome 2 of zebrafish. Our study is an attempt to establish a new and feasible method to advance the study of gene mapping and chromosome evolution in fish, and also to provide a new idea to distinguish each chromosome on the base of molecular markers for fish.

  18. Genetic Analysis and Mapping of TWH Gene in Rice Twisted Hull Mutant

    Institute of Scientific and Technical Information of China (English)

    LI Jin-bo; XIA Ming-yuan; WAN Bing-liang; DU Xue-shu; ZHA Zhong-ping; YU Da-zhao; QI Hua-xiong

    2009-01-01

    A mutant with twisted hulls was found in a breeding population of rice (Oryza sativa L.). The mutant shows less grain weight and inferior grain quality in addition to twisted hulls. Genetic analysis indicated that the phenotype of mutant was controlled by a single recessive gene (temporarily designated as TWH). To map the TWH gene, an F2 population was generated by crossing the twh mutant to R725, an indica rice variety with normal hulls. For bulked segregant analysis, the bulk of mutant plants was prepared by mixing equal amount of plant tissue from 10 twisted-hull plants and the bulk of normal plants was obtained by pooling equal amount tissue of 10 normal-hull plants. Two hundred and seven pairs of simple sequence repeat (SSR) primers, which are distributed on 12 rice chromosomes, were used for polymorphism analysis of the parents and the two bulks. The TWH locus was initially mapped close to the SSR marker RM526 on chromosome 2. Therefore, further mapping was performed using 50 pairs of SSR primers around the marker RM526. The TWH was delimited between the SSR markers RM14128 and RM208 on the long arm of chromosome 2 at the genetic distances of 1.4 cM and 2.7 cM, respectively. These results provide the foundation for further fine mapping, cloning and functional analysis of the TWH gene.

  19. Arabidopsis MAP kinase 4 regulates gene expression through transcription factor release in the nucleus.

    Science.gov (United States)

    Qiu, Jin-Long; Fiil, Berthe Katrine; Petersen, Klaus; Nielsen, Henrik Bjørn; Botanga, Christopher J; Thorgrimsen, Stephan; Palma, Kristoffer; Suarez-Rodriguez, Maria Cristina; Sandbech-Clausen, Signe; Lichota, Jacek; Brodersen, Peter; Grasser, Klaus D; Mattsson, Ole; Glazebrook, Jane; Mundy, John; Petersen, Morten

    2008-08-20

    Plant and animal perception of microbes through pathogen surveillance proteins leads to MAP kinase signalling and the expression of defence genes. However, little is known about how plant MAP kinases regulate specific gene expression. We report that, in the absence of pathogens, Arabidopsis MAP kinase 4 (MPK4) exists in nuclear complexes with the WRKY33 transcription factor. This complex depends on the MPK4 substrate MKS1. Challenge with Pseudomonas syringae or flagellin leads to the activation of MPK4 and phosphorylation of MKS1. Subsequently, complexes with MKS1 and WRKY33 are released from MPK4, and WRKY33 targets the promoter of PHYTOALEXIN DEFICIENT3 (PAD3) encoding an enzyme required for the synthesis of antimicrobial camalexin. Hence, wrky33 mutants are impaired in the accumulation of PAD3 mRNA and camalexin production upon infection. That WRKY33 is an effector of MPK4 is further supported by the suppression of PAD3 expression in mpk4-wrky33 double mutant backgrounds. Our data establish direct links between MPK4 and innate immunity and provide an example of how a plant MAP kinase can regulate gene expression by releasing transcription factors in the nucleus upon activation.

  20. Strategy for the mapping of interactive genes using bulked segregant analysis method and Mapmaker/Exp software

    Institute of Scientific and Technical Information of China (English)

    WU Weiren; HUANG Biguang

    2006-01-01

    A qualitative trait is usually controlled by a single gene, but it may be sometimes controlled by two or even more genes. This phenomenon is called gene interaction. Rapidly searching for linked molecular markers via bulked segregant analysis (BSA)and then constructing regional linkage map with Mapmaker/Exp has become a common approach to mapping single major genes. However, methods and computer programs developed for mapping single major genes cannot be simply applied to interactive genes because the genetic patterns of gene interactions are quite different from that of single-gene inheritance. Up to now, experimental methods for quickly screening molecular markers linked to interactive genes and statistical methods and corresponding computer softwares for simultaneously analyzing the linkage relationships of multiple molecular markers to an interactive gene have not been available. To solve this problem, in this paper, we propose a strategy for mapping interactive genes using BSA and Mapmaker/Exp. We demonstrate that Mapmaker/Exp' strategy using F2 generation (in a few cases, F3 generation is also needed). As BSA and Mapmaker/Exp have been broadly used in gene mapping studies and are well known by many researchers, the strategies proposed in this paper will be useful for practical researches.

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

    Energy Technology Data Exchange (ETDEWEB)

    Burt, M.J.; Smit, D.J.; Pyper, W.R. [Univ. of Queensland, Brisbane (Australia)

    1994-09-01

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

  2. Fine mapping of the red plant gene R1 in upland cotton(Gossypium hirsutum)

    Institute of Scientific and Technical Information of China (English)

    ZHAO Liang; CAI CaiPing; ZHANG TianZhen; GUO WangZhen

    2009-01-01

    Sub 16 is a substitution line with G. hirsutum cv. TM-1 genetic background except that the 16th chro-mosome (Chr. 16) is replaced by the corresponding homozygous chromosome of G. barbadense cv. 3-79, and T586 is a G. hirsutum multiple gene marker line with 8 dominant mutation genes. The R1 gene for anthocyanin pigmentation was tagged in Chr. 16 in T586. The objective of this research was to screen SSR markers tightly linked with R1 by using the F2 segregating population containing 1259 plants derived from the cross of Sub 16 and T586 and the backbone genetic linkage map from G. hir-sutumxG, barbadense BC1 newly updated by our laboratory. Genetic analysis suggested that the se-gregation ratio of red plants in the F2 population fit Mendelian 1:2:1 inheritance, confirming that the red plant trait was controlled by an incomplete dominance gene. Preliminary mapping of R1 was conducted using 237 randomLy selected F2 individuals and JoinMap v3.0 software. Then, a fine map of R1 was constructed using the F2 segregating population containing 1259 plants, and R1 was located between NAU4956 and NAU6752, with only 0.49 cM to the nearest maker loci (NAU6752). These results pro-vided a foundation for map-based cloning of R1 and further development of cotton cultivars with red fibers by transgenic technology.

  3. Genetic analysis and molecular mapping of maize (Zea mays L.) stalk rot resistant gene Rfg1.

    Science.gov (United States)

    Yang, D E; Zhang, C L; Zhang, D S; Jin, D M; Weng, M L; Chen, S J; Nguyen, H; Wang, B

    2004-02-01

    One single pathogen Fusarium graminearum Schw. was inoculated to maize inbred lines 1,145 (Resistant) and Y331 (Susceptive), and their progenies of F(1), F(2) and BC(1)F(1) populations. Field statistical data revealed that all of the F(1) individuals were resistant to the disease and that the ratio of resistant plants to susceptive plants was 3:1 in the F(2) population, and 1:1 in the BC(1)F(1 )population. The results revealed that a single dominant gene controls the resistance to F. graminearum Schw. The resistant gene to F. graminearum Schw. was denominated as Rfg1 according to the standard principle of the nomenclature of the plant disease resistant genes. RAPD (randomly amplified polymorphic DNA) combined with BSA (bulked segregant analysis) analysis was carried out in the developed F(2) and BC(1)F(1 )populations, respectively. Three RAPD products screened from the RAPD analysis with 820 Operon 10-mer primers showed the linkage relation with the resistant gene Rfg1. The three RAPD amplification products (OPD-20(1000), OPA-04(1100) and OPY-04(900)) were cloned and their copy numbers were determined. The results indicated that only OPY-04(900) was a single-copy sequence. Then, OPY-04(900) was used as a probe to map the Rfg1 gene with a RIL F(7) mapping population provided by Henry Nguyen, which was developed from the cross "S3xMo17". Rfg1 was primarily mapped on chromosome 6 between the two linked markers OPY-04(900) and umc21 (Bin 6.04-6.05). In order to confirm the primary mapping result, 25 SSR (simple sequence repeat) markers and six RFLP (restriction fragment length polymorphism) markers in the Rfg1 gene-encompassing region were selected, and their linkage relation with Rfg1 was analyzed in our F(2) population. Results indicated that SSR marker mmc0241 and RFLP marker bnl3.03 are flanking the Rfg1 gene with a genetic distance of 3.0 cM and 2.0 cM, respectively. This is the first time to name and to map a single resistant gene of maize stalk rot through a

  4. Isolation, characterization, and chromosomal mapping of the human Nkx6.1 gene (NKX6A), a new pancreatic islet homeobox gene

    Energy Technology Data Exchange (ETDEWEB)

    Inoue, Hiroshi; Permutt, M.A.; Veile, R. [Washington Univ. School of Medicine, St. Louis, MO (United States)] [and others

    1997-03-01

    Nkx6.1 (gene symbol NKX6A), a new member of the NK homeobox gene family, was recently identified in rodent pancreatic islet 13-cell lines. The pattern of expression suggested that this gene product might be important for control of islet development and/or regulation of insulin biosynthesis. We now report cloning of human NKX6A, characterization of its genomic structure, and its chromosomal localization. The predicted protein of human NKX6A contained 367 amino acids and had 97% identity to the hamster protein. The highly conserved NK decapeptide and homeodomain regions were identical between human and hamster, suggesting functional importance of these domains. The coding region spanned approximately 4.8 kb and was composed of three exons. The gene was localized to four CEPH {open_quotes}B{close_quotes} yeast artificial chromosome clones (914B4, 951G9, 981D6, and 847133), and a nearby polymorphic marker (D4S1538) on chromosome 4 was identified <1270 kb from the gene. Using fluorescence in situ hybridization, we also determined that NKX6A maps to 4q21.2-q22. 11 refs., 2 figs.

  5. Identification and mapping of two powdery mildew resistance genes in Triticum boeoticum L.

    Science.gov (United States)

    Chhuneja, Parveen; Kumar, Krishan; Stirnweis, Daniel; Hurni, Severine; Keller, Beat; Dhaliwal, Harcharan S; Singh, Kuldeep

    2012-04-01

    Powdery mildew (PM) caused by Blumeria graminis f. sp. tritici (Bgt), is one of the important foliar diseases of wheat that can cause serious yield losses. Breeding for cultivars with diverse resources of resistance is the most promising approach for combating this disease. The diploid A genome progenitor species of wheat are an important resource for new variability for disease resistance genes. An accession of Triticum boeoticum (A(b)A(b)) showed resistance against a number of Bgt isolates, when tested using detached leaf segments. Inheritance studies in a recombinant inbred line population (RIL), developed from crosses of PM resistant T. boeoticum acc. pau5088 with a PM susceptible T. monococcum acc. pau14087, indicated the presence of two powdery mildew resistance genes in T. boeoticum acc. pau5088. Analysis of powdery mildew infection and molecular marker data of the RIL population revealed that both powdery mildew resistance genes are located on the long arm of chromosome 7A. Mapping was conducted using an integrated linkage map of 7A consisting of SSR, RFLP, STS, and DArT markers. These powdery mildew resistance genes are tentatively designated as PmTb7A.1 and PmTb7A.2. The PmTb7A.2 is closely linked to STS markers MAG2185 and MAG1759 derived from RFLP probes which are linked to powdery mildew resistance gene Pm1. This indicated that PmTb7A.2 might be allelic to Pm1. The PmTb7A.1, flanked by a DArT marker wPt4553 and an SSR marker Xcfa2019 in a 4.3 cM interval, maps proximal to PmT7A.2. PmTb7A.1 is putatively a new powdery mildew resistance gene. The powdery mildew resistance genes from T. boeoticum are currently being transferred to cultivated wheat background through marker-assisted backcrossing, using T. durum as bridging species.

  6. Fine Mapping and Cloning of Leafy Head Mutant Gene pla1-5 in Rice

    Directory of Open Access Journals (Sweden)

    Gong-neng FENG

    2013-09-01

    Full Text Available We identified a leafy head mutant pla1-5 (plastochron 1-5 from the progeny of japonica rice cultivar Taipei 309 treated with 60Co-γ ray irradiation. The pla1-5 mutant has a dwarf phenotype and small leaves. Compared with its wild type, pla1-5 has more leaves and fewer tillers, and it fails to produce normal panicles at the maturity stage. Genetic analysis showed that the pla1-5 phenotype is controlled by a single recessive nuclear gene. Using the map-based cloning strategy, we narrowed down the location of the target gene to a 58-kb region between simple sequence repeat markers CHR1027 and CHR1030 on the long arm of chromosome 10. The target gene cosegregated with molecular markers CHR1028 and CHR1029. There were five predicted genes in the mapped region. The results from sequencing analysis revealed that there was one base deletion in the first exon of LOC_Os10g26340 encoding cytochrome P450 CYP78A11 in the pla1-5 mutant, which might result in a downstream frame shift and premature termination. These results suggest that the P450 CYP78A11 gene is the candidate gene of PLA1-5.

  7. Genetic Analysis and Gene Mapping of Light Brown Spotted Leaf Mutant in Rice

    Institute of Scientific and Technical Information of China (English)

    FENG Bao-hua; YANG Yang; SHI Yong-feng; LIN Lu; CHEN Jie; WEI Yan-lin; Hei LEUNG

    2013-01-01

    A light brown spotted-leaf mutant of rice was isolated from an ethane methyl sulfonate (EMS)induced IR64 mutant bank.The mutant,designated as Ibsl1 (light brown spotted-leaf 1),displayed light brown spot in the whole growth period from the first leaf to the flag leaf under natural summer field conditions.Agronomic traits including plant height,growth duration,number of filled grains per panicle,seed-setting rate and 1000-grain weight of the mutant were significantly affected.Genetic analysis showed that the mutation was controlled by a single recessive gene,tentatively named Ibsl1(t),which was mapped to the short arm of chromosome 6.By developing simple sequence repeat (SSR) markers,the gene was finally delimited to an interval of 130 kb between markers RM586 and RM588.The Ibsl1(t) gene is likely a novel rice spotted-leaf gene since no other similar genes have been identified near the chromosomal region.The genetic data and recombination populations provided will facilitate further fine-mapping and cloning of the gene.

  8. Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae

    Directory of Open Access Journals (Sweden)

    Shu Xia Sun

    2008-01-01

    Full Text Available We investigated inheritance and carried out gene fine mapping of aroma in crosses between the aromatic elite hybrid rice Oryza sativa indica variety Chuanxiang-29B (Ch-29B and the non-aromatic rice O. sativa indica variety R2 and O. sativa japonica Lemont (Le. The F1 grains and leaves were non-aromatic while the F2 non-aroma to aroma segregation pattern was 3:1. The F3 segregation ratio was consistent with the expected 1:2:1 for a single recessive aroma gene in Ch-29B. Linkage analysis between simple sequence repeat (SSR markers and the aroma locus for the aromatic F2 plants mapped the Ch-29B aroma gene to a chromosome 8 region flanked by SSR markers RM23120 at 0.52 cM and RM3459 at 1.23 cM, a replicate F2 population confirming these results. Three bacterial artificial chromosome (BAC clones cover chromosome 8 markers RM23120 and RM3459. Our molecular mapping data from the two populations indicated that the aroma locus occurs in a 142.85 kb interval on BAC clones AP005301 or AP005537, implying that it might be the same gene reported by Bradbury et al (2005a; Plant Biotec J. 3:363-370. The flanking markers Aro7, RM23120 and RM3459 identified by us could greatly accelerate the efficiency and precision of aromatic rice breeding programs.

  9. IDENTIFICATION AND MAPPING OF A GENE FOR RICE SLENDER KERNEL USING Oryza glumaepatula INTROGRESSION LINES

    Directory of Open Access Journals (Sweden)

    Sobrizal Sobrizal

    2016-10-01

    Full Text Available World demand for superior rice grain quality tends to increase. One of the  criteria of appearance quality of rice grain is grain shape. Rice consumers  exhibit wide preferences for grain shape, but most Indonesian rice consumers prefer long and slender grain. The objectives of this study were to identify and map a gene for rice slender kernel trait using Oryza  glumaepatula introgression lines with O. sativa cv. Taichung 65 genetic background. A segregation analysis of BC4F2 population derived from backcrosses of a donor parent O. glumaepatula into a recurrent parent Taichung 65 showed that the slender kernel was controlled by a single recessive gene. This new identified gene was designated as sk1 (slender kernel 1. Moreover, based on the RFLP analyses using 14 RFLP markers located on chromosomes 2, 8, 9, and 10 in which the O. glumaepatula chromosomal segments were retained in BC4F2 population, the sk1 was located between RFLP markers C679 and C560 on the long arm of chromosome 2, with map distances of 2.8 and 1.5 cM, respectively. The wild rice O. glumaepatula carried a recessive allele for slender kernel. This allele may be useful in breeding of rice with slender kernel types. In addition, the development of plant materials and RFLP map associated with slender kernel in this study is the preliminary works in the effort to isolate this important grain shape gene.

  10. Identification and genetic mapping of four novel genes that regulate leaf development in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Molecular and genetic characterizations of mutants have led to a better understanding of many developmental processes in the model system Arabidopsis thaliana. However, the leaf development that is specific to plants has been little studied. With the aim of contributing to the genetic dissection of leaf development, we have performed a large-scare screening for mutants with abnormal leaves. Among a great number of leaf mutants we have generated by T-DNA and transposon tagging and ethylmethae sulfonate (EMS) mutagenesis, four independent mutant lines have been identified and studied genetically. Phenotypes of these mutant lines represent the defects of four novel nuclear genes designated LL1 (LOTUS LEAF 1), LL2 (LOTUS LEAF 2), URO (UPRIGHT ROSETTE), and EIL (ENVIRONMENTCONDITION INDUCED LESION). The phenotypic analysis indicates that these genes play important roles during leaf development. For the further genetic analysis of these genes and the map-based cloning of LL1 and LL2, we have mapped these genes to chromosome regions with an efficient and rapid mapping method.

  11. Identification and genetic mapping of four novel genes that regulate leaf development in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    SUNYUE; YingLiGuo; 等

    2000-01-01

    Molecular and genetic characterizations of mutants have led to a better understanding of many developmental processes in the model system Arabidopsis thaliana.However,the leaf development that is specific to plants has been little studies.With the aim of contributing to the genetic dissection of leaf development,we have performed a large-scare screening for mutants with abnormal leaves.Among a great number of leaf mutants we have generated by T-DNA and transposon tagging and ethylmethae sulfonate (EMS) mutagenesis,four independent mutant lines have been identified and studied genetically.Phenotypes of these mutant lines represent the defects of four novel muclear genes designated LL1(LOTUS LEAF 1),LL2(LOTUS LEAF2),URO(UPRIGHT ROSETTE),and EIL(ENVIRONMENT CONDITION INDUCED LESION).The phenotypic analysis indicates that these genes play important roles during leaf development.For the further genetic analysis of these genes and the map-based cloning of LL1 and LL2,we have mapped these genes to chromosome regions with an efficient and rapid mapping method.

  12. On the structure of positive maps. II. Low dimensional matrix algebras

    Science.gov (United States)

    Majewski, Władysław A.; Tylec, Tomasz I.

    2013-07-01

    We use a new idea that emerged in the examination of exposed positive maps between matrix algebras to investigate in more detail the differences and similarities between unital positive maps on M2 ({C}) and M3({C}). Our main tool stems from classical Grothendieck theorem on tensor product of Banach spaces and is an older and more general version of Choi-Jamiołkowski isomorphism between positive maps and block positive Choi matrices. It takes into account the correct topology on the latter set that is induced by the uniform topology on positive maps. In this setting, we show that in M2({C}) case a large class of nice positive maps can be generated from the small set of maps represented by self-adjoint unitaries, 2Px with x maximally entangled vector and p⊗ {1} with p rank 1 projector. We indicate problems with passing this result to M3({C}) case. Among similarities, in both M2({C}) and M3({C}) cases any unital positive map represented by self-adjoint unitary is unitarily equivalent to the transposition map. Consequently, we obtain a large family of exposed maps. Furthermore, for M3({C}) there appear new non-trivial class of maps represented by Choi matrices with square equal to a projector. We examine this case. We also investigate a convex structure of the Choi map, the first example of non-decomposable map. As a result the nature of the Choi map will be explained.

  13. Cloning, structure, and chromosome localization of the mouse glutaryl-CoA dehydrogenase gene

    Energy Technology Data Exchange (ETDEWEB)

    Koeller, D.M.; DiGiulio, A.; Frerman, F.E. [Univ. of Colorado Health Sciences Center, Denver, CO (United States)] [and others

    1995-08-10

    Glutaryl-CoA dehydrogenase (GCDH) is a nuclear-encoded, mitochondrial matrix enzyme. In humans, deficiency of GCDH leads to glutaric acidemia type I, and inherited disorder of amino acid metabolism characterized by a progressive neurodegenerative disease. In this report we describe the cloning and structure of the mouse GCDH (Gcdh) gene and cDNA and its chromosomal localization. The mouse Gcdh cDNA is 1.75 kb long and contains and open reading frame of 438 amino acids. The amino acid sequences of mouse, human, and pig GCDH are highly conserved. The mouse Gcdh gene contains 11 exons and spans 7 kb of genomic DNA. Gcdh was mapped by backcross analysis to mouse chromosome 8 within a region that is homologous to a region of human chromosome 19, where the human gene was previously mapped. 14 refs., 3 figs.

  14. Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions and MapReduce.

    Science.gov (United States)

    Yehdego, Daniel T; Zhang, Boyu; Kodimala, Vikram K R; Johnson, Kyle L; Taufer, Michela; Leung, Ming-Ying

    2013-05-01

    Secondary structures of ribonucleic acid (RNA) molecules play important roles in many biological processes including gene expression and regulation. Experimental observations and computing limitations suggest that we can approach the secondary structure prediction problem for long RNA sequences by segmenting them into shorter chunks, predicting the secondary structures of each chunk individually using existing prediction programs, and then assembling the results to give the structure of the original sequence. The selection of cutting points is a crucial component of the segmenting step. Noting that stem-loops and pseudoknots always contain an inversion, i.e., a stretch of nucleotides followed closely by its inverse complementary sequence, we developed two cutting methods for segmenting long RNA sequences based on inversion excursions: the centered and optimized method. Each step of searching for inversions, chunking, and predictions can be performed in parallel. In this paper we use a MapReduce framework, i.e., Hadoop, to extensively explore meaningful inversion stem lengths and gap sizes for the segmentation and identify correlations between chunking methods and prediction accuracy. We show that for a set of long RNA sequences in the RFAM database, whose secondary structures are known to contain pseudoknots, our approach predicts secondary structures more accurately than methods that do not segment the sequence, when the latter predictions are possible computationally. We also show that, as sequences exceed certain lengths, some programs cannot computationally predict pseudoknots while our chunking methods can. Overall, our predicted structures still retain the accuracy level of the original prediction programs when compared with known experimental secondary structure.

  15. Structure contour map of the greater Green River basin, Wyoming, Colorado, and Utah

    Science.gov (United States)

    Lickus, M.R.; Law, B.E.

    1988-01-01

    The Greater Green River basin of Wyoming, Colorado, and Utah contains five basins and associated major uplifts (fig. 1). Published structure maps of the region have commonly used the top of the Lower Cretaceous Dakota Sandstone as a structural datum (Petroleum Ownership Map Company (POMCO), 1984; Rocky Mountain Association of Geologists, 1972). However, because relatively few wells in this area penetrate the Dakota, the Dakota structural datum has to be constructed by projecting down from shallower wells. Extrapolating in this manner may produce errors in the map. The primary purpose of this report is to present a more reliable structure contour map of the Greater Green River basin based on datums that are penetrated by many wells. The final map shows the large- to small-scale structures present in the Greater Green River basin. The availability of subsurface control and the map scale determined whether or not a structural feature was included on the map. In general, large structures such as the Moxa arch, Pinedale anticline, and other large folds were placed on the map based solely on the structure contours. In comparison, smaller folds and some faults were placed on the map based on structure contours and other reports (Bader 1987; Bradley 1961; Love and Christiansen, 1985; McDonald, 1975; Roehler, 1979; Wyoming Geological Association Oil and Gas Symposium Committee, 1979). State geologic maps and other reports were used to position basin margin faults (Bryant, 1985; Gries, 1983a, b; Hansen 1986; Hintze, 1980; Love and Christiansen, 1985; Tweto, 1979, 1983). In addition, an interpreted east-west-trending regional seismic line by Garing and Tainter (1985), which shows the basin configuration in cross-section, was helpful in locating buried faults, such as the high-angle reverse or thrust fault along the west flank of the Rock Springs uplift.

  16. Structure mapping for improved situational awareness, missions planning, and operator tracking

    Science.gov (United States)

    Williams, Jonathan; Reese, Matt; Calcutt, Wade; Morrison, James; Roehrich, Gregory J.

    2010-04-01

    McQ developed for the U.S. Army Armament Research, Development and Engineering Center (ARDEC) an acoustic and infrared measurement, node localization, and building characterization prototype system. The system is designed for both manned and unmanned use to develop greater situational awareness through the exploration of unknown structures and relay of mapping data through ARDEC's Firestorm network. This research covers ultrasonic and infrared ranging sensor performance, GPS-denied positioning solutions, sensor data fusion, and mapping algorithms. Applications of McQ's Structure Mapping system also include first responder mapping and positioning. McQ will present development methodology and performance.

  17. Exclusion map of Salla disease: attempts to localize the disease gene using a computer program.

    Science.gov (United States)

    Haataja, L; Schleutker, J; Renlund, M; Palotie, A; Peltonen, L; Aula, P

    1992-01-01

    Salla disease is a lysosomal storage disorder due to impaired transport of free sialic acid across the lysosomal membrane. The clinical presentation of this autosomal recessive trait is severe psychomotor retardation from early infancy on. In order to determine the gene locus for the disease we have initiated a genetic linkage study using polymorphic gene markers in representative family material comprising about 60% of all families known to be affected with Salla disease. Here we present an exclusion map based on combined linkage data from 64 informative loci on 19 autosomes. Theoretically, at least 55% of the genome has been excluded as a locus for the disease gene, while some chromosome areas, particularly the long arm of chromosome 2, are highlighted as possible sites for the gene locus.

  18. MAP kinase pathway gene copy alterations in NRAS/BRAF wild-type advanced melanoma.

    Science.gov (United States)

    Orouji, Elias; Orouji, Azadeh; Gaiser, Timo; Larribère, Lionel; Gebhardt, Christoffer; Utikal, Jochen

    2016-05-01

    Recent therapeutic advances have improved melanoma patientś clinical outcome. Novel therapeutics targeting BRAF, NRAS and cKit mutant melanomas are widely used in clinical practice. However therapeutic options in NRAS(wild-type) /BRAF(wild-type) /cKit(wild-type) melanoma patients are limited. Our study shows that gene copy numbers of members of the MAPK signaling pathway vary in different melanoma subgroups. NRAS(wild-type) /BRAF(wild-type) melanoma metastases are characterized by significant gains of MAP2K1 (MEK1) and MAPK3 (ERK1) gene loci. These additional gene copies could lead to an activation of the MAPK signaling pathway via a gene-dosage effect. Our results suggest that downstream analyses of the pMEK and pERK expression status in NRAS(wild-type) /BRAF(wild-type) melanoma patients identify patients that could benefit from targeted therapies with MEK and ERK inhibitors.

  19. High-resolution statistical mapping reveals gene territories in live yeast.

    Science.gov (United States)

    Berger, Axel B; Cabal, Ghislain G; Fabre, Emmanuelle; Duong, Tarn; Buc, Henri; Nehrbass, Ulf; Olivo-Marin, Jean-Christophe; Gadal, Olivier; Zimmer, Christophe

    2008-12-01

    The nonrandom positioning of genes inside eukaryotic cell nuclei is implicated in central nuclear functions. However, the spatial organization of the genome remains largely uncharted, owing to limited resolution of optical microscopy, paucity of nuclear landmarks and moderate cell sampling. We developed a computational imaging approach that creates high-resolution probabilistic maps of subnuclear domains occupied by individual loci in budding yeast through automated analysis of thousands of living cells. After validation, we applied the technique to genes involved in galactose metabolism and ribosome biogenesis. We found that genomic loci are confined to 'gene territories' much smaller than the nucleus, which can be remodeled during transcriptional activation, and that the nucleolus is an important landmark for gene positioning. The technique can be used to visualize and quantify territory positions relative to each other and to nuclear landmarks, and should advance studies of nuclear architecture and function.

  20. Genetic Analysis and Gene Mapping of Short Root Mutant Rice ksr1

    Institute of Scientific and Technical Information of China (English)

    NING Yong-qiang; DING Wo-na; ZHU Shi-hua; Yu Hang-wei; Yu Hang; Lu Kai-xing

    2011-01-01

    A short root mutant ksr1 with the Kasalath background was isolated from an EMS-mutagenized population in rice.The root length of 6-day-old ksr1 seedlings was only about 20% of the wild type.Genetic analysis indicated that the short root phenotype of ksr1 was controlled by a recessive mutation in a single nuclear-encoded gene.To map the ksr1 mutation,an F2 population was generated by crossing the ksr1 mutant with Nipponbare.The KSR1 locus was linked to the SSR marker RM1223 on rice chromosome 4.Eight new SSR markers and two InDet markers were developed around this marker.KSR1 gene was further mapped to a 155 kb region,flanked by the InDel marker 4-24725K and the SSR marker RM17182.

  1. Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice.

    Science.gov (United States)

    Gao, Zhenyu; Zeng, Dali; Cui, Xia; Zhou, Yihua; Yan, Meixian; Huang, Danian; Li, Jiayang; Qian, Qian

    2003-12-01

    Gelatinization temperature (GT) is an important parameter for evaluating the cooking and eating quality of rice besides amylose content (AC). The inheritance of the genes affecting GT has been widely studied and is considered to be controlled by a major gene. Here, we report the map-based cloning of rice ALK that encodes the soluble starch synthase II (SSSII). Comparison between the DNA sequences from different rice varieties, together with the results obtained with digestion of the rice seeds in alkali solution, indicates that the base substitutions in coding sequence of ALK may cause the alteration in GT.

  2. Linkage mapping of putative regulator genes of barley grain development characterized by expression profiling

    Directory of Open Access Journals (Sweden)

    Wobus Ulrich

    2009-01-01

    Full Text Available Abstract Background Barley (Hordeum vulgare L. seed development is a highly regulated process with fine-tuned interaction of various tissues controlling distinct physiological events during prestorage, storage and dessication phase. As potential regulators involved within this process we studied 172 transcription factors and 204 kinases for their expression behaviour and anchored a subset of them to the barley linkage map to promote marker-assisted studies on barley grains. Results By a hierachical clustering of the expression profiles of 376 potential regulatory genes expressed in 37 different tissues, we found 50 regulators preferentially expressed in one of the three grain tissue fractions pericarp, endosperm and embryo during seed development. In addition, 27 regulators found to be expressed during both seed development and germination and 32 additional regulators are characteristically expressed in multiple tissues undergoing cell differentiation events during barley plant ontogeny. Another 96 regulators were, beside in the developing seed, ubiquitously expressed among all tissues of germinating seedlings as well as in reproductive tissues. SNP-marker development for those regulators resulted in anchoring 61 markers on the genetic linkage map of barley and the chromosomal assignment of another 12 loci by using wheat-barley addition lines. The SNP frequency ranged from 0.5 to 1.0 SNP/kb in the parents of the various mapping populations and was 2.3 SNP/kb over all eight lines tested. Exploration of macrosynteny to rice revealed that the chromosomal orders of the mapped putative regulatory factors were predominantly conserved during evolution. Conclusion We identified expression patterns of major transcription factors and signaling related genes expressed during barley ontogeny and further assigned possible functions based on likely orthologs functionally well characterized in model plant species. The combined linkage map and reference

  3. High resolution genetic map of the adenomatous polyposis coli gene (APC) region

    Energy Technology Data Exchange (ETDEWEB)

    Olschwang, S.; Laurent-Puig, P.; Melot, T. [Institut Curie, Paris (France)

    1995-05-08

    Familial adenomatous polyposis coli (APC) is a dominantly inherited colorectal cancer susceptibility disease caused by mutation in a gene called APC located on chromosome 5q21. Presymptomatic diagnosis of this condition is recommended because it enables restriction of the efficient but demanding prevention program to those relatives that are genetically affected. The large size of the APC gene makes the direct search for the casual alteration difficult to implement in routine diagnostic laboratories. Because APC appears to be genetically homogeneous with alteration in a single locus causing the disease, cosegregation analysis may represent an alternative efficient method for presymptomatic diagnosis. However, the reliability of the risk estimation by linkage analysis in APC families is hampered by the lack of a short range genetic map of the APC locus. A combined approach including genotyping of 65 APC families, analysis of the CEPH database, and complementary typing of both APC and CEPH families has made it possible to derive the following genetic map: Centromere-[D5S82-D5S49]-0.02-D5S122-0.01-D5S136-0.01-D5S135-0.02-[APC-D5S346-MCC]-0.04-[D5S81-D5S64]-Telomere. This order, which differs from previously proposed genetic maps, is fully compatible with recent physical mapping data. These data should contribute to increase the reliability of the presymptomatic test for APC. 42 refs., 1 fig., 3 tabs.

  4. Genetic linkage map and expression analysis of genes expressed in the lamellae of the edible basidiomycete Pleurotus ostreatus.

    Science.gov (United States)

    Park, Sang-Kyu; Peñas, María M; Ramírez, Lucía; Pisabarro, Antonio G

    2006-05-01

    Pleurotus ostreatus is an industrially cultivated basidiomycete with nutritional and environmental applications. Its genome contains 35 Mbp organized in 11 chromosomes. There is currently available a genetic linkage map based predominantly on anonymous molecular markers complemented with the mapping of QTLs controlling growth rate and industrial productivity. To increase the saturation of the existing linkage maps, we have identified and mapped 82 genes expressed in the lamellae. Their manual annotation revealed that 34.1% of the lamellae-expressed and 71.5% of the lamellae-specific genes correspond to previously unknown sequences or to hypothetical proteins without a clearly established function. Furthermore, the expression pattern of some genes provides an experimental basis for studying gene regulation during the change from vegetative to reproductive growth. Finally, the identification of various differentially regulated genes involved in protein metabolism suggests the relevance of these processes in fruit body formation and maturation.

  5. Quantitative Chemical-Genetic Interaction Map Connects Gene Alterations to Drug Responses | Office of Cancer Genomics

    Science.gov (United States)

    In a recent Cancer Discovery report, CTD2 researchers at the University of California in San Francisco developed a new quantitative chemical-genetic interaction mapping approach to evaluate drug sensitivity or resistance in isogenic cell lines. Performing a high-throughput screen with isogenic cell lines allowed the researchers to explore the impact of a panel of emerging and established drugs on cells overexpressing a single cancer-associated gene in isolation.

  6. 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.

  7. How well do HapMap haplotypes identify common haplotypes of genes? A comparison with haplotypes of 334 genes resequenced in the environmental genome project.

    Science.gov (United States)

    Taylor, Jack A; Xu, Zong-Li; Kaplan, Norman L; Morris, Richard W

    2006-01-01

    One of the goals of the International HapMap Project is the identification of common haplotypes in genes. However, HapMap uses an incomplete catalogue of single nucleotide polymorphisms (SNPs) and might miss some common haplotypes. We examined this issue using data from the Environmental Genome Project (EGP) which resequenced 335 genes in 90 people, and thus, has a nearly complete catalogue of gene SNPs. The EGP identified a total of 45,243 SNPs, of which 10,780 were common SNPs (minor allele frequency >or=0.1). Using EGP common SNP genotype data, we identified 1,459 haplotypes with frequency >or=0.05 and we use these as "benchmark" haplotypes. HapMap release 16 had genotype information for 1,573 of 10,780 (15%) EGP common SNPs. Using these SNPs, we identified common HapMap haplotypes (frequency >or=0.05) in each of the four HapMap ethnic groups. To compare common HapMap haplotypes to EGP benchmark haplotypes, we collapsed benchmark haplotypes to the set of 1,573 SNPs. Ninety-eight percent of the collapsed benchmark haplotypes could be found as common HapMap haplotypes in one or more of the four HapMap ethnic groups. However, collapsing benchmark haplotypes to the set of SNPs available in HapMap resulted in a loss of haplotype information: 545 of 1,459 (37%) benchmark haplotypes were uniquely identified, and only 25% of genes had all their benchmark haplotypes uniquely identified. We resampled the EGP data to examine the effect of increasing the number of HapMap SNPs to 5 million, and estimate that approximately 40% of common SNPs in genes will be sampled and that half of the genes will have sufficient SNPs to identify all common haplotypes. This inability to distinguish common haplotypes of genes may result in loss of power when examining haplotype-disease association.

  8. Identification of mesoderm development (mesd) candidate genes by comparative mapping and genome sequence analysis.

    Science.gov (United States)

    Wines, M E; Lee, L; Katari, M S; Zhang, L; DeRossi, C; Shi, Y; Perkins, S; Feldman, M; McCombie, W R; Holdener, B C

    2001-02-15

    The proximal albino deletions identify several functional regions on mouse Chromosome 7 critical for differentiation of mesoderm (mesd), development of the hypothalamus neuroendocrine lineage (nelg), and function of the liver (hsdr1). Using comparative mapping and genomic sequence analysis, we have identified four novel genes and Il16 in the mesd deletion interval. Two of the novel genes, mesdc1 and mesdc2, are located within the mesd critical region defined by BAC transgenic rescue. We have investigated the fetal role of genes located outside the mesd critical region using BAC transgenic complementation of the mesd early embryonic lethality. Using human radiation hybrid mapping and BAC contig construction, we have identified a conserved region of human chromosome 15 homologous to the mesd, nelg, and hsdr1 functional regions. Three human diseases cosegregate with microsatellite markers used in construction of the human BAC/YAC physical map, including autosomal dominant nocturnal frontal lobe epilepsy (ENFL2; also known as ADNFLE), a syndrome of mental retardation, spasticity, and tapetoretinal degeneration (MRST); and a pyogenic arthritis, pyoderma gangrenosum, and acne syndrome (PAPA).

  9. Genetic mapping of sulfur assimilation genes reveals a QTL for onion bulb pungency.

    Science.gov (United States)

    McCallum, John; Pither-Joyce, Meeghan; Shaw, Martin; Kenel, Fernand; Davis, Sheree; Butler, Ruth; Scheffer, John; Jakse, Jernej; Havey, Michael J

    2007-03-01

    Onion exhibits wide genetic and environmental variation in bioactive organosulfur compounds that impart pungency and health benefits. A PCR-based molecular marker map that included candidate genes for sulfur assimilation was used to identify genomic regions affecting pungency in the cross 'W202A' x 'Texas Grano 438'. Linkage mapping revealed that genes encoding plastidic ferredoxin-sulfite reductase (SiR) and plastidic ATP sulfurylase (ATPS) are closely linked (1-2 cM) on chromosome 3. Inbred F(3) families derived from the F(2 )population used to construct the genetic map were grown in replicated trials in two environments and bulb pungency was evaluated as pyruvic acid or lachrymatory factor. Broad-sense heritability of pungency was estimated to be 0.78-0.80. QTL analysis revealed significant associations of both pungency and bulb soluble solids content with marker intervals on chromosomes 3 and 5, which have previously been reported to condition pleiotropic effects on bulb carbohydrate composition. Highly significant associations (LOD 3.7-8.7) were observed between ATPS and SiR Loci and bulb pungency but not with bulb solids content. This association was confirmed in two larger, independently derived F(2) families from the same cross. Single-locus models suggested that the partially dominant locus associated with these candidate genes controls 30-50% of genetic variation in pungency in these pedigrees. These markers may provide a practical means to select for lower pungency without correlated selection for lowered solids.

  10. The map-1 gene family in root-knot nematodes, Meloidogyne spp.: a set of taxonomically restricted genes specific to clonal species.

    Directory of Open Access Journals (Sweden)

    Iva Tomalova

    Full Text Available Taxonomically restricted genes (TRGs, i.e., genes that are restricted to a limited subset of phylogenetically related organisms, may be important in adaptation. In parasitic organisms, TRG-encoded proteins are possible determinants of the specificity of host-parasite interactions. In the root-knot nematode (RKN Meloidogyne incognita, the map-1 gene family encodes expansin-like proteins that are secreted into plant tissues during parasitism, thought to act as effectors to promote successful root infection. MAP-1 proteins exhibit a modular architecture, with variable number and arrangement of 58 and 13-aa domains in their central part. Here, we address the evolutionary origins of this gene family using a combination of bioinformatics and molecular biology approaches. Map-1 genes were solely identified in one single member of the phylum Nematoda, i.e., the genus Meloidogyne, and not detected in any other nematode, thus indicating that the map-1 gene family is indeed a TRG family. A phylogenetic analysis of the distribution of map-1 genes in RKNs further showed that these genes are specifically present in species that reproduce by mitotic parthenogenesis, with the exception of M. floridensis, and could not be detected in RKNs reproducing by either meiotic parthenogenesis or amphimixis. These results highlight the divergence between mitotic and meiotic RKN species as a critical transition in the evolutionary history of these parasites. Analysis of the sequence conservation and organization of repeated domains in map-1 genes suggests that gene duplication(s together with domain loss/duplication have contributed to the evolution of the map-1 family, and that some strong selection mechanism may be acting upon these genes to maintain their functional role(s in the specificity of the plant-RKN interactions.

  11. Tree structure-based bit-to-symbol mapping for multidimensional modulation format

    Science.gov (United States)

    Zhaoxi, Li; Yujuan, Si; Guijun, Hu

    2017-06-01

    Bit-to-symbol mapping is one of the key issues in multidimensional modulation. In an effort to resolve this issue, a tree structure based bit-to-symbol mapping scheme is proposed. By constructing a tree structure of constellation points, any neighboring constellation points become nearest-neighbor constellation points with minimum Euclidean distance, which in turn, changes the bit-to-symbol mapping problem in multidimensional signal modulation from random to orderly. Then, through the orderly distribution of labels, the minimum Hamming distance between the nearest neighboring constellation points is ensured, eventually achieving bit-to-symbol mapping optimization for multidimensional signals. Simulation analysis indicates that, compared with random search mapping, tree mapping can effectively improve the bit error rate performance of multidimensional signal modulation without multiple searching, reducing the computational cost.

  12. Gene therapy in glaucoma-part 2: Genetic etiology and gene mapping

    OpenAIRE

    Mohamed Abdel-Monem Soliman Mahdy

    2010-01-01

    Glaucoma diagnosis, identification of people at risk, initiation of treatment and timing of surgical intervention remains a problem. Despite new and improving diagnostic and therapeutic options for glaucoma, blindness from glaucoma is increasing and glaucoma remains a major public health problem. The role of heredity in ocular disease is attracting greater attention as the knowledge and recent advances of Human Genome Project and the HapMap Project have made genetic analysis of many human dis...

  13. On Line Segment Length and Mapping 4-regular Grid Structures in Network Infrastructures

    DEFF Research Database (Denmark)

    Riaz, Muhammad Tahir; Nielsen, Rasmus Hjorth; Pedersen, Jens Myrup;

    2006-01-01

    The paper focuses on mapping the road network into 4-regular grid structures. A mapping algorithm is proposed. To model the road network GIS data have been used. The Geographic Information System (GIS) data for the road network are composed with different size of line segment lengths....... The manipulation of the line segment length for mapping is analyzed. The algorithms and simulation results are given in the paper....

  14. A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates.

    Science.gov (United States)

    Everts-van der Wind, Annelie; Kata, Srinivas R; Band, Mark R; Rebeiz, Mark; Larkin, Denis M; Everts, Robin E; Green, Cheryl A; Liu, Lei; Natarajan, Shreedhar; Goldammer, Tom; Lee, Jun Heon; McKay, Stephanie; Womack, James E; Lewin, Harris A

    2004-07-01

    A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH(5000) panel to 1913. Of these, 1463 have significant BLASTN hits (E genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle-human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes. Copyright 2004 Cold Spring Harbor Laboratory Press ISSN

  15. Development and mapping of SSR markers linked to resistance-gene homologue clusters in common bean

    Institute of Scientific and Technical Information of China (English)

    Luz; Nayibe; Garzon; Matthew; Wohlgemuth; Blair

    2014-01-01

    Common bean is an important but often a disease-susceptible legume crop of temperate,subtropical and tropical regions worldwide. The crop is affected by bacterial, fungal and viral pathogens. The strategy of resistance-gene homologue(RGH) cloning has proven to be an efficient tool for identifying markers and R(resistance) genes associated with resistances to diseases. Microsatellite or SSR markers can be identified by physical association with RGH clones on large-insert DNA clones such as bacterial artificial chromosomes(BACs). Our objectives in this work were to identify RGH-SSR in a BAC library from the Andean genotype G19833 and to test and map any polymorphic markers to identify associations with known positions of disease resistance genes. We developed a set of specific probes designed for clades of common bean RGH genes and then identified positive BAC clones and developed microsatellites from BACs having SSR loci in their end sequences. A total of 629 new RGH-SSRs were identified and named BMr(bean microsatellite RGH-associated markers). A subset of these markers was screened for detecting polymorphism in the genetic mapping population DOR364 × G19833. A genetic map was constructed with a total of 264 markers,among which were 80 RGH loci anchored to single-copy RFLP and SSR markers. Clusters of RGH-SSRs were observed on most of the linkage groups of common bean and in positions associated with R-genes and QTL. The use of these new markers to select for disease resistance is discussed.

  16. Mapping of Fertility Restoring Gene for Aegilops kotschyi Cytoplasmic Male Sterility in Wheat Using SSR Markers

    Institute of Scientific and Technical Information of China (English)

    LIU Bao-shen; SUN Qi-xin; GAO Qing-rong; SUN Lan-zhen; XIE Chao-jie; LI Chuan-you; NI Zhong-fu; DOU Bing-de

    2002-01-01

    LK783 was found to be a good fertility restorer for K-type male sterility of wheat. Microsatellite markers were employed to map the major restoring gene in LK783. Maintainer and restorer DNA pools were established using the extreme sterile and fertile plants among (KJ5418A//911289/LK783)F1 population,respectively. Seventy-nine sets of SSR primers were screened for polymorphism between the two pools, 6 of which were found polymorphic. Linkage analysis showed that Xgwm11, Xgwm18 , Xgwm264a and Xgwm273were linked to the restoring gene in LK783, while Xgwm11, Xgwm18 and Xgwm273 were co-segregated. The distance between the Rf gene in LK783 and the three co-segregated markers was 6.54±4.37 cM, the distance between Rf gene and Xgwm264a was 5.71±4.10 cM. The four SSR markers were located on chromosome 1BS by amplifying the DNA of nulli-tetrasomics and ditelosomics of CS with the 4 sets of primers, indicating that the major restoring gene in LK783 was located on 1BS, but the relative location of the gene was different from Rfv1, allelism of the two genes should be further investigated. The breeding for new fertility restorer lines of K-type cytoplasmic male sterility in wheat would be facilitated by using the four polymorphic markers.

  17. The human renin-binding protein gene (RENBP) maps in Xq28

    Energy Technology Data Exchange (ETDEWEB)

    Ouweland, A.M.W. van der; Verdijk, M.; Oost, B.A. van (Univ. Hospital Nijmegen (Netherlands)); Kiochis, P.; Poustka, A. (Deutsches Krebsforschungszemtrum, Heidelberg (Germany))

    1994-05-01

    The authors report here the successful application of the method by which cDNA libraries are screened with positionally identified genomic clones. Human cosmid clones were selected from a cosmid library derived from the Q1Z cell line. This Q1Z cell line is a hamster-human somatic cell hybrid that contains the Xq28 region as its sole human component. To search for kidney-expressed genes, they screened a kidney cDNA library purchased from Clontech with cosmid-derived probes. Based on the physical mapping of the vasopressin V2 receptor gene close to the L1CAM gene, they analyzed cosmids derived from this region. One of the cosmids was 12B2, located 50 kb from the L1CAM gene. A 20-kb EcoRI subclone from the 12B2 cosmid was used as probe. This fragment did not hybridize to the probe 2-55 in contrast to the whole cosmid 12B2. Screening of 200,000 cDNA clones resulted in the identification of two positive clones. After sequence determination, it appeared that one of the positive cDNA clones contained Escherichia coli DNA as insert (data not shown). The other cDNA (pMV24) contained an open reading frame corresponding to the 243 amino-terminal amino acids of the human renin binding protein. The RENBP gene maps to interval 3 between the loci for DX52 and G-6-PD. This is the same interval as that for the color blindness gene, DXS707, and the AVPR2, L1CAM, and QM genes. This result confirms that the isolated RENBP cDNA originates from the same location as that from which the parental cosmid clone was derived. 28 refs., 1 fig.

  18. Fine Mapping and Transcriptome Analysis Reveal Candidate Genes Associated with Hybrid Lethality in Cabbage (Brassica Oleracea).

    Science.gov (United States)

    Xiao, Zhiliang; Hu, Yang; Zhang, Xiaoli; Xue, Yuqian; Fang, Zhiyuan; Yang, Limei; Zhang, Yangyong; Liu, Yumei; Li, Zhansheng; Liu, Xing; Liu, Zezhou; Lv, Honghao; Zhuang, Mu

    2017-06-05

    Hybrid lethality is a deleterious phenotype that is vital to species evolution. We previously reported hybrid lethality in cabbage (Brassica oleracea) and performed preliminary mapping of related genes. In the present study, the fine mapping of hybrid lethal genes revealed that BoHL1 was located on chromosome C1 between BoHLTO124 and BoHLTO130, with an interval of 101 kb. BoHL2 was confirmed to be between insertion-deletion (InDels) markers HL234 and HL235 on C4, with a marker interval of 70 kb. Twenty-eight and nine annotated genes were found within the two intervals of BoHL1 and BoHL2, respectively. We also applied RNA-Seq to analyze hybrid lethality in cabbage. In the region of BoHL1, seven differentially expressed genes (DEGs) and five resistance (R)-related genes (two in common, i.e., Bo1g153320 and Bo1g153380) were found, whereas in the region of BoHL2, two DEGs and four R-related genes (two in common, i.e., Bo4g173780 and Bo4g173810) were found. Along with studies in which R genes were frequently involved in hybrid lethality in other plants, these interesting R-DEGs may be good candidates associated with hybrid lethality. We also used SNP/InDel analyses and quantitative real-time PCR to confirm the results. This work provides new insight into the mechanisms of hybrid lethality in cabbage.

  19. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure.

    Science.gov (United States)

    Zuccolo, Andrea; Bowers, John E; Estill, James C; Xiong, Zhiyong; Luo, Meizhong; Sebastian, Aswathy; Goicoechea, José Luis; Collura, Kristi; Yu, Yeisoo; Jiao, Yuannian; Duarte, Jill; Tang, Haibao; Ayyampalayam, Saravanaraj; Rounsley, Steve; Kudrna, Dave; Paterson, Andrew H; Pires, J Chris; Chanderbali, Andre; Soltis, Douglas E; Chamala, Srikar; Barbazuk, Brad; Soltis, Pamela S; Albert, Victor A; Ma, Hong; Mandoli, Dina; Banks, Jody; Carlson, John E; Tomkins, Jeffrey; dePamphilis, Claude W; Wing, Rod A; Leebens-Mack, Jim

    2011-01-01

    Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome. Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella. When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.

  20. Structure and evolution of the mouse pregnancy-specific glycoprotein (Psg gene locus

    Directory of Open Access Journals (Sweden)

    Okumura Katsuzumi

    2005-01-01

    Full Text Available Abstract Background The pregnancy-specific glycoprotein (Psg genes encode proteins of unknown function, and are members of the carcinoembryonic antigen (Cea gene family, which is a member of the immunoglobulin gene (Ig superfamily. In rodents and primates, but not in artiodactyls (even-toed ungulates / hoofed mammals, there have been independent expansions of the Psg gene family, with all members expressed exclusively in placental trophoblast cells. For the mouse Psg genes, we sought to determine the genomic organisation of the locus, the expression profiles of the various family members, and the evolution of exon structure, to attempt to reconstruct the evolutionary history of this locus, and to determine whether expansion of the gene family has been driven by selection for increased gene dosage, or diversification of function. Results We collated the mouse Psg gene sequences currently in the public genome and expressed-sequence tag (EST databases and used systematic BLAST searches to generate complete sequences for all known mouse Psg genes. We identified a novel family member, Psg31, which is similar to Psg30 but, uniquely amongst mouse Psg genes, has a duplicated N1 domain. We also identified a novel splice variant of Psg16 (bCEA. We show that Psg24 and Psg30 / Psg31 have independently undergone expansion of N-domain number. By mapping BAC, YAC and cosmid clones we described two clusters of Psg genes, which we linked and oriented using fluorescent in situ hybridisation (FISH. Comparison of our Psg locus map with the public mouse genome database indicates good agreement in overall structure and further elucidates gene order. Expression levels of Psg genes in placentas of different developmental stages revealed dramatic differences in the developmental expression profile of individual family members. Conclusion We have combined existing information, and provide new information concerning the evolution of mouse Psg exon organization, the mouse

  1. Map updates in a dynamic Voronoi data structure

    DEFF Research Database (Denmark)

    Mioc, Darka; Antón Castro, Francesc/François; Gold, C. M.;

    2006-01-01

    the complex operations. This resulted in a new formal model for map updates, similar to "cellular encoding", where each update is uniquely characterized by the numbers of newly created and inactivated Voronoi regions. This research shows that the result of the formalization of the operations on the dynamic...

  2. Genetic linkage mapping of the dehydroepiandrosterone sulfotransferase (STD) gene on the chromosome 19q13.3 region

    Energy Technology Data Exchange (ETDEWEB)

    Durocher, F.; Morissette, J.; Dufort, I.; Simard, J.; Luu-The, V. [Laval Univ. Quebec (Canada)

    1995-10-10

    In the human liver and adrenal, there is a single hydroxysteroid sulfotransferase, which catalyzes the transformation of dehydroepiandrosterone to dehydroepiandrosterone sulfate, the most abundantly circulating steroid in humans, and also catalyzes the sulfation of a series of other 3{beta}-hydroxysteroids as well as cholesterol. Dehydroepiandrosterone sulfate serves as precursor for the formation of active androgens and estrogens in several peripheral tissues, indicating that hydroxysteroid sulfotransferase plays a pivotal role in controlling the hormonal action of sex steroids by regulating their bioavailability. We recently elucidated the structure of the gene encoding hydroxysteroid sulfotransferase (STD), also designated dehydroepiandrosterone sulfotransferase, which spans 17 kb and contains six exons. The STD gene was preliminarily assigned to chromosome 19 by polymerase chain reaction (PCR) amplification of DNA from a panel of human/rodent somatic cell hybrids. To locate the STD gene, the novel biallelic polymorphism found in intron 2 was genotyped in eight CEPH reference families by direct sequencing of PCR products. Two-point linkage analysis was first performed between the latter polymorphism and chromosome 19 markers from Genethon and NIH/CEPH. The closest linkage was observed with D19S412 (Z{sub max} = 9.23; {theta}{sub max} 0.038) and HRC (Z{sub max} =5.95; {theta}{sub max}0.036), located on the 19q13.3 region. A framework map including six Genethon markers flanking the polymorphic STD gene was created by multipoint linkage analysis. Thereafter, a high-resolution genetic map of the region was constructed, yielding to the following order: qter-D19S414-D19S224-D19S420-D19S217-(APOC2-D19S412)-(STD-HRC)-KLK-D19S22-D19S180-PRKCG-D19S418-tel. 24 refs., 2 figs.

  3. Polymorphism and genetic mapping of the human oxytocin receptor gene on chromosome 3

    Energy Technology Data Exchange (ETDEWEB)

    Michelini, S.; Urbanek, M.; Goldman, D. [National Institute of Health-National Institute of Alcohol Abuse and Alcoholism, Rockville, MD (United States)] [and others

    1995-06-19

    Centrally administered oxytocin has been reported to facilitate affiliative and social behaviors, in functional harmony with its well-known peripheral effects on uterine contraction and milk ejection. The biological effects of oxytocin could be perturbed by mutations occurring in the sequence of the oxytocin receptor gene, and it would be of interest to establish the position of this gene on the human linkage map. Therefore we identified a polymorphism at the human oxytocin receptor gene. A portion of the 3{prime} untranslated region containing a 30 bp CA repeat was amplified by polymerase chain reaction (PCR), revealing a polymorphism with two alleles occurring with frequencies of 0.77 and 0.23 in a sample of Caucasian CEPH parents (n = 70). The CA repeat polymorphism we detected was used to map the human oxytocin receptor to chromosome 3p25-3p26, in a region which contains several important genes, including loci for Von Hippel-Lindau disease (VHL) and renal cell carcinoma. 53 refs., 2 figs., 1 tab.

  4. Gene mapping in an anophthalmic pedigree of a consanguineous Pakistani family opened new horizons for research

    Directory of Open Access Journals (Sweden)

    Saleha S

    2016-07-01

    Full Text Available Clinical anophthalmia is a rare inherited disease of the eye and phenotype refers to the absence of ocular tissue in the orbit of eye. Patients may have unilateral or bilateral anophthalmia, and generally have short palpebral fissures and small orbits. Anophthalmia may be isolated or associated with a broader syndrome and may have genetic or environmental causes. However, genetic cause has been defined in only a small proportion of cases, therefore, a consanguineous Pakistani family of the Pashtoon ethnic group, with isolated clinical anophthalmia was investigated using linkage mapping. A family pedigree was created to trace the possible mode of inheritance of the disease. Blood samples were collected from affected as well as normal members of this family, and screened for disease-associated mutations. This family was analyzed for linkage to all the known loci of clinical anophthalmia, using microsatellite short tandem repeat (STR markers. Direct sequencing was performed to find out disease-associated mutations in the candidate gene. This family with isolated clinical anophthalmia, was mapped to the SOX2 gene that is located at chromosome 3q26.3-q27. However, on exonic and regulatory regions mutation screening of the SOX2 gene, the disease-associated mutation was not identified. It showed that another gene responsible for development of the eye might be present at chromosome 3q26.3-q27 and needs to be identified and screened for the disease-associated mutation in this family.

  5. Automatic Classification of Protein Structure Using the Maximum Contact Map Overlap Metric

    NARCIS (Netherlands)

    Andonov, R.; Djidjev, H.; Klau, G.W.; Le Boudic-Jamin, M.; Wohlers, I.

    2015-01-01

    In this work, we propose a new distance measure for comparing two protein structures based on their contact map representations. We show that our novel measure, which we refer to as the maximum contact map overlap (max-CMO) metric, satisfies all properties of a metric on the space of protein represe

  6. Case-control admixture mapping in Latino populations enriches for known asthma-associated genes

    Science.gov (United States)

    Torgerson, Dara G.; Gignoux, Christopher R.; Galanter, Joshua M.; Drake, Katherine A.; Roth, Lindsey A.; Eng, Celeste; Huntsman, Scott; Torres, Raul; Avila, Pedro C.; Chapela, Rocio; Ford, Jean G.; Rodríguez-Santana, José R.; Rodríguez-Cintrón, William; Hernandez, Ryan D.; Burchard, Esteban G.

    2012-01-01

    Background Polymorphisms in more than 100 genes have been associated with asthma susceptibility, yet much of the heritability remains to be explained. Asthma disproportionately affects different racial and ethnic groups in the United States, suggesting that admixture mapping is a useful strategy to identify novel asthma-associated loci. Objective We sought to identify novel asthma-associated loci in Latino populations using case-control admixture mapping. Methods We performed genome-wide admixture mapping by comparing levels of local Native American, European, and African ancestry between children with asthma and nonasthmatic control subjects in Puerto Rican and Mexican populations. Within candidate peaks, we performed allelic tests of association, controlling for differences in local ancestry. Results Between the 2 populations, we identified a total of 62 admixture mapping peaks at a P value of less than 10−3 that were significantly enriched for previously identified asthma-associated genes (P = .0051). One of the peaks was statistically significant based on 100 permutations in the Mexican sample (6q15); however, it was not significant in Puerto Rican subjects. Another peak was identified at nominal significance in both populations (8q12); however, the association was observed with different ancestries. Conclusion Case-control admixture mapping is a promising strategy for identifying novel asthma-associated loci in Latino populations and implicates genetic variation at 6q15 and 8q12 regions with asthma susceptibility. This approach might be useful for identifying regions that contribute to both shared and population-specific differences in asthma susceptibility. PMID:22502797

  7. Identification by Gene Coregulation Mapping of Novel Genes involved in Embryonic Stem Cell Differentiation

    NARCIS (Netherlands)

    Pennings, J.L.A.; Dartel, van D.A.M.; Pronk, T.E.; Hendriksen, P.J.M.; Piersma, A.H.

    2011-01-01

    A combined analysis of data from a series of literature studies can lead to more reliable results than that based on a single study. A common problem in performing combined analyses of literature microarray gene expression data is that the original raw data are not always available and not always ea

  8. MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined with de novo assembly of gap regions identifies the rice blast resistance gene Pii.

    Science.gov (United States)

    Takagi, Hiroki; Uemura, Aiko; Yaegashi, Hiroki; Tamiru, Muluneh; Abe, Akira; Mitsuoka, Chikako; Utsushi, Hiroe; Natsume, Satoshi; Kanzaki, Hiroyuki; Matsumura, Hideo; Saitoh, Hiromasa; Yoshida, Kentaro; Cano, Liliana M; Kamoun, Sophien; Terauchi, Ryohei

    2013-10-01

    Next-generation sequencing allows the identification of mutations responsible for mutant phenotypes by whole-genome resequencing and alignment to a reference genome. However, when the resequenced cultivar/line displays significant structural variation from the reference genome, mutations in the genome regions missing from the reference (gaps) cannot be identified by simple alignment. Here we report on a method called 'MutMap-Gap', which involves delineating a candidate region harboring a mutation of interest using the recently reported MutMap method, followed by de novo assembly, alignment, and identification of the mutation within genome gaps. We applied MutMap-Gap to isolate the blast resistant gene Pii from the rice cv Hitomebore using mutant lines that have lost Pii function. MutMap-Gap should prove useful for cloning genes that exhibit significant structural variations such as disease resistance genes of the nucleotide-binding site-leucine rich repeat (NBS-LRR) class.

  9. Fine genetic mapping of the gene for nevoid basal cell carcinoma syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Wicking, C.; Berkman, J.; Wainwright, B. [Univ. of Queensland, Brisbane (Australia)] [and others

    1994-08-01

    Nevoid basal cell carcinoma syndrome (NBCCS, or Gorlin syndrome) is a cancer predisposition syndrome characterized by multiple basal cell carcinomas and diverse developmental defects. The gene responsible for NBCCS, which is most likely to be a tumor suppressor gene, has previously been mapped to 9q22.3-q31 in a 12-cM interval between the microsatellite marker loci D9S12.1 and D9S109. Combined multipoint and haplotype analyses of additional polymorphisms in this region in our collection of Australasian pedigrees have further refined the localization of the gene to between the markers D9S196 and D9S180, an interval reported to be approximately 2 cM. 27 refs., 4 figs., 1 tab.

  10. iHAP – integrated haplotype analysis pipeline for characterizing the haplotype structure of genes

    Directory of Open Access Journals (Sweden)

    Lim Yun Ping

    2006-12-01

    Full Text Available Abstract Background The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows that genotype data from the International HapMap Project have a high degree of transferability to the wider population. This implies that the design of genotyping studies on local populations may be facilitated through inferences drawn from information contained in HapMap populations. Results To facilitate analysis of HapMap data for characterizing the haplotype structure of genes or any chromosomal regions, we have developed an integrated web-based resource, iHAP. In addition to incorporating genotype and haplotype data from the International HapMap Project and gene information from the UCSC Genome Browser Database, iHAP also provides capabilities for inferring haplotype blocks and selecting tag SNPs that are representative of haplotype patterns. These include block partitioning algorithms, block definitions, tag SNP definitions, as well as SNPs to be "force included" as tags. Based on the parameters defined at the input stage, iHAP performs on-the-fly analysis and displays the result graphically as a webpage. To facilitate analysis, intermediate and final result files can be downloaded. Conclusion The iHAP resource, available at http://ihap.bii.a-star.edu.sg, provides a convenient yet flexible approach for the user community to analyze HapMap data and identify candidate targets for genotyping studies.

  11. A gene expression map for the euchromatic genome of Drosophila melanogaster.

    Science.gov (United States)

    Stolc, Viktor; Gauhar, Zareen; Mason, Christopher; Halasz, Gabor; van Batenburg, Marinus F; Rifkin, Scott A; Hua, Sujun; Herreman, Tine; Tongprasit, Waraporn; Barbano, Paolo Emilio; Bussemaker, Harmen J; White, Kevin P

    2004-10-22

    We used a maskless photolithography method to produce DNA oligonucleotide microarrays with unique probe sequences tiled throughout the genome of Drosophila melanogaster and across predicted splice junctions. RNA expression of protein coding and nonprotein coding sequences was determined for each major stage of the life cycle, including adult males and females. We detected transcriptional activity for 93% of annotated genes and RNA expression for 41% of the probes in intronic and intergenic sequences. Comparison to genome-wide RNA interference data and to gene annotations revealed distinguishable levels of expression for different classes of genes and higher levels of expression for genes with essential cellular functions. Differential splicing was observed in about 40% of predicted genes, and 5440 previously unknown splice forms were detected. Genes within conserved regions of synteny with D. pseudoobscura had highly correlated expression; these regions ranged in length from 10 to 900 kilobase pairs. The expressed intergenic and intronic sequences are more likely to be evolutionarily conserved than nonexpressed ones, and about 15% of them appear to be developmentally regulated. Our results provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted.

  12. Mapping of bionic array electric field focusing in plasmid DNA-based gene electrotransfer.

    Science.gov (United States)

    Browne, C J; Pinyon, J L; Housley, D M; Crawford, E N; Lovell, N H; Klugmann, M; Housley, G D

    2016-04-01

    Molecular medicine through gene therapy is challenged to achieve targeted action. This is now possible utilizing bionic electrode arrays for focal delivery of naked (plasmid) DNA via gene electrotransfer. Here, we establish the properties of array-based electroporation affecting targeted gene delivery. An array with eight 300 μm platinum ring electrodes configured as a cochlear implant bionic interface was used to transduce HEK293 cell monolayers with a plasmid-DNA green fluorescent protein (GFP) reporter gene construct. Electroporation parameters were pulse intensity, number, duration, separation and electrode configuration. The latter determined the shape of the electric fields, which were mapped using a voltage probe. Electrode array-based electroporation was found to require ~100 × lower applied voltages for cell transduction than conventional electroporation. This was found to be due to compression of the field lines orthogonal to the array. A circular area of GFP-positive cells was created when the electrodes were ganged together as four adjacent anodes and four cathodes, whereas alternating electrode polarity created a linear area of GFP-positive cells. The refinement of gene delivery parameters was validated in vivo in the guinea pig cochlea. These findings have significant clinical ramifications, where spatiotemporal control of gene expression can be predicted by manipulation of the electric field via current steering at a cellular level.

  13. CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.

    Science.gov (United States)

    Carrillo-Tripp, Mauricio; Montiel-García, Daniel Jorge; Brooks, Charles L; Reddy, Vijay S

    2015-04-01

    Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the φ-ψ Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu.

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

    Science.gov (United States)

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

  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. p63 gene structure in the phylum mollusca.

    Science.gov (United States)

    Baričević, Ana; Štifanić, Mauro; Hamer, Bojan; Batel, Renato

    2015-08-01

    Roles of p53 family ancestor (p63) in the organisms' response to stressful environmental conditions (mainly pollution) have been studied among molluscs, especially in the genus Mytilus, within the last 15 years. Nevertheless, information about gene structure of this regulatory gene in molluscs is scarce. Here we report the first complete genomic structure of the p53 family orthologue in the mollusc Mediterranean mussel Mytilus galloprovincialis and confirm its similarity to vertebrate p63 gene. Our searches within the available molluscan genomes (Aplysia californica, Lottia gigantea, Crassostrea gigas and Biomphalaria glabrata), found only one p53 family member present in a single copy per haploid genome. Comparative analysis of those orthologues, additionally confirmed the conserved p63 gene structure. Conserved p63 gene structure can be a helpful tool to complement or/and revise gene annotations of any future p63 genomic sequence records in molluscs, but also in other animal phyla. Knowledge of the correct gene structure will enable better prediction of possible protein isoforms and their functions. Our analyses also pointed out possible mis-annotations of the p63 gene in sequenced molluscan genomes and stressed the value of manual inspection (based on alignments of cDNA and protein onto the genome sequence) for a reliable and complete gene annotation.

  17. Effects of prior knowledge and concept-map structure on disorientation, cognitive load, and learning

    NARCIS (Netherlands)

    Amadieu, Franck; Van Gog, Tamara; Paas, Fred; Tricot, André; Mariné, Claudette

    2009-01-01

    Citation: Amadieu, F., Van Gog, T., Paas, F., Tricot, A., & Mariné, C. (2009). Effects of prior knowledge and concept-map structure on disorientation, cognitive load, and learning. Learning and Instruction, 19, 376-386.

  18. Development of a molecular genetic linkage map for Colletotrichum lindemuthianum and segregation analysis of two avirulence genes.

    Science.gov (United States)

    Luna-Martínez, Francisco; Rodríguez-Guerra, Raúl; Victoria-Campos, Mayra; Simpson, June

    2007-02-01

    A framework genetic map was developed for the fungal pathogen Colletotrichum lindemuthianum, the causal agent of anthracnose of common bean (Phaseolus vulgaris L.). This is the first genetic map for any species within the family Melanconiaceae and the genus Colletotrichum and provides the first estimate of genome length for C. lindemuthianum. The map was generated using 106 haploid F1 progeny derived from crossing two Mexican C. lindemuthianum isolates differing in two avirulence genes (AvrclMex and AvrclTO). The map comprises 165 AFLP markers covering 1,897 cM with an average spacing of 11.49 cM. The markers are distributed over 19 major linkage groups containing between 5 and 25 markers each and the genome length was estimated to be approximately 3,241 cM. The avirulence genes AvrclMex and AvrclTO segregate in a 1:1 ratio supporting the gene for gene hypothesis for the incompatible reaction between C. lindemuthianum and P. vulgaris, but could not be incorporated into the genetic map. This initial outline map forms the basis for the development of a more detailed C. lindemuthianum linkage map, which would include other types of molecular markers and allow the location of genes previously isolated and characterized in this species.

  19. Construction of an integrated map and location of a bruchid resistance gene in mung bean

    Institute of Scientific and Technical Information of China (English)

    Lixia Wang; Chuanshu Wu; Min Zhong; Dan Zhao; Li Mei; Honglin Chen; Suhua Wang; Chunji Liu; Xuzhen Cheng

    2016-01-01

    Bruchid beetle (Callosobruchus chinensis) poses a serious threat to the production and storage of mung bean (Vigna radiata). Mapping bruchid resistance (Br) will provide an important basis for cloning the responsible gene(s) and elucidating its functional mechanism, and will also facilitate marker-assisted selection in mung bean breeding. Here, we report the construction of the genetic linkage groups of mung bean and mapping of the Br1 locus using an RIL population derived from a cross between Berken, a bruchid-susceptible line, and ACC41, a bruchid-resistant line. A total of 560 markers were mapped onto 11 linkage groups, with 38.0%of the markers showing distorted segregation. The lengths of the linkage groups ranged from 45.2 to 117.0 cM with a total coverage of 732.9 cM and an average interval of 1.3 cM between loci. Br1 was located on LG9 between BM202 (0.7 cM) and Vr2-627 (1.7 cM). Based on 270 shared SSR markers, most of the linkage groups were assigned to specific chromosomes. These results should further accelerate the genetic study of this crop.

  20. Construction of an integrated map and location of a bruchid resistance gene in mung bean

    Directory of Open Access Journals (Sweden)

    Lixia Wang

    2016-10-01

    Full Text Available Bruchid beetle (Callosobruchus chinensis poses a serious threat to the production and storage of mung bean (Vigna radiata. Mapping bruchid resistance (Br will provide an important basis for cloning the responsible gene(s and elucidating its functional mechanism, and will also facilitate marker-assisted selection in mung bean breeding. Here, we report the construction of the genetic linkage groups of mung bean and mapping of the Br1 locus using an RIL population derived from a cross between Berken, a bruchid-susceptible line, and ACC41, a bruchid-resistant line. A total of 560 markers were mapped onto 11 linkage groups, with 38.0% of the markers showing distorted segregation. The lengths of the linkage groups ranged from 45.2 to 117.0 cM with a total coverage of 732.9 cM and an average interval of 1.3 cM between loci. Br1 was located on LG9 between BM202 (0.7 cM and Vr2-627 (1.7 cM. Based on 270 shared SSR markers, most of the linkage groups were assigned to specific chromosomes. These results should further accelerate the genetic study of this crop.

  1. Structure of the gene encoding columbid annexin Icp35.

    Science.gov (United States)

    Hitti, Y S; Horseman, N D

    1991-07-22

    The cp35 gene, encoding an annexin I (AnxI) cropsac 35-kDa protein (cp35) from the pigeon, consists of 13 exons and twelve introns. The borders of exons 2-13 were mapped by comparison with the known cDNA sequence. A 5-kb sequence containing exons 1, 2, and 3, and 1.4 kb of 5'-flanking DNA, is presented. The transcription start point was mapped by S1 nuclease protection. The region of the cp35 mRNA sequence, which we had previously shown to be profoundly different from mammalian anxI, is located in the first half of exon 3. Whereas human anxI is known to be single copy, Southern analysis of pigeon genomic DNA and genomic clones demonstrated multiple anxI genes in the pigeon, diverging significantly in their 5'-termini. Pigeon vimentin, on the other hand, is encoded by a single-copy gene as it is in other birds and mammals. These experiments have demonstrated that the cp35 mRNA is transcribed from its individual gene and is not a product of alternative processing of the pigeon homolog of mammalian anxI. We speculate that the diversification of anxI genes in Columbid birds allowed the recruitment of one of these genes (cp35) for unique regulation by prolactin in the absence of post-translational regulation via residues encoded by exons 2 and 3.

  2. Gene Mapping of Brachytic Stem and Its Effect on Main Agronomic Traits in Soybean

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Brachytic stem is a major trait in plant type of soybean and its yield potential may be higher under high population when compared with normal stem. In the present investigation, 152 recombinant inbred line (RIL) families derived from the cross of Bogao (normal stem) and Nannong 94-156 (brachytic stem) were used to map genes and QTLs of three plant type traits and to identify the effects of brachytic stem on agronomic traits such as yield. The primary results indicated that brachytic stem (sb) and determinate growth habit (dtl) were mapped on linkage groups B2 and L, three major QTLs related to plant height were detected and mapped on linkage group L near dtl, another minor QTL was mapped near sb on linkage group B2-1. Lines with brachytic stem had shorter plant height, lower biomass, yield, harvest index and pods per plant, and essentially no differences in days to maturity and 100-seed weight when compared with normal stem lines. It was obvious that the effect of brachytic stem on yield was due to the decreased height, biomass and harvest index.

  3. Association of MAP4K4 gene single nucleotide polymorphism with mastitis and milk traits in Chinese Holstein cattle.

    Science.gov (United States)

    Bhattarai, Dinesh; Chen, Xing; Ur Rehman, Zia; Hao, Xingjie; Ullah, Farman; Dad, Rahim; Talpur, Hira Sajjad; Kadariya, Ishwari; Cui, Lu; Fan, Mingxia; Zhang, Shujun

    2017-02-01

    The objective of the studies presented in this Research Communication was to investigate the association of single nucleotide polymorphisms present in the MAP4K4 gene with different milk traits in dairy cows. Based on previous QTL fine mapping results on bovine chromosome 11, the MAP4K4 gene was selected as a candidate gene to evaluate its effect on somatic cell count and milk traits in ChineseHolstein cows. Milk production traits including milk yield, fat percentage, and protein percentage of each cow were collected using 305 d lactation records. Association between MAP4K4 genotype and different traits and Somatic Cell Score (SCS) was performed using General Linear Regression Model of R. Two SNPs at exon 18 (c.2061T > G and c.2196T > C) with genotype TT in both SNPs were found significantly higher for somatic SCS. We found the significant effect of exon 18 (c.2061T > G) on protein percentage, milk yield and SCS. We identified SNPs at different location of MAP4K4 gene of the cattle and several of them were significantly associated with the somatic cell score and other different milk traits. Thus, MAP4K4 gene could be a useful candidate gene for selection of dairy cattle against mastitis and the identified polymorphisms might potentially be strong genetic markers.

  4. Monitoring Scientific Developments from a Dynamic Perspective: Self-Organized Structuring To Map Neural Network Research.

    Science.gov (United States)

    Noyons, E. C. M.; van Raan, A. F. J.

    1998-01-01

    Using bibliometric mapping techniques, authors developed a methodology of self-organized structuring of scientific fields which was applied to neural network research. Explores the evolution of a data generated field structure by monitoring the interrelationships between subfields, the internal structure of subfields, and the dynamic features of…

  5. 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.

  6. Spatio-temporal map generalizations with the hierarchical Voronoi data structure

    DEFF Research Database (Denmark)

    Mioc, Darka; Anton, François; Gold, Christopher M.

    of map objects, together with their temporal and spatial adjacency relationships. In this paper, we present new solutions to the problems of spatio-temporal generalizations using the hierarchical Voronoi spatio-temporal data structure. The application of the hierarchical Voronoi data structure presented...... in this research is in spatio-temporal map generalization, which is needed for reasoning about dynamic aspects of the world, primarily about actions, events and processes. This provides an advance in the domain of map generalization as we are able to deal not only with the cartographic objects, but also...... implemented in commercial GIS systems. In this research, we used the Voronoi spatial data model for map generalizations. We were able to demonstrate that the map generalization does not affect only spatial objects (points, lines or polygons), but also the events corresponding to the creation and modification...

  7. Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber.

    Science.gov (United States)

    Zhang, Zhonghua; Mao, Linyong; Chen, Huiming; Bu, Fengjiao; Li, Guangcun; Sun, Jinjing; Li, Shuai; Sun, Honghe; Jiao, Chen; Blakely, Rachel; Pan, Junsong; Cai, Run; Luo, Ruibang; Van de Peer, Yves; Jacobsen, Evert; Fei, Zhangjun; Huang, Sanwen

    2015-06-01

    Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated break-induced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.

  8. 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).

  9. The structure and expression of the human neuroligin-3 gene.

    Science.gov (United States)

    Philibert, R A; Winfield, S L; Sandhu, H K; Martin, B M; Ginns, E I

    2000-04-04

    The neuroligins are a family of proteins that are thought to mediate cell to cell interactions between neurons. During the sequencing at an Xq13 locus associated with a mental retardation syndrome in some studies, we discovered a portion of the human orthologue of the rat neuroligin-3 gene. We now report the structure and the expression of that gene. The gene spans approximately 30kb and contains eight exons. Unlike the rat gene, it codes for at least two mRNAs and at least one of which is expressed outside the CNS. Interestingly, the putative promoter for the gene overlaps the last exon of the neighboring HOPA gene and is located less than 1kb from an OPA element in which a polymorphism associated with mental retardation is found. These findings suggest a possible role for the neuroligin gene in mental retardation and that the role of the gene in humans may differ from its role in rats.

  10. Protein contact maps: A binary depiction of protein 3D structures

    Science.gov (United States)

    Emerson, Isaac Arnold; Amala, Arumugam

    2017-01-01

    In recent years, there has been a considerable interest in examining the structure and dynamics of complex networks. Proteins in 3D space may also be considered as complex systems emerged through the interactions of their constituent amino acids. This representation provides a powerful framework to uncover the general organized principle of protein contact network. Here we reviewed protein contact map in terms of protein structure prediction and analyses. In addition, we had also discussed the various computational techniques for the prediction of protein contact maps and the tools to visualize contact maps.

  11. AutoMap & AutoLink: Tools for Communicating Complex & DynamicData-Structures using MPI

    OpenAIRE

    Goujon, Delphine; Michel, Martial; Peeters, Jasper; Devaney, Judith Ellen

    1998-01-01

    Colloque avec actes et comité de lecture.; This article describes two software tools, AutoMap and AutoLink, that facilitate the use of data-structures in MPI. AutoMap is a program that parses a file of user-defined data-structures and generates new MPI types out of basic and previously defined MPI data-types. Our software tool automatically handles specialized error checking related to memory mapping. AutoLink is an MPI library that allows the transfert of complex, dynimacally linked, and pos...

  12. A gene for distal arthrogryposis Type I maps to the pericentromeric region of chromosome 9

    Energy Technology Data Exchange (ETDEWEB)

    Bamshad, M.; Watkins, W.S.; Zenger, R.K.; Bohnsack, J.F.; Carey, J.C.; Otterud, B.; Krakowiak, P.A.; Robertson, M.; Jorde, L.B. [Univ. of Utah Health Sciences Center, Salt Lake City, UT (United States)

    1994-12-01

    Club foot is one of the most common human congenital malformations. Distal arthrogryposis type I (DA-1) is a frequent cause of dominantly inherited club foot. Performing a genomewide search using short tandem repeat (STR) polymorphisms, we have mapped a DA-1 gene to the pericentromeric region of chromosome 9 in a large kindred. Linkage analysis has generated a positive lod score of 5.90 at {theta} = 0, with the marker GS-4. Multiple recombinants bracketing the region have been identified. Analysis of an additional family demonstrated no linkage to the same locus, indicating likely locus heterogeneity. Of the autosomal congenital contracture disorders causing positional foot deformities, this is the first to be mapped.

  13. Molecular mapping of leaf rust resistance genes in the wheat line Yu 356-9

    Institute of Scientific and Technical Information of China (English)

    HAN Liu-sha; LI Zai-feng; WANG Jia-zhen; SHI Ling-zhi; ZHU Lin; LI Xing; LIU Da-qun; Syed J A Shah

    2015-01-01

    The Chinese wheat line Yu 356-9 exhibits a high level of resistance to leaf rust. In order to decipher the genetic base of resistance in Yu 356-9, gene postulation, inheritance analyses, and chromosome linkage mapping were carried out. Gene postulation completed using 15 leaf rust pathotypes and 36 isogenic lines indicated that Yu 356-9 was resistant to al pathotypes tested. F1 and F2 plants from the cross Yu 356-9 (resistant)/Zhengzhou 5389 (susceptible) were tested with leaf rust pathotype“FHNQ”in the greenhouse. Results indicated a 3:1 segregation ratio, indicative of the presence of a single dominant leaf rust resistance gene in Yu 356-9 which was temporarily designated as LrYu. Bulk segregant analysis and molecular marker assays were used to map LrYu. Five simple sequence repeat (SSR) markers on chromosome 2BS were found closely linked to LrYu. Among these markers, Xwmc770 is the most closely linked, with a genetic distance of 5.7 cM.

  14. Genome-wide mapping of furfural tolerance genes in Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Tirzah Y Glebes

    Full Text Available Advances in genomics have improved the ability to map complex genotype-to-phenotype relationships, like those required for engineering chemical tolerance. Here, we have applied the multiSCale Analysis of Library Enrichments (SCALEs; Lynch et al. (2007 Nat. Method. approach to map, in parallel, the effect of increased dosage for >10(5 different fragments of the Escherichia coli genome onto furfural tolerance (furfural is a key toxin of lignocellulosic hydrolysate. Only 268 of >4,000 E. coli genes (∼ 6% were enriched after growth selections in the presence of furfural. Several of the enriched genes were cloned and tested individually for their effect on furfural tolerance. Overexpression of thyA, lpcA, or groESL individually increased growth in the presence of furfural. Overexpression of lpcA, but not groESL or thyA, resulted in increased furfural reduction rate, a previously identified mechanism underlying furfural tolerance. We additionally show that plasmid-based expression of functional LpcA or GroESL is required to confer furfural tolerance. This study identifies new furfural tolerant genes, which can be applied in future strain design efforts focused on the production of fuels and chemicals from lignocellulosic hydrolysate.

  15. Genome-wide mapping of furfural tolerance genes in Escherichia coli.

    Science.gov (United States)

    Glebes, Tirzah Y; Sandoval, Nicholas R; Reeder, Philippa J; Schilling, Katherine D; Zhang, Min; Gill, Ryan T

    2014-01-01

    Advances in genomics have improved the ability to map complex genotype-to-phenotype relationships, like those required for engineering chemical tolerance. Here, we have applied the multiSCale Analysis of Library Enrichments (SCALEs; Lynch et al. (2007) Nat. Method.) approach to map, in parallel, the effect of increased dosage for >10(5) different fragments of the Escherichia coli genome onto furfural tolerance (furfural is a key toxin of lignocellulosic hydrolysate). Only 268 of >4,000 E. coli genes (∼ 6%) were enriched after growth selections in the presence of furfural. Several of the enriched genes were cloned and tested individually for their effect on furfural tolerance. Overexpression of thyA, lpcA, or groESL individually increased growth in the presence of furfural. Overexpression of lpcA, but not groESL or thyA, resulted in increased furfural reduction rate, a previously identified mechanism underlying furfural tolerance. We additionally show that plasmid-based expression of functional LpcA or GroESL is required to confer furfural tolerance. This study identifies new furfural tolerant genes, which can be applied in future strain design efforts focused on the production of fuels and chemicals from lignocellulosic hydrolysate.

  16. Fine-mapping of genes determining extrafusal fiber properties in murine soleus muscle.

    Science.gov (United States)

    Carroll, A M; Cheng, R; Collie-Duguid, E S R; Meharg, C; Scholz, M E; Fiering, S; Fields, J L; Palmer, A A; Lionikas, A

    2017-03-01

    Muscle fiber cross-sectional area (CSA) and proportion of different fiber types are important determinants of muscle function and overall metabolism. Genetic variation plays a substantial role in phenotypic variation of these traits; however, the underlying genes remain poorly understood. This study aimed to map quantitative trait loci (QTL) affecting differences in soleus muscle fiber traits between the LG/J and SM/J mouse strains. Fiber number, CSA, and proportion of oxidative type I fibers were assessed in the soleus of 334 genotyped female and male mice of the F34 generation of advanced intercross lines (AIL) derived from the LG/J and SM/J strains. To increase the QTL detection power, these data were combined with 94 soleus samples from the F2 intercross of the same strains. Transcriptome of the soleus muscle of LG/J and SM/J females was analyzed by microarray. Genome-wide association analysis mapped four QTL (genome-wide P < 0.05) affecting the properties of muscle fibers to chromosome 2, 3, 4, and 11. A 1.5-LOD QTL support interval ranged between 2.36 and 4.67 Mb. On the basis of the genomic sequence information and functional and transcriptome data, we identified candidate genes for each of these QTL. The combination of analyses in F2 and F34 AIL populations with transcriptome and genomic sequence data in the parental strains is an effective strategy for refining QTL and nomination of the candidate genes.

  17. Dynamic QTL analysis and candidate gene mapping for waterlogging tolerance at maize seedling stage.

    Directory of Open Access Journals (Sweden)

    Khalid A Osman

    Full Text Available Soil waterlogging is one of the major abiotic stresses adversely affecting maize growth and yield. To identify dynamic expression of genes or quantitative trait loci (QTL, QTL associated with plant height, root length, root dry weight, shoot dry weight and total dry weight were identified via conditional analysis in a mixed linear model and inclusive composite interval mapping method at three respective periods under waterlogging and control conditions. A total of 13, 19 and 23 QTL were detected at stages 3D|0D (the period during 0-3 d of waterlogging, 6D|3D and 9D|6D, respectively. The effects of each QTL were moderate and distributed over nine chromosomes, singly explaining 4.14-18.88% of the phenotypic variation. Six QTL (ph6-1, rl1-2, sdw4-1, sdw7-1, tdw4-1 and tdw7-1 were identified at two consistent stages of seedling development, which could reflect a continuous expression of genes; the remaining QTL were detected at only one stage. Thus, expression of most QTL was influenced by the developmental status. In order to provide additional evidence regarding the role of corresponding genes in waterlogging tolerance, mapping of Expressed Sequence Tags markers and microRNAs were conducted. Seven candidate genes were observed to co-localize with the identified QTL on chromosomes 1, 4, 6, 7 and 9, and may be important candidate genes for waterlogging tolerance. These results are a good starting point for understanding the genetic basis for selectively expressing of QTL in different stress periods and the common genetic control mechanism of the co-localized traits.

  18. Sub-diffuse structured light imaging provides macroscopic maps of microscopic tissue structure (Conference Presentation)

    Science.gov (United States)

    Kanick, Stephen C.

    2016-03-01

    The onset and progression of cancer introduces changes to the intra-cellular ultrastructural components and to the morphology of the extracellular matrix. While previous work has shown that localized scatter imaging is sensitive to pathology-induced differences in these aspects of tissue microstructure, wide adaptation this knowledge for surgical guidance is limited by two factors. First, the time required to image with confocal-level localization of the remission signal can be substantial. Second, localized (i.e. sub-diffuse) scatter remission intensity is influenced interchangeably by parameters that define scattering frequency and anisotropy. This similarity relationship must be carefully considered in order to obtain unique estimates of biomarkers that define either the scatter density or features that describe the distribution (e.g. shape, size, and orientation) of scatterers. This study presents a novel approach that uses structured light imaging to address both of these limitations. Monte Carlo data were used to model the reflectance intensity over a wide range of spatial frequencies, reduced scattering coefficients, absorption coefficients, and a metric of the scattering phase function that directly maps to the fractal dimension of scatter sizes. The approach is validated in tissue-simulating phantoms constructed with user-tuned scattering phase functions. The validation analysis shows that the phase function can be described in the presence of different scatter densities or background absorptions. Preliminary data from clinical tissue specimens show quantitative images of both the scatter density and the tissue fractal dimension for various tissue types and pathologies. These data represent a novel wide-field quantitative approach to mapping microscopic structural biomarkers that cannot be obtained with standard diffuse imaging. Implications for the use of this approach to assess surgical margins will be discussed.

  19. QTL and candidate gene mapping for polyphenolic composition in apple fruit

    Directory of Open Access Journals (Sweden)

    Chagné David

    2012-01-01

    Full Text Available Abstract Background The polyphenolic products of the phenylpropanoid pathway, including proanthocyanidins, anthocyanins and flavonols, possess antioxidant properties that may provide health benefits. To investigate the genetic architecture of control of their biosynthesis in apple fruit, various polyphenolic compounds were quantified in progeny from a 'Royal Gala' × 'Braeburn' apple population segregating for antioxidant content, using ultra high performance liquid chromatography of extracts derived from fruit cortex and skin. Results Construction of genetic maps for 'Royal Gala' and 'Braeburn' enabled detection of 79 quantitative trait loci (QTL for content of 17 fruit polyphenolic compounds. Seven QTL clusters were stable across two years of harvest and included QTLs for content of flavanols, flavonols, anthocyanins and hydroxycinnamic acids. Alignment of the parental genetic maps with the apple whole genome sequence in silico enabled screening for co-segregation with the QTLs of a range of candidate genes coding for enzymes in the polyphenolic biosynthetic pathway. This co-location was confirmed by genetic mapping of markers derived from the gene sequences. Leucoanthocyanidin reductase (LAR1 co-located with a QTL cluster for the fruit flavanols catechin, epicatechin, procyanidin dimer and five unknown procyanidin oligomers identified near the top of linkage group (LG 16, while hydroxy cinnamate/quinate transferase (HCT/HQT co-located with a QTL for chlorogenic acid concentration mapping near the bottom of LG 17. Conclusion We conclude that LAR1 and HCT/HQT are likely to influence the concentration of these compounds in apple fruit and provide useful allele-specific markers for marker assisted selection of trees bearing fruit with healthy attributes.

  20. Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells

    Science.gov (United States)

    Looney, Timothy J.; Zhang, Li; Chen, Chih-Hsin; Lee, Jae Hyun; Chari, Sheila; Mao, Frank Fuxiang; Pelizzola, Mattia; Zhang, Lu; Lister, Ryan; Baker, Samuel W.; Fernandes, Croydon J.; Gaetz, Jedidiah; Foshay, Kara M.; Clift, Kayla L.; Zhang, Zhenyu; Li, Wei-Qiang; Vallender, Eric J.; Wagner, Ulrich; Qin, Jane Yuxia; Michelini, Katelyn J.; Bugarija, Branimir; Park, Donghyun; Aryee, Emmanuel; Stricker, Thomas; Zhou, Jie; White, Kevin P.; Ren, Bing; Schroth, Gary P.; Ecker, Joseph R.; Xiang, Andy Peng; Lahn, Bruce T.

    2014-01-01

    Both diffusible factors acting in trans and chromatin components acting in cis are implicated in gene regulation, but the extent to which either process causally determines a cell's transcriptional identity is unclear. We recently used cell fusion to define a class of silent genes termed “cis-silenced” (or “occluded”) genes, which remain silent even in the presence of trans-acting transcriptional activators. We further showed that occlusion of lineage-inappropriate genes plays a critical role in maintaining the transcriptional identities of somatic cells. Here, we present, for the first time, a comprehensive map of occluded genes in somatic cells. Specifically, we mapped occluded genes in mouse fibroblasts via fusion to a dozen different rat cell types followed by whole-transcriptome profiling. We found that occluded genes are highly prevalent and stable in somatic cells, representing a sizeable fraction of silent genes. Occluded genes are also highly enriched for important developmental regulators of alternative lineages, consistent with the role of occlusion in safeguarding cell identities. Alongside this map, we also present whole-genome maps of DNA methylation and eight other chromatin marks. These maps uncover a complex relationship between chromatin state and occlusion. Furthermore, we found that DNA methylation functions as the memory of occlusion in a subset of occluded genes, while histone deacetylation contributes to the implementation but not memory of occlusion. Our data suggest that the identities of individual cell types are defined largely by the occlusion status of their genomes. The comprehensive reference maps reported here provide the foundation for future studies aimed at understanding the role of occlusion in development and disease. PMID:24310002

  1. Interpreting Patterns of Gene Expression with Self-Organizing Maps: Methods and Application to Hematopoietic Differentiation

    Science.gov (United States)

    Tamayo, Pablo; Slonim, Donna; Mesirov, Jill; Zhu, Qing; Kitareewan, Sutisak; Dmitrovsky, Ethan; Lander, Eric S.; Golub, Todd R.

    1999-03-01

    Array technologies have made it straightforward to monitor simultaneously the expression pattern of thousands of genes. The challenge now is to interpret such massive data sets. The first step is to extract the fundamental patterns of gene expression inherent in the data. This paper describes the application of self-organizing maps, a type of mathematical cluster analysis that is particularly well suited for recognizing and classifying features in complex, multidimensional data. The method has been implemented in a publicly available computer package, GENECLUSTER, that performs the analytical calculations and provides easy data visualization. To illustrate the value of such analysis, the approach is applied to hematopoietic differentiation in four well studied models (HL-60, U937, Jurkat, and NB4 cells). Expression patterns of some 6,000 human genes were assayed, and an online database was created. GENECLUSTER was used to organize the genes into biologically relevant clusters that suggest novel hypotheses about hematopoietic differentiation--for example, highlighting certain genes and pathways involved in "differentiation therapy" used in the treatment of acute promyelocytic leukemia.

  2. Genetic analysis and mapping of gene fzp(t) controlling spikelet differentiation in rice

    Institute of Scientific and Technical Information of China (English)

    段远霖; 李维明; 吴为人; 潘润森; 周元昌; 祁建民; 林荔辉; 陈志伟; 毛大梅; 刘华清; 张丹凤; 薛勇彪

    2003-01-01

    A mutant of spikelet differentiation in rice called frizzle panicle (fzp) was discovered in the progeny of a cross between Oryza sativa ssp. indica cv. V20B and cv. Hua1B. The mutant exhibits normal plant morphology but has apparently fewer tillers. The most striking change in fzp is that its spikelet differentiation is completely blocked, with unlimited subsequent rachis branches generated from the positions where spikelets normally develop in wild-type plants. Genetic analysis suggests that fzp is controlled by a single recessive gene, which is temporarily named fzp (t). Based on its mutant phenotype, fzp (t) represents a key gene controlling spikelet differentiation. Some F2 mutant plants derived from various genetic background appeared as the "middle type", suggesting that the action of fzp (t) is influenced by the presence of redundant, modifier or interactive genes. By using simple sequence repeat (SSR) markers and bulked segregant analysis (BSA) method, fzp (t) gene was mapped in the terminal region of the long arm of chromosome 7, with RM172 and RM248 on one side, 3.2 cM and 6.4 cM from fzp (t), and RM18 and RM234 on the other side, 23.1 cM and 26.3 cM from fzp(t), respectively. These results will facilitate the positional cloning and function studies of the gene.

  3. Demyelination determinants map to the spike glycoprotein gene of coronavirus mouse hepatitis virus.

    Science.gov (United States)

    Das Sarma, J; Fu, L; Tsai, J C; Weiss, S R; Lavi, E

    2000-10-01

    Demyelination is the pathologic hallmark of the human immune-mediated neurologic disease multiple sclerosis, which may be triggered or exacerbated by viral infections. Several experimental animal models have been developed to study the mechanism of virus-induced demyelination, including coronavirus mouse hepatitis virus (MHV) infection in mice. The envelope spike (S) glycoprotein of MHV contains determinants of properties essential for virus-host interactions. However, the molecular determinants of MHV-induced demyelination are still unknown. To investigate the mechanism of MHV-induced demyelination, we examined whether the S gene of MHV contains determinants of demyelination and whether demyelination is linked to viral persistence. Using targeted RNA recombination, we replaced the S gene of a demyelinating virus (MHV-A59) with the S gene of a closely related, nondemyelinating virus (MHV-2). Recombinant viruses containing an S gene derived from MHV-2 in an MHV-A59 background (Penn98-1 and Penn98-2) exhibited a persistence-positive, demyelination-negative phenotype. Thus, determinants of demyelination map to the S gene of MHV. Furthermore, viral persistence is insufficient to induce demyelination, although it may be a prerequisite for the development of demyelination.

  4. Identification, mapping, and cloning of the gene encoding cyanase in Escherichia coli K-12.

    Science.gov (United States)

    Sung, Y C; Parsell, D; Anderson, P M; Fuchs, J A

    1987-06-01

    The gene in Escherichia coli for cyanase, designated cynS, was localized to a BglII restriction site approximately 1.7 kilobases from the lacA end of the lac operon. The gene was cloned into the pUC13 vector. Maxicell analysis of plasmid-encoded proteins confirmed that the BglII site is in the region encoding the structural gene for cyanase. Cyanase-deficient strains had increased sensitivity to cyanate and were not able to use cyanate as a nitrogen source.

  5. Identification, mapping, and cloning of the gene encoding cyanase in Escherichia coli K-12.

    OpenAIRE

    Sung, Y C; Parsell, D; Anderson, P. M.; Fuchs, J A

    1987-01-01

    The gene in Escherichia coli for cyanase, designated cynS, was localized to a BglII restriction site approximately 1.7 kilobases from the lacA end of the lac operon. The gene was cloned into the pUC13 vector. Maxicell analysis of plasmid-encoded proteins confirmed that the BglII site is in the region encoding the structural gene for cyanase. Cyanase-deficient strains had increased sensitivity to cyanate and were not able to use cyanate as a nitrogen source.

  6. Mapping chemical performance on molecular structures using locally interpretable explanations

    CERN Document Server

    Whitmore, Leanne S; Hudson, Corey M

    2016-01-01

    In this work, we present an application of Locally Interpretable Machine-Agnostic Explanations to 2-D chemical structures. Using this framework we are able to provide a structural interpretation for an existing black-box model for classifying biologically produced fuel compounds with regard to Research Octane Number. This method of "painting" locally interpretable explanations onto 2-D chemical structures replicates the chemical intuition of synthetic chemists, allowing researchers in the field to directly accept, reject, inform and evaluate decisions underlying inscrutably complex quantitative structure-activity relationship models.

  7. Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

    Science.gov (United States)

    Burt, Andrew J; William, H Manilal; Perry, Gregory; Khanal, Raja; Pauls, K Peter; Kelly, James D; Navabi, Alireza

    2015-01-01

    Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

  8. Evaluating HapMap SNP data transferability in a large-scale genotyping project involving 175 cancer-associated genes.

    Science.gov (United States)

    Ribas, Gloria; González-Neira, Anna; Salas, Antonio; Milne, Roger L; Vega, Ana; Carracedo, Begoña; González, Emilio; Barroso, Eva; Fernández, Lara P; Yankilevich, Patricio; Robledo, Mercedes; Carracedo, Angel; Benítez, Javier

    2006-02-01

    One of the many potential uses of the HapMap project is its application to the investigation of complex disease aetiology among a wide range of populations. This study aims to assess the transferability of HapMap SNP data to the Spanish population in the context of cancer research. We have carried out a genotyping study in Spanish subjects involving 175 candidate cancer genes using an indirect gene-based approach and compared results with those for HapMap CEU subjects. Allele frequencies were very consistent between the two samples, with a high positive correlation (R) of 0.91 (PHapMap CEU data using pairwise r (2) thresholds of 0.8 and 0.5 was assessed by applying these to the Spanish and current HapMap data for 66 genes. In general, the HapMap tagSNPs performed very well. Our results show generally high concordance with HapMap data in allele frequencies and haplotype distributions and confirm the applicability of HapMap SNP data to the study of complex diseases among the Spanish population.

  9. Fine mapping of the epistatic suppressor gene (esp) of a recessive genic male sterility in rapeseed (Brassica napus L.).

    Science.gov (United States)

    Xu, Zhenghua; Xie, Yanzhou; Hong, Dengfeng; Liu, Pingwu; Yang, Guangsheng

    2009-09-01

    9012AB, a recessive genic male sterility (RGMS) line derived from spontaneous mutation in Brassica napus, has been playing an important role in rapeseed hybrid production in China. The male sterility of 9012AB is controlled by two recessive genes (ms3 and ms4) interacting with one recessive epistatic suppressor gene (esp). The objective of this study was to develop PCR-based markers tightly linked to the esp gene and construct a high-resolution map surrounding the esp gene. From the survey of 512 AFLP primer combinations, 3 tightly linked AFLP markers were obtained and successfully converted to codominant or dominant SCAR markers. Furthermore, a codominant SSR marker (Ra2G08) associated with the esp gene was identified through genetic map integration. For fine mapping of the esp gene, these PCR-based markers were analyzed in a large BC1 population of 2545 plants. The esp gene was then genetically restricted to a region of 1.03 cM, 0.35 cM from SSR marker Ra2G08 and 0.68 cM from SCAR marker WSC6. The SCAR marker WSC5 co-segregated with the target gene. These results lay a solid foundation for map-based cloning of esp and will facilitate the selection of RGMS lines and their temporary maintainers.

  10. Phylogenetic conservation and physical mapping of members of the H6 homeobox gene family.

    Science.gov (United States)

    Stadler, H S; Murray, J C; Leysens, N J; Goodfellow, P J; Solursh, M

    1995-06-01

    Homeobox genes represent a class of transcription factors that play key roles in the regulation of embryogenesis and development. Here we report the identification of a homeobox-containing gene family that is highly conserved at both the nucleotide and amino acid levels in a diverse number of species. These species encompass both vertebrate and invertebrate phylogenies, ranging from Homo sapiens to Drosophila melanogaster. In humans, at least two homeobox sequences from this family were identified representing a previously reported member of this family as well as a novel homeobox sequence that we physically mapped to the 10q25.2-q26.3 region of human Chromosome (Chr) 10. Multiple members of this family were also detected in three additional vertebrate species including Equus caballus (horse), Gallus gallus (Chicken), and Mus musculus (mouse), whereas only single members were detected in Tripneustes gratilla (sea urchin), Petromyzon marinus (lamprey), Salmo salar (salmon), Ovis aries (sheep), and D. melanogaster (fruit fly).

  11. Paramyotonia congenita and hyperkalemic periodic paralysis map to the same sodium-channel gene locus.

    Science.gov (United States)

    Ptacek, L J; Trimmer, J S; Agnew, W S; Roberts, J W; Petajan, J H; Leppert, M

    1991-01-01

    Paramyotonia congenita (PC), an autosomal dominant muscle disease, shares some clinical and electrophysiological similarities with another myotonic muscle disorder, hyperkalemic periodic paralysis (HYPP). However, clinical and electrophysiologic differences allow differentiation of the two disorders. The HYPP locus was recently shown to be linked to a skeletal muscle sodium-channel gene probe. We now report that PC maps to the same locus (LOD score 4.4, theta = 0 at assumed penetrance of .95). These linkage results, coupled with physiological data demonstrating abnormal sodium-channel function in patients with PC, implicate a sodium-channel gene as an important candidate for the site of mutation responsible for PC. Furthermore, this is strong evidence for the hypothesis that PC and HYPP are allelic disorders. PMID:1654742

  12. Mapping of a BYDV resistance gene from Thinopyrum intermedium in wheat background by molecular markers

    Institute of Scientific and Technical Information of China (English)

    张增艳; 辛志勇; 马有志; 陈孝; 徐琼芳; 林志珊

    1999-01-01

    The wheat line H960642 is a homozygous wheat-Thinopyrum intermedium translocation line with resistance to BYDV by genomie in situ hybridization (GISH) and RFLP analysis. The genomie DNA of Th. intermedium was used as a probe, and eonunon wheat genomie DNA as a blocking in GISH experiment. The results showed that the chromosome segments of Th. intermedium were transferred to the distal end of a pair of wheat chromosomes. RFLP analysis indicated that the transloeation line H960642 is a T7DS·7DL-7XL translocation by using 8 probes mapped on the homoeologous group 7 in wheat. The tranalocation breakpoint is located between Xpsr680 and Xpsr965 about 90—99 cM from the centromere. The RFLP markers psr680 and psr687 were closoly linked with the BYDV resistance gene. The gene is located on the distal end of 7XL around Xpsr680 and Xpsr687.

  13. Characterization and mapping of a white panicle mutant gene in rice

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    A spontaneous white panicle mutant was found from the F6 progenies of an indica/japonica cross. The mutant exhibits white stripes on its basal leaves while the panicles, rachis and pedicel are milky white colored at flowering stage. Genetic analysis in an F2 population from the cross of Zhi7/white panicle mutant indicates that the white panicle phenotype is controlled by a single recessive nuclear gene, tentatively termed as wp(t). Using microsatellite markers, the wp(t) gene was anchored between the markers of SSR101 and SSR63.9 with a map distance of 2.3 and 0.8 cM, respectively, and co-segregated with the marker of SSR17 on rice chromosome 1.

  14. The gamma fibrinogen gene (FGG) maps to chromosome 17 in both cattle and sheep.

    Science.gov (United States)

    Johnson, S E; Barendse, W; Hetzel, D J

    1993-01-01

    The gamma fibrinogen gene (FGG) was localised in both cattle and sheep using in situ hybridisation. The probe employed was a 1-kb bovine cDNA fragment. Based on observations of QFQ-banded chromosome preparations, this locus is on bovine chromosome 17q12-->q13 and on the homologous sheep chromosome 17. This localisation is, to our knowledge, the first assignment to chromosome 17 in either the bovine or ovine genome. In addition to localising FGG to this chromosome, the assignment provisionally maps the previously unassigned syntenic group U23, containing (besides FGG) the genes for mitochondrial aldehyde dehydrogenase 2 (ALDH2), interleukin 2 (IL2), immunoglobulin lambda (IGL), and beta fibrinogen (FGB), to chromosome 17 in cattle and probably to the same chromosome in sheep.

  15. Genetic Analysis and Mapping of Dominant Minute Grain Gene Mi3(t) in Rice

    Institute of Scientific and Technical Information of China (English)

    LIU Ming-wei; LIU Yong; WANG Shi-quan; DENG Qi-ming; LI Ping

    2005-01-01

    Grain size, determined chiefly by grain Iength, is one of the main factors affecting the grain yield in rice production. To study the trait of rice grain size, F1 and F2 populations were developed from crosses Shuhui 881/Y34 and Shuhui 527/Y34, and genetic analysis for minute grain was performed. The F1 populations showed minute grains, and grain size segregations in the two F2 populations were both in accordance with the ratio of 3:1, indicating that minute grain in Y34 was controlled by a completely dominant gene. By using the F2 population from Shuhui 881/Y34, this dominant gene, tentatively designated as Mi3(t), was mapped based on SSR markers in the interval between RM282 (genetic distance of 5.1 cM) and RM6283 (genetic distance of 0.9 cM) on the short arm of chromosome 3.

  16. Comparative genomics of the relationship between gene structure and expression

    NARCIS (Netherlands)

    Ren, X.

    2006-01-01

    The relationship between the structure of genes and their expression is a relatively new aspect of genome organization and regulation. With more genome sequences and expression data becoming available, bioinformatics approaches can help the further elucidation of the relationships between gene struc

  17. Structure and in vitro transcription of human globin genes.

    Science.gov (United States)

    Proudfoot, N J; Shander, M H; Manley, J L; Gefter, M L; Maniatis, T

    1980-09-19

    The alpha-like and beta-like subunits of human hemoglobin are encoded by a small family of genes that are differentially expressed during development. Through the use of molecular cloning procedures, each member of this gene family has been isolated and extensively characterized. Although the alpha-like and beta-like globin genes are located on different chromosomes, both sets of genes are arranged in closely linked clusters. In both clusters, each of the genes is transcribed from the same DNA strand, and the genes are arranged in the order of their expressions during development. Structural comparisons of immediately adjacent genes within each cluster have provided evidence for the occurrence of gene duplication and correction during evolution and have led to the discovery of pseudogenes, genes that have acquired numerous mutations that prevent their normal expression. Recently, in vivo and in vitro systems for studying the expression of cloned eukaryotic genes have been developed as a means of identifying DNA sequences that are necessary for normal gene function. This article describes the application of an in vitro transcription procedure to the study of human globin gene expression.

  18. Relationship between autophagy-related genes Beclin-1 and MAP1LC3 expression and biological characteristics of oral cancer

    Institute of Scientific and Technical Information of China (English)

    Xiao-Dong Li; Xiao-Chen Sun; Xin-Mei Li; Jia-Wei Gu

    2016-01-01

    Objective:To study the relationship between autophagy-related genes Beclin-1 and MAP1LC3 expression and biological characteristics of oral cancer. Methods:Oral cancer tissues and precancerous tissues were collected to detect mRNA expression levels of Beclin-1 and MAP1LC3;tongue cancer cell lines CTST-2 and primary epithelial cells of normal buccal mucosa were cultured to detect mRNA expression levels of autophagy marker molecues (Beclin-1 and MAP1LC3), pro-apoptosis genes (P53 and Caspase-3) and anti-apoptosis genes (Survivin, Bcl-2 and Bmi-1). Results:mRNA contents of Beclin-1 and MAP1LC3 in tongue cancer, buccal mucosa cancer, gingival cancer and mouth floor cancer tissues were significantly lower than those in corresponding precancerous tissues; mRNA contents of Beclin-1 and MAP1LC3 in tongue cancer cells CTST-2 were lower than those in normal mucosal cells;mRNA contents of P53 and Caspase-3 in tongue cancer cells CTST-2 were lower than those in normal mucosal cells and positively correlated with mRNA contents of Beclin-1 and MAP1LC3; mRNA contents of survivin, Bcl-2 and Bmi-1 in CTST-2 were higher than those in normal mucosal cells and negatively correlated with mRNA contents of Beclin-1 and MAP1LC3. Conclusion:Expression levels of autophagy-related genes Beclin-1 and MAP1LC3 abnormally reduce in oral cancer and have significant correlation with the expression of pro-apoptosis genes and anti-apoptosis genes of cancer cells.

  19. Mapping the genes for susceptibility and response to Leishmania tropica in mouse.

    Directory of Open Access Journals (Sweden)

    Yahya Sohrabi

    Full Text Available BACKGROUND: L. tropica can cause both cutaneous and visceral leishmaniasis in humans. Although the L. tropica-induced cutaneous disease has been long known, its potential to visceralize in humans was recognized only recently. As nothing is known about the genetics of host responses to this infection and their clinical impact, we developed an informative animal model. We described previously that the recombinant congenic strain CcS-16 carrying 12.5% genes from the resistant parental strain STS/A and 87.5% genes from the susceptible strain BALB/c is more susceptible to L. tropica than BALB/c. We used these strains to map and functionally characterize the gene-loci regulating the immune responses and pathology. METHODS: We analyzed genetics of response to L. tropica in infected F2 hybrids between BALB/c×CcS-16. CcS-16 strain carries STS-derived segments on nine chromosomes. We genotyped these segments in the F2 hybrid mice and tested their linkage with pathological changes and systemic immune responses. PRINCIPAL FINDINGS: We mapped 8 Ltr (Leishmania tropica response loci. Four loci (Ltr2, Ltr3, Ltr6 and Ltr8 exhibit independent responses to L. tropica, while Ltr1, Ltr4, Ltr5 and Ltr7 were detected only in gene-gene interactions with other Ltr loci. Ltr3 exhibits the recently discovered phenomenon of transgenerational parental effect on parasite numbers in spleen. The most precise mapping (4.07 Mb was achieved for Ltr1 (chr.2, which controls parasite numbers in lymph nodes. Five Ltr loci co-localize with loci controlling susceptibility to L. major, three are likely L. tropica specific. Individual Ltr loci affect different subsets of responses, exhibit organ specific effects and a separate control of parasite load and organ pathology. CONCLUSION: We present the first identification of genetic loci controlling susceptibility to L. tropica. The different combinations of alleles controlling various symptoms of the disease likely co-determine different

  20. Fine Mapping of RppP25, a Southern Rust Resistance Gene in Maize

    Institute of Scientific and Technical Information of China (English)

    Panfeng Zhao; Guobin Zhang; Xiaojun Wu; Na Li; Dianyi Shi; Dengfeng Zhang; Chunfang Ji

    2013-01-01

    Southern rust (Puccinia polysora Underw.) is a major disease that can cause severe yield losses in maize (Zea mays L.).In our previous study,a major gene RppP25 that confers resistance to southern rust was identified in inbred line P25.Here,we report the fine mapping and candidate gene analysis of RppP25from the near-isogenic line F939,which harbors RppP25 in the genetic background of the susceptible inbred line F349.The inheritance of resistance to southern rust was investigated in the BC1F1 and BC3F1 populations,which were derived from a cross between F939 and F349 (as the recurrent parent).The 1:1 segregation ratio of resistance to susceptible plants in these two populations indicated that the resistance is controlled by a single dominant gene.Ten markers,including three simple sequence repeat (SSR) markers and seven insertion/deletion (InDel) markers,were developed in the RppP25 region.RppP25 was delimited to an interval between P091 and M271,with an estimated length of 40 kb based on the physical map of B73.In this region,a candidate gene was identified that was predicted to encode a putative nucleotide-binding site leucine-rich repeat (NBS-LRR) protein.Two co-segregated markers will aid in pyramiding diverse southern rust resistance alleles into elite materials,and thereby improve southern rust resistance worldwide.

  1. Genetic mapping of two genes conferring resistance to powdery mildew in common bean (Phaseolus vulgaris L.).

    Science.gov (United States)

    Pérez-Vega, Elena; Trabanco, Noemí; Campa, Ana; Ferreira, Juan José

    2013-06-01

    Powdery mildew (PM) is a serious disease in many legume species, including the common bean (Phaseolus vulgaris L.). This study investigated the genetic control behind resistance reaction to PM in the bean genotype, Cornell 49242. The results revealed evidence supporting a qualitative mode of inheritance for resistance and the involvement of two independent genes in the resistance reaction. The location of these resistance genes was investigated in a linkage genetic map developed for the XC RIL population. Contingency tests revealed significant associations for 28 loci out of a total of 329 mapped loci. Fifteen were isolated or formed groups with less than two loci. The thirteen remaining loci were located at three regions in linkage groups Pv04, Pv09, and Pv11. The involvement of Pv09 was discarded due to the observed segregation in the subpopulation obtained from the Xana genotype for the loci located in this region. In contrast, the two subpopulations obtained from the Xana genotype for the BM161 locus, linked to the Co-3/9 anthracnose resistance gene (Pv04), and from the Xana genotype for the SCAReoli locus, linked to the Co-2 anthracnose resistance gene (Pv11), exhibited monogenic segregations, suggesting that both regions were involved in the genetic control of resistance. A genetic dissection was carried out to verify the involvement of both regions in the reaction to PM. Two resistant recombinant lines were selected, according to their genotypes, for the block of loci included in the Co-2 and Co-3/9 regions, and they were crossed with the susceptible parent, Xana. Linkage analysis in the respective F2 populations supported the hypothesis that a dominant gene (Pm1) was located in the linkage group Pv11 and another gene (Pm2) was located in the linkage group Pv04. This is the first report showing the localization of resistance genes against powdery mildew in Phaseolus vulgaris and the results offer the opportunity to increase the efficiency of breeding

  2. Mapping of the nuclear fertility restorer gene for HL cytoplasmic male sterility in rice using microsatellite markers

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Bulked segregant analysis (BSA) of a BC1 population derived from Congguang 41A//Miyang 23/Congguang 41B was used to map the nuclear fertility restorer gene for Honglian (HL) cytoplasmic male sterility.One hundred and fifty-nine microsatellite primer pairs were screened for polymorphisms between the parents and between two bulks representing fertile and sterile plants.One microsatellite marker RM258 produced polymorphic products.The nuclear fertility restorer gene for HL cytoplasmic male sterility was mapped on chromosome 10,7.8cM from RM258.The restorer gene may be clustered on chromosome.

  3. Refinement of the background genetic map of Xq26-q27 and gene localisation for Boerjeson-Forssman-Lehmann syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Gedeon, A.K.; Kozman, H.M.; Mulley, J.C. [Univ. of Adelaide (Australia)] [and others

    1996-07-12

    A detailed map of genetic markers was constructed around the gene for the X-linked mental retardation syndrome of Borjeson-Forssman-Lehmann (BFLS). A multipoint linkage map of framework markers across Xq26-27, based on CEPH families, was integrated with the physical map, based on a YAC contig, to confirm marker order. The remaining genetic markers, which could not be ordered by linkage, were added to create the comprehensive genetic background map, in the order determined by physical mapping, to determine genetic distances between adjacent markers. This background genetic map is applicable to the refinement of the regional localization for any disease gene mapping to this region. The BFLS gene was localized using this background map in an extended version of the family described by Turner et al. The regional localization for BFLS extends between recombination events at DXS425 and DXS105, an interval of 24.6 cM on the background genetic map. The phenotypic findings commonly seen in the feet of affected males and obligate carrier females may represent a useful clinical indicator of carrier status in potential female carriers in the family. Recombination between DXS425 and DXS105 in a female with such characteristic feet suggests that the distal limit of the regional localization for the BFLS gene might reasonably be reduced to DXS294 for the purpose of selecting candidate genes, reducing the interval for the BFLS gene to 15.5 cM. Positional candidate genes from the interval between DXS425 and DXS105 include the SOX3 gene, mapped between DXS51(52A) and DXS98(4D-8). SOX3 may have a role in regulating the development of the nervous system. The HMG-box region of this single exon gene was examined by PCR for a deletion and then sequenced. No deviation from normal was observed, excluding mutations in the conserved HMG-box region as the cause of BFLS in this family. 27 refs., 1 fig., 2 tabs.

  4. Modeling Three-Dimensional Chromosome Structures Using Gene Expression Data.

    Science.gov (United States)

    Xiao, Guanghua; Wang, Xinlei; Khodursky, Arkady B

    2011-03-01

    Recent genomic studies have shown that significant chromosomal spatial correlation exists in gene expression of many organisms. Interestingly, coexpression has been observed among genes separated by a fixed interval in specific regions of a chromosome chain, which is likely caused by three-dimensional (3D) chromosome folding structures. Modeling such spatial correlation explicitly may lead to essential understandings of 3D chromosome structures and their roles in transcriptional regulation. In this paper, we explore chromosomal spatial correlation induced by 3D chromosome structures, and propose a hierarchical Bayesian method based on helical structures to formally model and incorporate the correlation into the analysis of gene expression microarray data. It is the first study to quantify and infer 3D chromosome structures in vivo using expression microarrays. Simulation studies show computing feasibility of the proposed method and that, under the assumption of helical chromosome structures, it can lead to precise estimation of structural parameters and gene expression levels. Real data applications demonstrate an intriguing biological phenomenon that functionally associated genes, which are far apart along the chromosome chain, are brought into physical proximity by chromosomal folding in 3D space to facilitate their coexpression. It leads to important biological insight into relationship between chromosome structure and function.

  5. A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure.

    Science.gov (United States)

    Greenbury, Sam F; Johnston, Iain G; Louis, Ard A; Ahnert, Sebastian E

    2014-06-01

    The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here, we introduce a rich, intuitive and biologically realistic genotype-phenotype (GP) map that serves as a model of self-assembling biological structures, such as protein complexes, and remains computationally and analytically tractable. Our GP map arises naturally from the self-assembly of polyomino structures on a two-dimensional lattice and exhibits a number of properties: redundancy (genotypes vastly outnumber phenotypes), phenotype bias (genotypic redundancy varies greatly between phenotypes), genotype component disconnectivity (phenotypes consist of disconnected mutational networks) and shape space covering (most phenotypes can be reached in a small number of mutations). We also show that the mutational robustness of phenotypes scales very roughly logarithmically with phenotype redundancy and is positively correlated with phenotypic evolvability. Although our GP map describes the assembly of disconnected objects, it shares many properties with other popular GP maps for connected units, such as models for RNA secondary structure or the hydrophobic-polar (HP) lattice model for protein tertiary structure. The remarkable fact that these important properties similarly emerge from such different models suggests the possibility that universal features underlie a much wider class of biologically realistic GP maps.

  6. A tractable genotype–phenotype map modelling the self-assembly of protein quaternary structure

    Science.gov (United States)

    Greenbury, Sam F.; Johnston, Iain G.; Louis, Ard A.; Ahnert, Sebastian E.

    2014-01-01

    The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here, we introduce a rich, intuitive and biologically realistic genotype–phenotype (GP) map that serves as a model of self-assembling biological structures, such as protein complexes, and remains computationally and analytically tractable. Our GP map arises naturally from the self-assembly of polyomino structures on a two-dimensional lattice and exhibits a number of properties: redundancy (genotypes vastly outnumber phenotypes), phenotype bias (genotypic redundancy varies greatly between phenotypes), genotype component disconnectivity (phenotypes consist of disconnected mutational networks) and shape space covering (most phenotypes can be reached in a small number of mutations). We also show that the mutational robustness of phenotypes scales very roughly logarithmically with phenotype redundancy and is positively correlated with phenotypic evolvability. Although our GP map describes the assembly of disconnected objects, it shares many properties with other popular GP maps for connected units, such as models for RNA secondary structure or the hydrophobic-polar (HP) lattice model for protein tertiary structure. The remarkable fact that these important properties similarly emerge from such different models suggests the possibility that universal features underlie a much wider class of biologically realistic GP maps. PMID:24718456

  7. Quantitative gene-gene and gene-environment mapping for leaf shape variation using tree-based models

    Science.gov (United States)

    Leaf shape traits have long been a focus of many disciplines, but searching for complex genetic and environmental interactive mechanisms regulating leaf shape variation has not yet been well developed. The question of the respective roles of gene and environment and how they interplay to modulate l...

  8. Linkage disequilibrium blocks, haplotype structure, and htSNPs of human CYP7A1 gene

    Directory of Open Access Journals (Sweden)

    Wan Yu-Jui

    2006-05-01

    Full Text Available Abstract Background Cholesterol 7-alpha-hydroxylase (CYP7A1 is the rate limiting enzyme for converting cholesterol into bile acids. Genetic variations in the CYP7A1 gene have been associated with metabolic disorders of cholesterol and bile acids, including hypercholesterolemia, hypertriglyceridemia, arteriosclerosis, and gallstone disease. Current genetic studies are focused mainly on analysis of a single nucleotide polymorphism (SNP at A-278C in the promoter region of the CYP7A1 gene. Here we report a genetic approach for an extensive analysis on linkage disequilibrium (LD blocks and haplotype structures of the entire CYP7A1 gene and its surrounding sequences in Africans, Caucasians, Asians, Mexican-Americans, and African-Americans. Result The LD patterns and haplotype blocks of CYP7A1 gene were defined in Africans, Caucasians, and Asians using genotyping data downloaded from the HapMap database to select a set of haplotype-tagging SNPs (htSNP. A low cost, microarray-based platform on thin-film biosensor chips was then developed for high-throughput genotyping to study transferability of the HapMap htSNPs to Mexican-American and African-American populations. Comparative LD patterns and haplotype block structure was defined across all test populations. Conclusion A constant genetic structure in CYP7A1 gene and its surrounding sequences was found that may lead to a better design for association studies of genetic variations in CYP7A1 gene with cholesterol and bile acid metabolism.

  9. Genetic analysis and gene fine mapping for a rice novel mutant (rl9(t)) with rolling leaf character

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Leaf shape is an important parameter for ideotype breeding in rice, and the rolling of leaf is also beneficial to efficient ripening of grains. This encourages the explorations of new genes that regulate leaf shape. In this study, genetic analysis and gene mapping were carried out for a novel rolling leaf mutant identified from japonica variety Zhonghua 11. The SSR marker analysis showed that the mutant was controlled by a single recessive gene (rl9(t)) located on chromosome 9. Fine mapping of the Rl9(t) locus was conducted with 30 new STS markers developed around Rl9(t) anchored region based on the sequence diversity between Nipponbare and 93-11. The fine mapping necessitated the contruction of a PAC contig encompassing the Rl9(t) locus, which was delimited to a 42 kb region. This could therefore enhance the cloning of the target gene in further studies.

  10. BodyMap-Xs: anatomical breakdown of 17 million animal ESTs for cross-species comparison of gene expression.

    Science.gov (United States)

    Ogasawara, Osamu; Otsuji, Makiko; Watanabe, Kouji; Iizuka, Takayasu; Tamura, Takuro; Hishiki, Teruyoshi; Kawamoto, Shoko; Okubo, Kousaku

    2006-01-01

    BodyMap-Xs (http://bodymap.jp) is a database for cross-species gene expression comparison. It was created by the anatomical breakdown of 17 million animal expressed sequence tag (EST) records in DDBJ using a sorting program tailored for this purpose. In BodyMap-Xs, users are allowed to compare the expression patterns of orthologous and paralogous genes in a coherent manner. This will provide valuable insights for the evolutionary study of gene expression and identification of a responsive motif for a particular expression pattern. In addition, starting from a concise overview of the taxonomical and anatomical breakdown of all animal ESTs, users can navigate to obtain gene expression ranking of a particular tissue in a particular animal. This method may lead to the understanding of the similarities and differences between the homologous tissues across animal species. BodyMap-Xs will be automatically updated in synchronization with the major update in DDBJ, which occurs periodically.

  11. A gene-based map of the Nod factor-independent Aeschynomene evenia sheds new light on the evolution of nodulation and legume genomes.

    Science.gov (United States)

    Chaintreuil, Clémence; Rivallan, Ronan; Bertioli, David J; Klopp, Christophe; Gouzy, Jérôme; Courtois, Brigitte; Leleux, Philippe; Martin, Guillaume; Rami, Jean-François; Gully, Djamel; Parrinello, Hugues; Séverac, Dany; Patrel, Delphine; Fardoux, Joël; Ribière, William; Boursot, Marc; Cartieaux, Fabienne; Czernic, Pierre; Ratet, Pascal; Mournet, Pierre; Giraud, Eric; Arrighi, Jean-François

    2016-08-01

    Aeschynomene evenia has emerged as a new model legume for the deciphering of the molecular mechanisms of an alternative symbiotic process that is independent of the Nod factors. Whereas most of the research on nitrogen-fixing symbiosis, legume genetics and genomics has so far focused on Galegoid and Phaseolid legumes, A. evenia falls in the more basal and understudied Dalbergioid clade along with peanut (Arachis hypogaea). To provide insights into the symbiotic genes content and the structure of the A. evenia genome, we established a gene-based genetic map for this species. Firstly, an RNAseq analysis was performed on the two parental lines selected to generate a F2 mapping population. The transcriptomic data were used to develop molecular markers and they allowed the identification of most symbiotic genes. The resulting map comprised 364 markers arranged in 10 linkage groups (2n = 20). A comparative analysis with the sequenced genomes of Arachis duranensis and A. ipaensis, the diploid ancestors of peanut, indicated blocks of conserved macrosynteny. Altogether, these results provided important clues regarding the evolution of symbiotic genes in a Nod factor-independent context. They provide a basis for a genome sequencing project and pave the way for forward genetic analysis of symbiosis in A. evenia.

  12. EcoTILLING-based association mapping efficiently delineates functionally relevant natural allelic variants of candidate genes governing agronomic traits in chickpea

    Directory of Open Access Journals (Sweden)

    Deepak eBajaj

    2016-04-01

    Full Text Available The large-scale mining and high-throughput genotyping of novel gene-based allelic variants in natural mapping population are essential for association mapping to identify functionally relevant molecular tags governing useful agronomic traits in chickpea. The present study employs an alternative time-saving, non-laborious and economical pool-based EcoTILLING approach coupled with agarose gel detection assay to discover 1133 novel SNP allelic variants from diverse coding and regulatory sequence components of 1133 transcription factor (TF genes by genotyping in 192 diverse desi and kabuli chickpea accessions constituting a seed weight association panel. Integrating these SNP genotyping data with seed weight field phenotypic information of 192 structured association panel identified eight SNP alleles in the eight TF genes regulating seed weight of chickpea. The associated individual and combination of all SNPs explained 10-15 and 31% phenotypic variation for seed weight, respectively. The EcoTILLING-based large-scale allele mining and genotyping strategy implemented for association mapping is found much effective for a diploid genome crop species like chickpea with narrow genetic base and low genetic polymorphism. This optimized approach thus can be deployed for various genomics-assisted breeding applications with optimal expense of resources in domesticated chickpea. The seed weight-associated natural allelic variants and candidate TF genes delineated have potential to accelerate marker-assisted genetic improvement of chickpea.

  13. Remnants of the Legume Ancestral Genome Preserved in Gene-Rich Regions: Insights from Lupinus angustifolius Physical, Genetic, and Comparative Mapping.

    Science.gov (United States)

    Książkiewicz, Michał; Zielezinski, Andrzej; Wyrwa, Katarzyna; Szczepaniak, Anna; Rychel, Sandra; Karlowski, Wojciech; Wolko, Bogdan; Naganowska, Barbara

    The narrow-leafed lupin (Lupinus angustifolius) was recently considered as a legume reference species. Genetic resources have been developed, including a draft genome sequence, linkage maps, nuclear DNA libraries, and cytogenetic chromosome-specific landmarks. Here, we used a complex approach, involving DNA fingerprinting, sequencing, genetic mapping, and molecular cytogenetics, to localize and analyze L. angustifolius gene-rich regions (GRRs). A L. angustifolius genomic bacterial artificial chromosome (BAC) library was screened with short sequence repeat (SSR)-based probes. Selected BACs were fingerprinted and assembled into contigs. BAC-end sequence (BES) annotation allowed us to choose clones for sequencing, targeting GRRs. Additionally, BESs were aligned to the scaffolds of the genome sequence. The genetic map was supplemented with 35 BES-derived markers, distributed in 14 linkage groups and tagging 37 scaffolds. The identified GRRs had an average gene density of 19.6 genes/100 kb and physical-to-genetic distance ratios of 11 to 109 kb/cM. Physical and genetic mapping was supported by multi-BAC-fluorescence in situ hybridization (FISH), and five new linkage groups were assigned to the chromosomes. Syntenic links to the genome sequences of five legume species (Medicago truncatula, Glycine max, Lotus japonicus, Phaseolus vulgaris, and Cajanus cajan) were identified. The comparative mapping of the two largest lupin GRRs provides novel evidence for ancient duplications in all of the studied species. These regions are conserved among representatives of the main clades of Papilionoideae. Furthermore, despite the complex evolution of legumes, some segments of the nuclear genome were not substantially modified and retained their quasi-ancestral structures. Cytogenetic markers anchored in these regions constitute a platform for heterologous mapping of legume genomes.

  14. Molecular mapping of two semidwarf genes in an indica rice variety Aitaiyin3(Oryza sativa L.)

    Institute of Scientific and Technical Information of China (English)

    Zhao Xiangqiang; Liang Guohua; Zhou Jingsong; Yan Changjie; Cao Xiaoying; Gu Minghong

    2006-01-01

    Genetic analysis established that Aitaiyin3,a dwarf rice variety derived from a semidwarf cultivar Taiyin1,carries two recessive semidwarf genes.By using simple sequence repeat(SSR)markers,we mapped the two semidwarf genes,sd-1 and sd-t2 on chromosomes 1 and 4,respectively.Sd-t2 was thus named because the semidrawf gene sd-t has already been identified from Aitaiyin 2 whose origin could be traced back to Taivin1.The result of the molecular mappingof sd-1 gene revealed it is linked to four SSR markers found on chromosome 1.These markers are:RM297,RM302,RM212,and OSR3 spaced at 4.7 cM,0 cM,0.8cM and 0 cM,respectively.Sd-t2 was found to be located on chromosome 4 using five SSR markers:two markers,SSR332 and RM1305 located proximal to sd-t2 are spaced 11.6 cM,3.8 cM,respectively,while the three distally located primers,RM5633,RM307,and RM401 are separated by distances of 0.4 cM,0.0 cM,and 0.4 cM,respectively.

  15. Physical mapping of the elephant X chromosome: conservation of gene order over 105 million years.

    Science.gov (United States)

    Delgado, Claudia Leticia Rodríguez; Waters, Paul D; Gilbert, Clément; Robinson, Terence J; Graves, Jennifer A Marshall

    2009-01-01

    All therian mammals (eutherians and marsupials) have an XX female/XY male sex chromosome system or some variant of it. The X and Y evolved from a homologous pair of autosomes over the 166 million years since therian mammals diverged from monotremes. Comparing the sex chromosomes of eutherians and marsupials defined an ancient X conserved region that is shared between species of these mammalian clades. However, the eutherian X (and the Y) was augmented by a recent addition (XAR) that is autosomal in marsupials. XAR is part of the X in primates, rodents, and artiodactyls (which belong to the eutherian clade Boreoeutheria), but it is uncertain whether XAR is part of the X chromosome in more distantly related eutherian mammals. Here we report on the gene content and order on the X of the elephant (Loxodonta africana)-a representative of Afrotheria, a basal endemic clade of African mammals-and compare these findings to those of other documented eutherian species. A total of 17 genes were mapped to the elephant X chromosome. Our results support the hypothesis that the eutherian X and Y chromosomes were augmented by the addition of autosomal material prior to eutherian radiation. Not only does the elephant X bear the same suite of genes as other eutherian X chromosomes, but gene order appears to have been maintained across 105 million years of evolution, perhaps reflecting strong constraints posed by the eutherian X inactivation system.

  16. Genetic Analysis and Mapping of the Dominant Dwarfing Gene D-53 in Rice

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The dwarfing gene D-53 is one of a few dominant genes for dwarfing in rice (Oryza sativa L.). In the present study, our genetic analysis confirmed that mutant characteristics including dwarfing, profuse tillering, thin stems and small panicles are all controlled by the dominant D-53 gene. We measured the length of each internode of KL908, a D-53-carrying line, and classified the dwarfism of KL908 into the dn-type. In addition, we measured elongation of the second sheath and α-amylase activity in the endosperm, and we characterized KL908 as a dwarf mutant that was neither gibberellic acid-deficient nor gibberellic acid-insensitive. Using a large F2 population obtained by crossing KL908 with a wild-type variety, NJ6, the D-53 gene was mapped to the terminal region of the short arm of chromosome 11, with one simple sequence repeat marker, Ds3, co-segregating, and the other, K81114, located 0.6 cM away.

  17. Gene mapping of autosomal dominant retinitis pigmentosa in a Chinese family

    Institute of Scientific and Technical Information of China (English)

    DAI Li-li; SUN Da-wei; WANG Zheng; FU Song-bin; HUANG Shang-zhi; ZHANG Zhong-yu; ZENG Guang; PENG Shao-min

    2009-01-01

    Background The autosomal dominant form of retinitis pigmentosa (ADRP) can be caused by mutations in 14 genes and further loci remains to be identified. This study was intended to identify mutations in a Chinese pedigree with ADRP. Methods A large Chinese family with retinitis pigmentosa was collected. The genetic analysis of the family suggested an autosomal dominant pattern. Microsatellite (STR) markers tightly linked to genes known to be responsible for ADRP were selected for linkage analysis. Exons along with adjacent splice junctions of PRPF31 were amplified by polymerase chain reaction (PCR) and screened by direct sequencing.Results The caused gene of ADRP was mapped to 19q13.4 between markers D19S572 and D19S877, with a maximum LOD score of 3.01 at marker D19S418 (recombination fraction=0).Conclusion The affected gene linked to the 19q13.4 in a Chinese family with ADRP, which is different from other mutations at the same loci in other Chinese families.

  18. Mapping of a new gene for brown planthopper resistance in cultivated rice introgressed from Oryza eichingeri

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Wild rice species is an important source of useful genes for cultivated rice improvement. Some accessions of Oryza eichingeri (2n = 24, CC) from Africa confer strong resistance to brown planthopper (BPH), whitebacked planthopper (WBPH) and bacterial blight (BB). In the present study, restriction fragments length polymorphism (RFLP) and simple sequence repeats (SSR) analysis were performed on disomic backcross plants between Oryza sativa (2n = 24, AA) and O. eichingeri in order to identify the presenee of O. eichingeri segments and further to localize BPH-resistant gene. In the introgression lines, 1-6O. eichingeri segments were detected on rice chromosomes 1, 2, 6, or/and 10. The dominant BPH resistant gene, tentatively named Bph13(t), was mapped to chromosome 2, being 6.1 and 5.5 cM away from two microsatellite markers RM240 and RM250, respectively. The transfer and localization of this gene from O. eichingeri will contribute to the improvement of BPH resistance in cultivated rice.``

  19. Transcriptional mapping of a late gene coding for the p12 attachment protein of African swine fever virus.

    OpenAIRE

    1993-01-01

    The transcriptional characterization of the gene coding for the p12 attachment protein of the African swine fever virus is presented. The results obtained have been used to generate the first detailed transcriptional map of an African swine fever virus late gene. Novel experimental evidence indicating the existence of major differences between the mechanisms controlling the transcription of late genes in African swine fever virus and poxviruses is provided.

  20. Gene order data from a model amphibian (Ambystoma: new perspectives on vertebrate genome structure and evolution

    Directory of Open Access Journals (Sweden)

    Voss S Randal

    2006-08-01

    Full Text Available Abstract Background Because amphibians arise from a branch of the vertebrate evolutionary tree that is juxtaposed between fishes and amniotes, they provide important comparative perspective for reconstructing character changes that have occurred during vertebrate evolution. Here, we report the first comparative study of vertebrate genome structure that includes a representative amphibian. We used 491 transcribed sequences from a salamander (Ambystoma genetic map and whole genome assemblies for human, mouse, rat, dog, chicken, zebrafish, and the freshwater pufferfish Tetraodon nigroviridis to compare gene orders and rearrangement rates. Results Ambystoma has experienced a rate of genome rearrangement that is substantially lower than mammalian species but similar to that of chicken and fish. Overall, we found greater conservation of genome structure between Ambystoma and tetrapod vertebrates, nevertheless, 57% of Ambystoma-fish orthologs are found in conserved syntenies of four or more genes. Comparisons between Ambystoma and amniotes reveal extensive conservation of segmental homology for 57% of the presumptive Ambystoma-amniote orthologs. Conclusion Our analyses suggest relatively constant interchromosomal rearrangement rates from the euteleost ancestor to the origin of mammals and illustrate the utility of amphibian mapping data in establishing ancestral amniote and tetrapod gene orders. Comparisons between Ambystoma and amniotes reveal some of the key events that have structured the human genome since diversification of the ancestral amniote lineage.

  1. Self-similarities of periodic structures for a discrete model of a two-gene system

    Energy Technology Data Exchange (ETDEWEB)

    Souza, S.L.T. de, E-mail: thomaz@ufsj.edu.br [Departamento de Física e Matemática, Universidade Federal de São João del-Rei, Ouro Branco, MG (Brazil); Lima, A.A. [Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, MG (Brazil); Caldas, I.L. [Instituto de Física, Universidade de São Paulo, São Paulo, SP (Brazil); Medrano-T, R.O. [Departamento de Ciências Exatas e da Terra, Universidade Federal de São Paulo, Diadema, SP (Brazil); Guimarães-Filho, Z.O. [Aix-Marseille Univ., CNRS PIIM UMR6633, International Institute for Fusion Science, Marseille (France)

    2012-03-12

    We report self-similar properties of periodic structures remarkably organized in the two-parameter space for a two-gene system, described by two-dimensional symmetric map. The map consists of difference equations derived from the chemical reactions for gene expression and regulation. We characterize the system by using Lyapunov exponents and isoperiodic diagrams identifying periodic windows, denominated Arnold tongues and shrimp-shaped structures. Period-adding sequences are observed for both periodic windows. We also identify Fibonacci-type series and Golden ratio for Arnold tongues, and period multiple-of-three windows for shrimps. -- Highlights: ► The existence of noticeable periodic windows has been reported recently for several nonlinear systems. ► The periodic window distributions appear highly organized in two-parameter space. ► We characterize self-similar properties of Arnold tongues and shrimps for a two-gene model. ► We determine the period of the Arnold tongues recognizing a Fibonacci-type sequence. ► We explore self-similar features of the shrimps identifying multiple period-three structures.

  2. Linkage disequilibrium mapping places the gene causing familial Mediterranean fever close to D16S246

    Energy Technology Data Exchange (ETDEWEB)

    Levy, E. N.; Aksentijevich, I.; Pras, E. [National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD (United States)] [and others

    1996-03-01

    This report presents refined genetic mapping data for the gene causing familial Mediterranean fever (FMF), a recessively inherited disorder of inflammation. We sampled 65 Jewish, Armenian, and Arab families and typed them for eight markers from chromosome 16p. Using a new algorithm that permits multipoint calculations for a dense map of markers in consanguineous families, we obtained a maximal LOD score of 49.2 at a location 1.6 cM centromeric to D16S246. A specific haplotype at D16S283-D16S94-D16S246 was found in 76% of Moroccan and 32% of non-Moroccan Jewish carrier chromosomes, but this haplotype was not overrepresented in Armenian or Arab FMF carriers. Moreover, the 2.5-kb allele at D16S246 was significantly associated with FMF in Moroccan and non-Moroccan Jews but not in Armenians or Arabs. Since the Moroccan Jewish community represents a relatively recently established and genetically isolated founder population, we analyzed the Moroccan linkage-disequilibrium data by using Luria-Delbruck formulas and simulations based on a Poisson branching process. These methods place the FMF susceptibility gene within 0.305 cM of D16S246 (2-LOD-unit range 0.02-0.64 cM). 41 refs., 3 figs., 5 tabs.

  3. Comparative gene mapping in cattle, Indian muntjac, and Chinese muntjac by fluorescence in situ hybridization.

    Science.gov (United States)

    Murmann, Andrea E; Mincheva, Antoaneta; Scheuermann, Markus O; Gautier, Mathieu; Yang, Fentang; Buitkamp, Johannes; Strissel, Pamela L; Strick, Reiner; Rowley, Janet D; Lichter, Peter

    2008-11-01

    The Indian muntjac (Muntiacus muntjak vaginalis) has a karyotype of 2n = 6 in the female and 2n = 7 in the male. The karyotypic evolution of Indian muntjac via extensive tandem fusions and several centric fusions are well documented by molecular cytogenetic studies mainly utilizing chromosome paints. To achieve higher resolution mapping, a set of 42 different genomic clones coding for 37 genes and the nucleolar organizer region were used to examine homologies between the cattle (2n = 60), human (2n = 46), Indian muntjac (2n = 6/7) and Chinese muntjac (2n = 46) karyotypes. These genomic clones were mapped by fluorescence in situ hybridization (FISH). Localization of genes on all three pairs of M. m. vaginalis chromosomes and on the acrocentric chromosomes of M. reevesi allowed not only the analysis of the evolution of syntenic regions within the muntjac genus but also allowed a broader comparison of synteny with more distantly related species, such as cattle and human, to shed more light onto the evolving genome organization.

  4. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  5. Structure-performance maps of polymeric, metal, and ceramic matrix composites

    Science.gov (United States)

    Chou, Tsu-Wei; Yang, Jenn-Ming

    1986-09-01

    This paper presents the results of extensive analytical studies of the thermo-elastic properties of unidirectional laminated composites, as well as two-dimensional and three-dimensional textile structural composites with polymeric, metal, and ceramic matrices. Some comparisons of the theoretical predictions with experimental data have been made. By the construction of the structure-performance maps, the effective composite properties based upon various reinforcement forms and fiber and matrix combinations can be easily assessed. The uniqueness of various textile structural reinforcements also has been demonstrated. These comprehensive performance maps can provide the data base necessary for material selections and guidance for future investigations of advanced composites.

  6. Molecular mapping and candidate gene analysis of a new epicuticular wax locus in sorghum (Sorghum bicolor L. Moench).

    Science.gov (United States)

    Uttam, G Anurag; Praveen, M; Rao, Y Venkateswara; Tonapi, Vilas A; Madhusudhana, R

    2017-07-12

    A new epicuticular wax (bloom) locus has been identified and fine mapped to the 207.89 kb genomic region on chromosome 1. A putative candidate gene, Sobic.001G269200, annotated as GDSL-like lipase/acylhydrolase, is proposed as the most probable candidate gene involved in bloom synthesis/deposition. Deposition of epicuticular wax on plant aerial surface is one strategy that plants adapt to reduce non-transpiration water loss. Epicuticular wax (bloom)-less mutants in sorghum with their glossy phenotypes exhibit changes in the accumulation of epicuticular wax on leaf and culm surfaces. We report molecular mapping of a new sorghum locus, bloomless mutant (bm39), involved in epicuticular wax biosynthesis in sorghum. Inheritance studies involving a profusely bloom parent (BTx623) and a spontaneous bloomless mutant (RS647) indicated that the parents differed in a single gene for bloom synthesis. Bloomless was recessive to bloom deposition. Genetic mapping involving F2 and F7 mapping populations in diverse genetic backgrounds (BTx623 × RS647; 296A × RS647 and 27A × RS647) identified and validated the map location of bm39 to a region of 207.89 kb on chromosome 1. SSR markers, Sblm13 and Sblm16, flanked the bm39 locus to a map interval of 0.3 cM on either side. Nine candidate genes were identified, of which Sobic.001G269200 annotated for GDSL-like lipase/acylhydrolase is the most likely gene associated with epicuticular wax deposition. Gene expression analysis in parents, isogenic lines and sets of near isogenic lines also confirmed the reduced expression of the putative candidate gene. The study opens possibilities for a detailed molecular analysis of the gene, its role in epicuticular wax synthesis and deposition, and may help to understand its function in moisture stress tolerance and insect and pathogen resistance in sorghum.

  7. Maps Showing Geology, Structure, and Geophysics of the Central Black Hills, South Dakota

    Science.gov (United States)

    Redden, Jack A.; DeWitt, Ed

    2008-01-01

    This 1:100,000-scale digital geologic map details the complex Early Proterozoic granitic rocks, Early Proterozoic supracrustal metamorphic rocks, and Archean crystalline basement of the Black Hills. The granitic rocks host pegmatite deposits renowned for their feldspar, mica, spodumene, and beryl. The supracrustal rocks host the Homestake gold mine, which produced more than 40 million ounces of gold over a 125-year lifetime. The map documents the Laramide deformation of Paleozoic and Mesozoic cover rocks; and shows the distribution of Laramide plutonic rocks associated with precious-metals deposits. Four 1:300,000-scale maps summarize Laramide structures; Early Proterozoic structures; aeromagnetic anomalies; and gravity anomalies. Three 1:500,000-scale maps show geophysical interpretations of buried Early Proterozoic to Archean rocks in western South Dakota and eastern Wyoming.

  8. Structure and Function of Cytochrome P-450 Genes

    Science.gov (United States)

    1988-01-25

    UNIT Bolling Air Force Base, D.C. 20332 ELEMENT NO. NO. NO. ACCESSION NO. 61102F 2312 A5 11. TITLE (Include Security Clasification ) Structure and...chromatin structure of these genes and to characterize nuclear proteins that bind to the genes. Accesion For hRIS A-RA&I d OVIrC TAB LISUrc’t,:oimnc...nuclear proteins that bind to the genes. ........ .. A. RESEARCH OBJECTIVES The overall goal and the specific aims of this project remain the same as

  9. Mapping beech (Fagus sylvatica L.) forest structure with airborne hyperspectral imagery

    NARCIS (Netherlands)

    Cho, M.A.; Skidmore, A.K.; Sobhan, I.

    2009-01-01

    Estimating forest structural attributes using multispectral remote sensing is challenging because of the saturation of multispectral indices at high canopy cover. The objective of this study was to assess the utility of hyperspectral data in estimating and mapping forest structural parameters includ

  10. Fractal patterns on the onset of coherent structures in a coupled map lattice

    Indian Academy of Sciences (India)

    G Ambika; Kamala Menon

    2002-07-01

    We report the formation of Cantor set-like fractals during the development of coherent structures in a coupled map lattice (CML). The dependence of these structures on the size of the lattice as well as the first three dimensions of the associated fractal patterns are analyzed numerically.

  11. Intriguing structures in iterative maps motivated by N-body problem

    Science.gov (United States)

    Mittal, Ashok Kumar; Gupta, Ashok Kumar

    2011-03-01

    Conventional approaches to modeling any system try to incorporate increasingly realistic features into the model, thereby making it more and more complex. An opposite approach seeks to build simpler and simpler conceptual models capable of capturing some observed features of a system. This trend began with Lorenz, who simplified models of the atmosphere to obtain the Lorenz model consisting of a system of only three equations. Despite the simplicity of these equations, this system displayed surprisingly rich properties, and has been used as a conceptual model in diverse disciplines. Poincare maps help study ordinary differential equations from a qualitative perspective. Several investigators like Henon and Feigenbaum followed this simplification approach. Instead of investigating Poincare maps of realistic systems, they, along with several others, investigated simple maps for their own sake. Despite lack of realism, this approach proved to be very fruitful. A map, as simple as the Logistic map, became an important conceptual modeling paradigm. It provided a tool for understanding bifurcation routes to chaos, which were verified experimentally through various experiments in diverse fields. Coupled map lattices (CML) help explore partial differential equations (PDE). Further simplification led to the introduction of Cellular Automata (CA). These fields continue to be explored with vigor and have given rise to a rich body of knowledge, conceptually useful over a wide spectrum of disciplines. In this paper, we follow the simplification approach for modeling the N-body problem. N-body simulations, say in Gravitation, give rise to filamentary structures. Such structures are observed in the actual observed Galactic distribution. The mechanism for creation of such structures is not well understood. We present a simple iterative dynamical model, motivated by the N-body problem, which, though unrealistic, produces such filamentary structures. This model also exhibits a

  12. QTL analysis and candidate gene mapping for the polyphenol content in cider apple.

    Science.gov (United States)

    Verdu, Cindy F; Guyot, Sylvain; Childebrand, Nicolas; Bahut, Muriel; Celton, Jean-Marc; Gaillard, Sylvain; Lasserre-Zuber, Pauline; Troggio, Michela; Guilet, David; Laurens, François

    2014-01-01

    Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.

  13. QTL analysis and candidate gene mapping for the polyphenol content in cider apple.

    Directory of Open Access Journals (Sweden)

    Cindy F Verdu

    Full Text Available Polyphenols have favorable antioxidant potential on human health suggesting that their high content is responsible for the beneficial effects of apple consumption. They control the quality of ciders as they predominantly account for astringency, bitterness, color and aroma. In this study, we identified QTLs controlling phenolic compound concentrations and the average polymerization degree of flavanols in a cider apple progeny. Thirty-two compounds belonging to five groups of phenolic compounds were identified and quantified by reversed phase liquid chromatography on both fruit extract and juice, over three years. The average polymerization degree of flavanols was estimated in fruit by phloroglucinolysis coupled to HPLC. Parental maps were built using SSR and SNP markers and used for the QTL analysis. Sixty-nine and 72 QTLs were detected on 14 and 11 linkage groups of the female and male maps, respectively. A majority of the QTLs identified in this study are specific to this population, while others are consistent with previous studies. This study presents for the first time in apple, QTLs for the mean polymerization degree of procyanidins, for which the mechanisms involved remains unknown to this day. Identification of candidate genes underlying major QTLs was then performed in silico and permitted the identification of 18 enzymes of the polyphenol pathway and six transcription factors involved in the apple anthocyanin regulation. New markers were designed from sequences of the most interesting candidate genes in order to confirm their co-localization with underlying QTLs by genetic mapping. Finally, the potential use of these QTLs in breeding programs is discussed.

  14. Development of genomic SSR markers for fingerprinting lettuce (Lactuca sativa L.) cultivars and mapping genes.

    Science.gov (United States)

    Rauscher, Gilda; Simko, Ivan

    2013-01-22

    Lettuce (Lactuca sativa L.) is the major crop from the group of leafy vegetables. Several types of molecular markers were developed that are effectively used in lettuce breeding and genetic studies. However only a very limited number of microsattelite-based markers are publicly available. We have employed the method of enriched microsatellite libraries to develop 97 genomic SSR markers. Testing of newly developed markers on a set of 36 Lactuca accession (33 L. sativa, and one of each L. serriola L., L. saligna L., and L. virosa L.) revealed that both the genetic heterozygosity (UHe = 0.56) and the number of loci per SSR (Na = 5.50) are significantly higher for genomic SSR markers than for previously developed EST-based SSR markers (UHe = 0.32, Na = 3.56). Fifty-four genomic SSR markers were placed on the molecular linkage map of lettuce. Distribution of markers in the genome appeared to be random, with the exception of possible cluster on linkage group 6. Any combination of 32 genomic SSRs was able to distinguish genotypes of all 36 accessions. Fourteen of newly developed SSR markers originate from fragments with high sequence similarity to resistance gene candidates (RGCs) and RGC pseudogenes. Analysis of molecular variance (AMOVA) of L. sativa accessions showed that approximately 3% of genetic diversity was within accessions, 79% among accessions, and 18% among horticultural types. The newly developed genomic SSR markers were added to the pool of previously developed EST-SSRs markers. These two types of SSR-based markers provide useful tools for lettuce cultivar fingerprinting, development of integrated molecular linkage maps, and mapping of genes.

  15. Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

    Directory of Open Access Journals (Sweden)

    de Miguel Marina

    2012-10-01

    Full Text Available Abstract Background Pinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15 belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers. Results We obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency. Conclusions This study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

  16. A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block

    Directory of Open Access Journals (Sweden)

    Ma Wujun

    2010-05-01

    Full Text Available Abstract Background The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features. Results BAC shotgun sequencing of the hexaploid wheat (Triticum aestivum cv. Chinese Spring genome has been used to assemble a group of 15 wheat BACs from the chromosome 3B physical map FPC contig ctg1034 into a 783,553 bp genomic sequence. This ctg1034 sequence was annotated for biological features such as genes and transposable elements. A three-gene island was identified among >80% repetitive DNA sequence. Using bioinformatics analysis there were no observable similarity in their gene functions. The ctg1034 gene island also displayed complete conservation of gene order and orientation with syntenic gene islands found in publicly available genome sequences of Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays, even though the intergenic space and introns were divergent. Conclusion We propose that ctg1034 is located within the heterochromatic C-band region of deletion bin 3BL7 based on the identification of heterochromatic tandem repeats and presence of significant matches to chromodomain-containing gypsy LTR retrotransposable elements. We also speculate that this location, among other highly repetitive sequences, may account for the relative stability in gene order and

  17. A novel color image encryption scheme using alternate chaotic mapping structure

    Science.gov (United States)

    Wang, Xingyuan; Zhao, Yuanyuan; Zhang, Huili; Guo, Kang

    2016-07-01

    This paper proposes an color image encryption algorithm using alternate chaotic mapping structure. Initially, we use the R, G and B components to form a matrix. Then one-dimension logistic and two-dimension logistic mapping is used to generate a chaotic matrix, then iterate two chaotic mappings alternately to permute the matrix. For every iteration, XOR operation is adopted to encrypt plain-image matrix, then make further transformation to diffuse the matrix. At last, the encrypted color image is obtained from the confused matrix. Theoretical analysis and experimental results has proved the cryptosystem is secure and practical, and it is suitable for encrypting color images.

  18. Structure and Evolution of Mediterranean Forest Research: A Science Mapping Approach

    OpenAIRE

    Pierfrancesco Nardi; Giovanni Di Matteo; Marc Palahi; Giuseppe Scarascia Mugnozza

    2016-01-01

    This study aims at conducting the first science mapping analysis of the Mediterranean forest research in order to elucidate its research structure and evolution. We applied a science mapping approach based on co-term and citation analyses to a set of scientific publications retrieved from the Elsevier's Scopus database over the period 1980-2014. The Scopus search retrieved 2,698 research papers and reviews published by 159 peer-reviewed journals. The total number of publications was around 1%...

  19. Spatio-Temporal Story Mapping Animation Based On Structured Causal Relationships Of Historical Events

    Science.gov (United States)

    Inoue, Y.; Tsuruoka, K.; Arikawa, M.

    2014-04-01

    In this paper, we proposed a user interface that displays visual animations on geographic maps and timelines for depicting historical stories by representing causal relationships among events for time series. We have been developing an experimental software system for the spatial-temporal visualization of historical stories for tablet computers. Our proposed system makes people effectively learn historical stories using visual animations based on hierarchical structures of different scale timelines and maps.

  20. Mapping Out the Structure of a Spinach Light-Harvester

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    @@ The major light-harvesting complex of photosystem Ⅱ(LHC-Ⅱ) serves as the principal solar energy collector in the photosynthesis of green plants and presumably also functions in photoprotection under high-light conditions. Many of its structures were revealed by a work of a 3.2A electron crystallographic model of LHC-Ⅱ in 1994. Since then researchers have eagerly awaited a higher-resolution structure to extend knowledge of the light harvesting and energy transfer processes involved in photosynthesis to the level of full atomic data.

  1. Mapping relational database into OWL Structure with data semantic preservation

    CERN Document Server

    Gherabi, Noreddine; Bahaj, Mohamed

    2012-01-01

    This paper proposes a solution for migrating an RDB into Web semantic. The solution takes an existing RDB as input, and extracts its metadata representation (MTRDB). Based on the MTRDB, a Canonical Data Model (CDM) is generated. Finally, the structure of the classification scheme in the CDM model is converted into OWL ontology and the recordsets of database are stored in owl document. A prototype has been implemented, which migrates a RDB into OWL structure, for demonstrate the practical applicability of our approach by showing how the results of reasoning of this technique can help improve the Web systems.

  2. Gathering structured reflection in the furniture business by Trend Mapping

    DEFF Research Database (Denmark)

    Frei, Andrea Erika; Eriksen, Kaare Riise

    2015-01-01

    Setting up the direction for new product designs in the furniture business can be more or less structured and in many situations the idea for new design concepts, constructions, details, coloring or choice of material are directed by random input from retailers or external designers or from...... studying trend agency reports besides considering other matters like new market strategies etc. In this paper the authors describe an attempt to create a richer discussion among a manufacturer and its retail partners by structured play/interviews using research data collected by design students...

  3. Increased complexity of gene structure and base composition in vertebrates

    Institute of Scientific and Technical Information of China (English)

    Ying Wu; Huizhong Yuan; Shengjun Tan; Jian-Qun Chen; Dacheng Tian; Haiwang Yang

    2011-01-01

    How the structure and base composition of genes changed with the evolution of vertebrates remains a puzzling question. Here we analyzed 895 orthologous protein-coding genes in six multicellular animals: human, chicken, zebrafish, sea squirt, fruit fly, and worm. Our analyses reveal that many gene regions, particularly intron and 3' UTR, gradually expanded throughout the evolution of vertebrates from their invertebrate ancestors, and that the number of exons per gene increased. Studies based on all protein-coding genes in each genome provide consistent results.We also find that GC-content increased in many gene regions (especially 5' UTR) in the evolution of endotherms, except in coding-exons.Analysis of individual genomes shows that 3′ UTR demonstrated stronger length and CC-content correlation with intron than 5' UTR, and gene with large intron in all six species demonstrated relatively similar GC-content. Our data indicates a great increase in complexity in vertebrate genes and we propose that the requirement for morphological and functional changes is probably the driving force behind the evolution of structure and base composition complexity in multicellular animal genes.

  4. Fine mapping of the MLK-3 gene within 11q13 and its exclusion as the MEN1 susceptibility gene.

    Science.gov (United States)

    Lassam, N J; Lin, Z; Shennan, M G; Courseaux, A; Teh, B T; Gaudray, P; Larsson, C

    1997-06-01

    MLK-3 kinase is a widely expressed serine/ threonine kinase that bears multiple protein interaction domains and regulates signals mediated by the stress-responsive pathway. Thus, MLK-3 signaling affects numerous cellular processes, raising the possibility that MLK-3 might play a role in oncogenesis. In this report, we describe the fine mapping of the MLK-3 gene within the 11q13.1 chromosomal region. By integrating data from somatic cell hybrids and double color fluorescence in situ hybridization on metaphase chromosomes and DNA fibers. MLK-3 has been assigned approximately 1 Mb telomeric of PYGM, close to the D11S546 locus. Since the MEN1 susceptibility locus is also located within the 11q13.1 region, we have carried out Southern and Northern blot analyses, as well as protein truncation assays to establish whether abnormalities in MLK-3 lead to the development of this familial cancer syndrome. Our observations exclude MLK-3 as the MEN1 gene.

  5. Genetic mapping of stem rust resistance gene Sr13 in tetraploid wheat (Triticum turgidum ssp. durum L.).

    Science.gov (United States)

    Simons, Kristin; Abate, Zewdie; Chao, Shiaoman; Zhang, Wenjun; Rouse, Matt; Jin, Yue; Elias, Elias; Dubcovsky, Jorge

    2011-02-01

    Wheat stem rust caused by Puccinia graminis f. sp. tritici, can cause significant yield losses. To combat the disease, breeders have deployed resistance genes both individually and in combinations to increase resistance durability. A new race, TTKSK (Ug99), identified in Uganda in 1999 is virulent on most of the resistance genes currently deployed, and is rapidly spreading to other regions of the world. It is therefore important to identify, map, and deploy resistance genes that are still effective against TTKSK. One of these resistance genes, Sr13, was previously assigned to the long arm of chromosome 6A, but its precise map location was not known. In this study, the genome location of Sr13 was determined in four tetraploid wheat (T. turgidum ssp. durum) mapping populations involving the TTKSK resistant varieties Kronos, Kofa, Medora and Sceptre. Our results showed that resistance was linked to common molecular markers in all four populations, suggesting that these durum lines carry the same resistance gene. Based on its chromosome location and infection types against different races of stem rust, this gene is postulated to be Sr13. Sr13 was mapped within a 1.2-2.8 cM interval (depending on the mapping population) between EST markers CD926040 and BE471213, which corresponds to a 285-kb region in rice chromosome 2, and a 3.1-Mb region in Brachypodium chromosome 3. These maps will be the foundation for developing high-density maps, identifying diagnostic markers, and positional cloning of Sr13.

  6. Comments on the Bifurcation Structure of 1D Maps

    DEFF Research Database (Denmark)

    Belykh, V.N.; Mosekilde, Erik

    1997-01-01

    -within-a-box structure of the total bifurcation set. This presents a picture in which the homoclinic orbit bifurcations act as a skeleton for the bifurcational set. At the same time, experimental results on continued subharmonic generation for piezoelectrically amplified sound waves, predating the Feigenbaum theory...

  7. Cognitive governance, cognitive mapping and cognitive conflicts: Structural analysis with the MICMAC method

    Directory of Open Access Journals (Sweden)

    Garoui Nassreddine

    2014-12-01

    Full Text Available This research aims to achieve a better understanding of the modes of conceptualization and thinking on issues of governance. It is part of a cognitive approach, to our knowledge unprecedented. This research has shown that the mapping concepts of governance can provide the original performance and meaningful. The purpose was to plot the thought of governance actors in the form of a cognitive map and analyze it. The results highlighted the relative importance of the concepts they used, the dimensions from which they structured more or less consciously, here own thoughts, and the nature and characteristics of the concepts they considered primarily as an explanation or consequences. They allowed characterizing very special or very precise structure and content of the thought of these actors. The construction of collective cognitive maps is to help structure the relationship between governance actors in the sense that it will detect the conflict relations of cognitive order. The cognitive map is by definition a representation of mental models of actors on any topic. Actors of governance do not have the same definitions of the concepts of governance that represents for us a sort of cognitive conflict and hence through cognitive mapping can map the concentration of these conflicts and we are still looking for more to show the effectiveness governance mechanisms to resolve these conflicts.

  8. Fine mapping of the rice bacterial blight resistance gene Xa-4 and its co-segregation marker

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    An F2 population developed from the Xa-4 near isogenic lines,IR24 and IRBB4,was used for fine mapping of the rice bacterial blight resistance gene,Xa-4.Some restriction fragment length polymorphism (RFLP) markers on the high-density map constructed by Harushima et al.and the amplified DNA fragments homologous to the conserved domains of plant disease resistance (R) genes were used to construct the genetic linkage map around the gene Xa-4 by scoring susceptible individuals in the population.Xa-4 was mapped between the RFLP marker G181 and the polymerase chain reaction (PCR) marker M55.The R gene homologous fragment marker RS13 was found co-segregating with Xa-4 by analyzing all the plants in the population.This result opened an approach to map-based cloning of this gene,and marker RS13 can be applied to molecular marker-assisted selection of Xa-4 in rice breeding programs.

  9. Fine Mapping of Virescent Leaf Gene v-1 in Cucumber (Cucumis sativus L.

    Directory of Open Access Journals (Sweden)

    Han Miao

    2016-09-01

    Full Text Available Leaf color mutants are common in higher plants that can be used as markers in crop breeding or as an important tool in understanding regulatory mechanisms in chlorophyll biosynthesis and chloroplast development. In virescent leaf mutants, young leaves are yellow in color, which gradually return to normal green when the seedlings grow large. In the present study, we conducted phenotypic characterization and genetic mapping of the cucumber virescent leaf mutant 9110Gt conferred by the v-1 locus. Total chlorophyll and carotenoid content in 9110Gt was reduced by 44% and 21%, respectively, as compared with its wild type parental line 9110G. Electron microscopic investigation revealed fewer chloroplasts per cell and thylakoids per chloroplast in 9110Gt than in 9110G. Fine genetic mapping allowed for the assignment of the v-1 locus to a 50.4 kb genomic DNA region in chromosome 6 with two flanking markers that were 0.14 and 0.16 cM away from v-1, respectively. Multiple lines of evidence supported CsaCNGCs as the only candidate gene for the v-1 locus, which encoded a cyclic-nucleotide-gated ion channel protein. A single nucleotide change in the promoter region of v-1 seemed to be associated with the virescent color change in 9110Gt. Real-time PCR revealed significantly lower expression of CsaCNGCs in the true leaves of 9110Gt than in 9110G. This was the first report that connected the CsaCNGCs gene to virescent leaf color change, which provided a useful tool to establish linkages among virescent leaf color change, chloroplast development, chlorophyll biosynthesis, and the functions of the CsaCNGCs gene.

  10. Use of SNPs to determine the breakpoints of complex deficiencies, facilitating gene mapping in Caenorhabditis elegans

    Directory of Open Access Journals (Sweden)

    Hoffmann Melissa

    2005-05-01

    Full Text Available Abstract Background Genetic deletions or deficiencies have been used for gene mapping and discovery in various organisms, ranging from the nematode Caenorhabditis elegans all the way to humans. One problem with large deletions is the determination of the location of their breakpoints. This is exacerbated in the case of complex deficiencies that delete a region of the genome, while retaining some of the intervening sequence. Previous methods, using genetic complementation or cytology were hampered by low marker density and were consequently not very precise at positioning the breakpoints of complex deficiencies. The identification of increasing numbers of Single Nucleotide Polymorphisms (SNPs has resulted in the use of these as genetic markers, and consequently in their utilization for defining the breakpoints of deletions using molecular biology methods. Results Here, we show that SNPs can be used to help position the breakpoints of a complex deficiency in C. elegans. The technique uses a combination of genetic crosses and molecular biology to generate robust and highly reproducible results with strong internal controls when trying to determine the breakpoints of deficiencies. The combined use of this technique and standard genetic mapping allowed us to rapidly narrow down the region of interest in our attempts to clone a gene. Conclusion Unlike previous methods used to locate deficiency breakpoints, our technique has the advantage of not being limited by the amount of starting material. It also incorporates internal controls to eliminate false positives and negatives. The technique can also easily be adapted for use in other organisms in which both genetic deficiencies and SNPs are available, thereby aiding gene discovery in these other models.

  11. Genomic and protein structural maps of adaptive evolution of human influenza A virus to increased virulence in the mouse.

    Directory of Open Access Journals (Sweden)

    Jihui Ping

    Full Text Available Adaptive evolution is characterized by positive and parallel, or repeated selection of mutations. Mouse adaptation of influenza A virus (IAV produces virulent mutants that demonstrate positive and parallel evolution of mutations in the hemagglutinin (HA receptor and non-structural protein 1 (NS1 interferon antagonist genes. We now present a genomic analysis of all 11 genes of 39 mouse adapted IAV variants from 10 replicate adaptation experiments. Mutations were mapped on the primary and structural maps of each protein and specific mutations were validated with respect to virulence, replication, and RNA polymerase activity. Mouse adapted (MA variants obtained after 12 or 20-21 serial infections acquired on average 5.8 and 7.9 nonsynonymous mutations per genome of 11 genes, respectively. Among a total of 115 nonsynonymous mutations, 51 demonstrated properties of natural selection including 27 parallel mutations. The greatest degree of parallel evolution occurred in the HA receptor and ribonucleocapsid components, polymerase subunits (PB1, PB2, PA and NP. Mutations occurred in host nuclear trafficking factor binding sites as well as sites of virus-virus protein subunit interaction for NP, NS1, HA and NA proteins. Adaptive regions included cap binding and endonuclease domains in the PB2 and PA polymerase subunits. Four mutations in NS1 resulted in loss of binding to the host cleavage and polyadenylation specificity factor (CPSF30 suggesting that a reduction in inhibition of host gene expression was being selected. The most prevalent mutations in PB2 and NP were shown to increase virulence but differed in their ability to enhance replication and demonstrated epistatic effects. Several positively selected RNA polymerase mutations demonstrated increased virulence associated with >300% enhanced polymerase activity. Adaptive mutations that control host range and virulence were identified by their repeated selection to comprise a defined model for

  12. Gene-based and semantic structure of the Gene Ontology as a complex network

    Science.gov (United States)

    Coronnello, Claudia; Tumminello, Michele; Miccichè, Salvatore

    2016-09-01

    The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The Gene Ontology (GO) is constantly evolving over time. The information accumulated time-by-time and included in the GO is encoded in the definition of terms and in the setting up of semantic relations amongst terms. Here we investigate the Gene Ontology from a complex network perspective. We consider the semantic network of terms naturally associated with the semantic relationships provided by the Gene Ontology consortium. Moreover, the GO is a natural example of bipartite network of terms and genes. Here we are interested in studying the properties of the projected network of terms, i.e. a gene-based weighted network of GO terms, in which a link between any two terms is set if at least one gene is annotated in both terms. One aim of the present paper is to compare the structural properties of the semantic and the gene-based network. The relative importance of terms is very similar in the two networks, but the community structure changes. We show that in some cases GO terms that appear to be distinct from a semantic point of view are instead connected, and appear in the same community when considering their gene content. The identification of such gene-based communities of terms might therefore be the basis of a simple protocol aiming at improving the semantic structure of GO. Information about terms that share large gene content might also be important from a biomedical point of view, as it might reveal how genes over-expressed in a certain term also affect other biological processes, molecular functions and cellular components not directly linked according to GO semantics.

  13. 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.

  14. 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.

  15. Enhancing the usability and performance of structured association mapping algorithms using automation, parallelization, and visualization in the GenAMap software system

    Directory of Open Access Journals (Sweden)

    Curtis Ross E

    2012-04-01

    Full Text Available Abstract Background Structured association mapping is proving to be a powerful strategy to find genetic polymorphisms associated with disease. However, these algorithms are often distributed as command line implementations that require expertise and effort to customize and put into practice. Because of the difficulty required to use these cutting-edge techniques, geneticists often revert to simpler, less powerful methods. Results To make structured association mapping more accessible to geneticists, we have developed an automatic processing system called Auto-SAM. Auto-SAM enables geneticists to run structured association mapping algorithms automatically, using parallelization. Auto-SAM includes algorithms to discover gene-networks and find population structure. Auto-SAM can also run popular association mapping algorithms, in addition to five structured association mapping algorithms. Conclusions Auto-SAM is available through GenAMap, a front-end desktop visualization tool. GenAMap and Auto-SAM are implemented in JAVA; binaries for GenAMap can be downloaded from http://sailing.cs.cmu.edu/genamap.

  16. Gene structure and chromosomal localization of plasma kallikrein

    Energy Technology Data Exchange (ETDEWEB)

    Beaubien, G.; Mbikay, M.; Chretien, M.; Seidah, N.G. (Clinical Research Institute of Montreal, Quebec (Canada)); Rosinski-Chupin, I. (Inst. Pasteur, Paris (France)); Mattei, M.G. (Groupe hospitalier de a Timone, Marseille (France))

    1991-02-12

    Plasma kallikrein (Fletcher factor) is a hepatic serine proteinase that participates in the early phase of blood coagulation. From two genomic libraries, the authors succeeded to isolate four overlapping clones representing the entire rat plasma kallikrein gene. Using selective DNA sequencing, polymerase chain reactions, and restriction mapping, the authors demonstrated that the gene for rat plasma kallikrein was 22 kb in length. Similar to human factor XI the authors also found that the plasma kallikrein gene is composed of 15 exons and 14 introns. A potential transcription initiation step was determined by a novel application of the polymerase chain reaction technique. Computer analysis of the 5{prime}-promoter region of this gene revealed some putative control elements that might regulate the rat plasma kallikrein gene expression. These data and the results of chromosomal localization reported in the present study for mouse (chromosome 8) and human (chromosome 4) plasma kallikrein genes strongly corroborate a genic duplication event from a common ancestor to both plasma kallikrein and factor XI.

  17. Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean

    Science.gov (United States)

    Burt, Andrew J.; William, H. Manilal; Perry, Gregory; Khanal, Raja; Pauls, K. Peter; Kelly, James D.; Navabi, Alireza

    2015-01-01

    Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris). Alleles at the Co–4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08) where Co–4 is localized. Three SCAR markers with known linkage to Co–4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK–4 loci found in previous studies. It is possible that the Co–4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases. PMID:26431031

  18. Candidate Gene Identification with SNP Marker-Based Fine Mapping of Anthracnose Resistance Gene Co-4 in Common Bean.

    Directory of Open Access Journals (Sweden)

    Andrew J Burt

    Full Text Available Anthracnose, caused by Colletotrichum lindemuthianum, is an important fungal disease of common bean (Phaseolus vulgaris. Alleles at the Co-4 locus confer resistance to a number of races of C. lindemuthianum. A population of 94 F4:5 recombinant inbred lines of a cross between resistant black bean genotype B09197 and susceptible navy bean cultivar Nautica was used to identify markers associated with resistance in bean chromosome 8 (Pv08 where Co-4 is localized. Three SCAR markers with known linkage to Co-4 and a panel of single nucleotide markers were used for genotyping. A refined physical region on Pv08 with significant association with anthracnose resistance identified by markers was used in BLAST searches with the genomic sequence of common bean accession G19833. Thirty two unique annotated candidate genes were identified that spanned a physical region of 936.46 kb. A majority of the annotated genes identified had functional similarity to leucine rich repeats/receptor like kinase domains. Three annotated genes had similarity to 1, 3-β-glucanase domains. There were sequence similarities between some of the annotated genes found in the study and the genes associated with phosphoinositide-specific phosphilipases C associated with Co-x and the COK-4 loci found in previous studies. It is possible that the Co-4 locus is structured as a group of genes with functional domains dominated by protein tyrosine kinase along with leucine rich repeats/nucleotide binding site, phosphilipases C as well as β-glucanases.

  19. Gathering structured reflection in the furniture business by Trend Mapping

    DEFF Research Database (Denmark)

    Frei, Andrea Erika; Eriksen, Kaare Riise

    2015-01-01

    studying trend agency reports besides considering other matters like new market strategies etc. In this paper the authors describe an attempt to create a richer discussion among a manufacturer and its retail partners by structured play/interviews using research data collected by design students...... at an international furniture fair. The experiment was developed and carried out by design engineering students and design researchers in collaboration with a furniture manufacturer and the results and methodology are presented and discussed in this paper.......Setting up the direction for new product designs in the furniture business can be more or less structured and in many situations the idea for new design concepts, constructions, details, coloring or choice of material are directed by random input from retailers or external designers or from...

  20. Determination of contact maps in proteins: A combination of structural and chemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw (Poland); Gómez-Sicilia, Àngel [Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid (Spain); Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/Faraday 9, 28049 Cantoblanco (Madrid) (Spain)

    2015-12-28

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.

  1. Mapping acute systemic effects of inhaled particulate matter and ozone: multiorgan gene expression and glucocorticoid activity.

    Science.gov (United States)

    Thomson, Errol M; Vladisavljevic, Djordje; Mohottalage, Susantha; Kumarathasan, Prem; Vincent, Renaud

    2013-09-01

    Recent epidemiological studies have demonstrated associations between air pollution and adverse effects that extend beyond respiratory and cardiovascular disease, including low birth weight, appendicitis, stroke, and neurological/neurobehavioural outcomes (e.g., neurodegenerative disease, cognitive decline, depression, and suicide). To gain insight into mechanisms underlying such effects, we mapped gene profiles in the lungs, heart, liver, kidney, spleen, cerebral hemisphere, and pituitary of male Fischer-344 rats immediately and 24h after a 4-h exposure by inhalation to particulate matter (0, 5, and 50mg/m(3) EHC-93 urban particles) and ozone (0, 0.4, and 0.8 ppm). Pollutant exposure provoked differential expression of genes involved in a number of pathways, including antioxidant response, xenobiotic metabolism, inflammatory signalling, and endothelial dysfunction. The mRNA profiles, while exhibiting some interorgan and pollutant-specific differences, were remarkably similar across organs for a set of genes, including increased expression of redox/glucocorticoid-sensitive genes and decreased expression of inflammatory genes, suggesting a possible hormonal effect. Pollutant exposure increased plasma levels of adrenocorticotropic hormone and the glucocorticoid corticosterone, confirming activation of the hypothalamic-pituitary-adrenal axis, and there was a corresponding increase in markers of glucocorticoid activity. Although effects were transient and presumably represent an adaptive response to acute exposure in these healthy animals, chronic activation and inappropriate regulation of the hypothalamic-pituitary-adrenal axis are associated with adverse neurobehavioral, metabolic, immune, developmental, and cardiovascular effects. The experimental data are consistent with epidemiological associations of air pollutants with extrapulmonary health outcomes and suggest a mechanism through which such health effects may be induced.

  2. Positional and functional mapping of a neuroblastoma differentiation gene on chromosome 11

    Directory of Open Access Journals (Sweden)

    Bader Scott

    2005-07-01

    Full Text Available Abstract Background Loss of chromosome 11q defines a subset of high-stage aggressive neuroblastomas. Deletions are typically large and mapping efforts have thus far not lead to a well defined consensus region, which hampers the identification of positional candidate tumour suppressor genes. In a previous study, functional evidence for a neuroblastoma suppressor gene on chromosome 11 was obtained through microcell mediated chromosome transfer, indicated by differentiation of neuroblastoma cells with loss of distal 11q upon introduction of chromosome 11. Interestingly, some of these microcell hybrid clones were shown to harbour deletions in the transferred chromosome 11. We decided to further exploit this model system as a means to identify candidate tumour suppressor or differentiation genes located on chromosome 11. Results In a first step, we performed high-resolution arrayCGH DNA copy-number analysis in order to evaluate the chromosome 11 status in the hybrids. Several deletions in both parental and transferred chromosomes in the investigated microcell hybrids were observed. Subsequent correlation of these deletion events with the observed morphological changes lead to the delineation of three putative regions on chromosome 11: 11q25, 11p13->11p15.1 and 11p15.3, that may harbour the responsible differentiation gene. Conclusion Using an available model system, we were able to put forward some candidate regions that may be involved in neuroblastoma. Additional studies will be required to clarify the putative role of the genes located in these chromosomal segments in the observed differentiation phenotype specifically or in neuroblastoma pathogenesis in general.

  3. Three-dimensional mapping of microcircuit correlation structure

    Directory of Open Access Journals (Sweden)

    R. James eCotton

    2013-10-01

    Full Text Available Great progress has been made towards understanding the properties of single neurons, yet the principles underlying interactions between neurons remain poorly understood. Given that connectivity in the neocortex is locally dense through both horizontal and vertical con-nections, it is of particular importance to characterize the activity structure of local popula-tions of neurons arranged in three dimensions. However, techniques for simultaneously measuring microcircuit activity are lacking. We developed an in vivo 3D high-speed, ran-dom-access two-photon microscope that is capable of simultaneous 3D motion tracking. This allows imaging from hundreds of neurons at several hundred Hz, while monitoring tissue movement. Given that motion will induce common artifacts across the population, accurate motion tracking is absolutely necessary for studying population activity with ran-dom-access based imaging methods. We demonstrate the potential of this imaging tech-nique by measuring the correlation structure of large populations of nearby neurons in the mouse visual cortex, and find that the microcircuit correlation structure is stimulus-dependent. Three-dimensional random access multiphoton imaging with concurrent mo-tion tracking provides a novel powerful method to characterize the microcircuit activity in vivo.

  4. Identification and genetic mapping of a homeobox gene to the 4p16. 1 region of human chromosome 4

    Energy Technology Data Exchange (ETDEWEB)

    Stadler, H.S.; Padanilam, B.J.; Solursh, M. (Univ. of Iowa, Iowa City (United States)); Buetow, K. (Fox Chase Cancer Center, Philadelphia, PA (United States)); Murray, J.C. (Univ. of Iowa Hospitals and Clinics, Iowa City (United States))

    1992-12-01

    A human craniofacial cDNA library was screened with a degenerate oligonucleotide probe based on the conserved third helix of homeobox genes. From this screening, we identified a homeobox gene, H6, which shared only 57-65% amino acid identity to previously reported homeodomains. H6 was physically mapped to the 4P16.1 region by using somatic cell hybrids containing specific deletions of human chromosome 4. Linkage data from a single-stranded conformational polymorphism derived from the 3[prime] untranslated region of the H6 cDNA placed this homeobox gene more than 20 centimorgans proximal of the previously mapped HOX7 gene on chromosome 4. Identity comparisons of the H6 Homeodomain with previously reported homeodomains reveal the highest identities to be with the Nk class of homeobox genes in Drosophila melanogaster. 53 refs., 5 figs., 2 tabs.

  5. Identification and genetic mapping of a homeobox gene to the 4p16.1 region of human chromosome 4.

    Science.gov (United States)

    Stadler, H S; Padanilam, B J; Buetow, K; Murray, J C; Solursh, M

    1992-12-01

    A human craniofacial cDNA library was screened with a degenerate oligonucleotide probe based on the conserved third helix of homeobox genes. From this screening, we identified a homeobox gene, H6, which shared only 57-65% amino acid identity to previously reported homeodomains. H6 was physically mapped to the 4p16.1 region by using somatic cell hybrids containing specific deletions of human chromosome 4. Linkage data from a single-stranded conformational polymorphism derived from the 3' untranslated region of the H6 cDNA placed this homeobox gene more than 20 centimorgans proximal of the previously mapped HOX7 gene on chromosome 4. Identity comparisons of the H6 homeodomain with previously reported homeodomains reveal the highest identities to be with the Nk class of homeobox genes in Drosophila melanogaster.

  6. A simple method for the design of tension structures combining topological mapping and nonlinear structural analysis

    Directory of Open Access Journals (Sweden)

    Jurado-Piña, R.

    2014-12-01

    Full Text Available When designing a tension structure the shape is not known at the beginning of the process. Form-finding methods allow the designer to obtain an initial shape from given boundary conditions. Several form-finding methods for tension structures are already available in the technical literature; all of them posses certain limitations and drawbacks and no single method is optimal for all problems. The engineer may select the proper combination of methods best suited to the designer’s needs. In this paper it is proposed a combined method to achieve satisfactory equilibrium configurations for fabric tension structures. The force density method (FDM implemented with topological mapping (TM is used as a search engine for the preliminary design, and a procedure that employs nonlinear structural analysis is proposed for final refinement of the initial equilibrium configuration hence allowing the use of the same analysis tool for both refinement of the solution and analysis under loading.Al diseñar una estructura tensada la forma inicial es normalmente desconocida. Los métodos de búsqueda de forma permiten al ingeniero obtener una geometría inicial dadas unas condiciones de contorno. Existen diferentes métodos de búsqueda de formas de equilibrio, pero todos tienen limitaciones y no existe uno único óptimo para cualquier tipo de problema. El ingeniero debe elegir la combinación de métodos que mejor se adapte a sus necesidades. En este artículo se propone un método combinado para generar configuraciones de equilibrio satisfactorias en estructuras tensadas. Como motor de búsqueda para el diseño preliminar se emplea el método de las densidades de fuerza (FDM implementado con mallado en topología (TM, y se propone un procedimiento basado en análisis no lineal de estructuras para el refinamiento de la configuración inicial de equilibrio, permitiéndose así el empleo de las mismas herramientas tanto para el refinamiento de la solución inicial

  7. Linkage analysis and physical mapping near the gene for x-linked agammaglobulinemia at Xq22

    Energy Technology Data Exchange (ETDEWEB)

    Parolini, O.; Lassiter, G.L.; Henry, M.J.; Conley, M.E. (Univ. of Tennessee College of Medicine, Memphis (United States) St. Jude Children' s Research Hospital, Memphis, TN (United States)); Hejtmancik, J.F. (National Inst. of Health, Bethesda, MD (United States)); Allen, R.C.; Belmont, J.W. (Baylor College of Medicine, Houston, TX (United States)); Barker, D.F. (Univ. of Utah, Salt Lake City (United States))

    1993-02-01

    The gene for x-linked agammaglobulinemia (XLA) has been mapped to Xq22. No recombinations have been reported between the gene and the prob p212 at DXS178; however, this probe is informative in only 30-40% of women and the reported flanking markers, DXS3 and DXS94, and 10-15 cM apart. To identify additional probes that might be useful in genetic counseling, we examined 11 polymorphisms that have been mapped to the Xq21.3-q22 region in 13 families with XLA. In addition, pulsed-field gel electrophoresis and yeast artificial chromosomes (YACs) were used to further characterize the segman of DNA within which the gene for SLA must lie. The results demonstrated that DXS366 and DXS442, which share a 430-kb pulsed-field fragment, could replace DXS3 as proximal flanking markers. Probes at DXS178 and DXS265 identified the same 145-kb pulsed-field fragment, and both loci were contained within a 200-kb YAC identified with the probe p212. A highly polymorphic CA repeat (DCS178CA) was isolated from one end of this YAC and used in linkage analysis. Probes at DXS101 and DXS328 shared several pulsed-field fragments, the smallest of which was 250 kb. No recombinations were seen between XLA and the DXS178-DXS265-DXS178CA complex, DXS101, DXS328, DXS87, or the gene for proteolipid protein (PLP). Key crossovers, when combined with the linkage data from families with Alport syndrome, suggested the following order of loci: cen-DXS3-DXS366-DXS442-(PLP, DXS101, DXS328, DXS178-DXS265-DXS178CA complex, XL)-(DXS87, DXS94)-DXS327-(DXS350, DXS362)-tel. Our studies also limit the segment of DNA within which the XLA gene must lie to the 3- to 4-cM distance between DCS442 and DXS94 and they identify and orient polymorphisms that can be used in genetic counseling not only for XLA but also for Pelizaeus-Merzbacher disease (PLP deficiency), Alport syndrome (COL4A5 deficiency), and Fabry disease ([alpha]-galactosidase A difficiency). 31 refs., 5 figs., 2 tabs.

  8. A new physical mapping approach refines the sex-determining gene positions on the Silene latifolia Y-chromosome

    Science.gov (United States)

    Kazama, Yusuke; Ishii, Kotaro; Aonuma, Wataru; Ikeda, Tokihiro; Kawamoto, Hiroki; Koizumi, Ayako; Filatov, Dmitry A.; Chibalina, Margarita; Bergero, Roberta; Charlesworth, Deborah; Abe, Tomoko; Kawano, Shigeyuki

    2016-01-01

    Sex chromosomes are particularly interesting regions of the genome for both molecular genetics and evolutionary studies; yet, for most species, we lack basic information, such as the gene order along the chromosome. Because they lack recombination, Y-linked genes cannot be mapped genetically, leaving physical mapping as the only option for establishing the extent of synteny and homology with the X chromosome. Here, we developed a novel and general method for deletion mapping of non-recombining regions by solving “the travelling salesman problem”, and evaluate its accuracy using simulated datasets. Unlike the existing radiation hybrid approach, this method allows us to combine deletion mutants from different experiments and sources. We applied our method to a set of newly generated deletion mutants in the dioecious plant Silene latifolia and refined the locations of the sex-determining loci on its Y chromosome map.

  9. Fine genetic mapping of cp: a recessive gene for compact (dwarf) plant architecture in cucumber, Cucumis sativus L.

    Science.gov (United States)

    Li, Yuhong; Yang, Luming; Pathak, Mamta; Li, Dawei; He, Xiaoming; Weng, Yiqun

    2011-10-01

    The compact (dwarf) plant architecture is an important trait in cucumber (Cucumis sativus L.) breeding that has the potential to be used in once-over mechanical harvest of cucumber production. Compact growth habit is controlled by a simply inherited recessive gene cp. With 150 F(2:3) families derived from two inbred cucumber lines, PI 308915 (compact vining) and PI 249561 (regular vining), we conducted genome-wide molecular mapping with microsatellite (simple sequence repeat, SSR) markers. A framework genetic map was constructed consisting of 187 SSR loci in seven linkage groups (chromosomes) covering 527.5 cM. Linkage analysis placed cp at the distal half of the long arm of cucumber Chromosome 4. Molecular markers cosegregating with the cp locus were identified through whole genome scaffold-based chromosome walking. Fine genetic mapping with 1,269 F(2) plants delimited the cp locus to a 220 kb genomic DNA region. Annotation and function prediction of genes in this region identified a homolog of the cytokinin oxidase (CKX) gene, which may be a potential candidate of compact gene. Alignment of the CKX gene homologs from both parental lines revealed a 3-bp deletion in the first exon of PI 308915, which can serve as a marker for marker-assisted selection of the compact phenotype. This work also provides a solid foundation for map-based cloning of the compact gene and understanding the molecular mechanisms of the dwarfing in cucumber.

  10. CREST maps somatic structural variation in cancer genomes with base-pair resolution.

    Science.gov (United States)

    Wang, Jianmin; Mullighan, Charles G; Easton, John; Roberts, Stefan; Heatley, Sue L; Ma, Jing; Rusch, Michael C; Chen, Ken; Harris, Christopher C; Ding, Li; Holmfeldt, Linda; Payne-Turner, Debbie; Fan, Xian; Wei, Lei; Zhao, David; Obenauer, John C; Naeve, Clayton; Mardis, Elaine R; Wilson, Richard K; Downing, James R; Zhang, Jinghui

    2011-06-12

    We developed 'clipping reveals structure' (CREST), an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution. Application of CREST to whole-genome sequencing data from five pediatric T-lineage acute lymphoblastic leukemias (T-ALLs) and a human melanoma cell line, COLO-829, identified 160 somatic structural variations. Experimental validation exceeded 80%, demonstrating that CREST had a high predictive accuracy.

  11. CREST maps somatic structural variation in cancer genomes with base-pair resolution

    OpenAIRE

    2011-01-01

    We developed CREST (Clipping REveals STructure), an algorithm that uses next-generation sequencing reads with partial alignments to a reference genome to directly map structural variations at the nucleotide level of resolution. Application of CREST to whole-genome sequencing data from five pediatric T-lineage acute lymphoblastic leukemias (T-ALLs) and a human melanoma cell line, COLO-829, identified 160 somatic structural variations. Experimental validation exceeded 80% demonstrating that CRE...

  12. The ornithine decarboxylase gene of Caenorhabditis elegans: Cloning, mapping and mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Macrae, M.; Coffino, P. [Univ. of California, San Francisco, CA (United States); Plasterk, R.H.A. [Netherlands Cancer Institute, Amsterdam (Netherlands)

    1995-06-01

    The gene (odc-1) encoding ornithine decarboxylase, a key enzyme in polyamine biosynthesis, was cloned and characterized. Two introns interrupt the coding sequence of the gene. The deduced protein contains 442 amino acids and is homologous to ornithine decarboxylases of other eukaryotic species. In vitro translation of a transcript of the cDNA yielded an enzymatically active product. The mRNA is 1.5 kb in size and is formed by trans-splicing to SL1, a common 5{prime} RNA segment. odc-1 maps to the middle of LG V, between dpy-11 and unc-42 and near a breakpoint of the nDf32 deficiency strain. Enzymatic activity is low in starved 1 (L1) larva and, after feeding, rises progressively as the worms develop. Targeted gene disruption was used to create a null allele. Homozygous mutants are normally viable and show no apparent defects, with the exception of a somewhat reduced brood size. In vitro assays for ornithine decarboxylase activity, however, show no detectable enzymatic activity, suggesting that ornithine decarboxylase is dispensible for nematode growth in the laboratory. 37 refs., 6 figs., 1 tab.

  13. Characterization and fine mapping of a female fertility associated gene Ff1(t) in rice

    Indian Academy of Sciences (India)

    Lei Zhao; Song Yan; Renliang Huang; Shan Zhu; Hongliang Xiong; Zhiqin Peng; Qingyou Zhou; Yingjin Huang; Xianhua Shen

    2015-03-01

    Female-sterile line can be used as a pollinator which has a great potential for hybrid seeds production. However, reports on female fertility are fewer than male fertility. Here, we characterized a recessive female fertility weakening mutant ff1(t) from rice. The spikelet fertility was seriously affected in the mutant. Reciprocal crosses and pollen vitality assay suggest that the decreased fertility was caused by the defective female gametophytes. Further investigation indicated that the mutant ovary development was inhibited before fertilization and failed swelling after flowering. Genetic analysis and fine mapping showed that the mutant was controlled by a single recessive gene, residing on a 16.8 kb region on the long arm of chromosome 1. The gene annotation indicated that there was only one putative gene encoding lysine decarboxylase-like protein in this region, which was allelic to LOG. Further, the sequence analysis was carried out and a substitution at the splice site of intron 2 / exon 3 was revealed in ff1(t) mutant, resulting in the change of reading frame. The finding of novel allele of LOG locus will facilitate the understanding of the mechanisms of female gametophyte development.

  14. High-resolution mapping of the gene for cystinosis, using combined biochemical and linkage analysis.

    Science.gov (United States)

    Jean, G; Fuchshuber, A; Town, M M; Gribouval, O; Schneider, J A; Broyer, M; van't Hoff, W; Niaudet, P; Antignac, C

    1996-03-01

    Infantile nephropathic cystinosis is an autosomal recessive disorder characterized biochemically by an abnormally high intracellular content of free cystine in different organs and tissues due to a transport defect of cystine through the lysosomal membrane. Affected children present with the Fanconi syndrome and usually develop progressive renal failure within the 1st decade of life. Measurement of free cystine in purified polymorphonuclear leukocytes provides an accurate method for diagnosis and detection of heterozygous carriers. In order to localize the gene locus for cystinosis we performed linkage analysis in 18 cystinosis families. However, since 17 of these were simplex families, we decided to include the phenotypes of the heterozygous carriers previously determined by their leukocyte cystine content in the linkage analysis. This approach allowed us to obtain highly significant results, confirming the localization of the cystinosis gene locus recently mapped to the short arm of chromosome 17 by the Cystinosis Collaborative Research Group. Crucial recombination events allowed us to refine the interval of the cystinosis gene to a genetic distance of 1 cM. No evidence of genetic heterogeneity was found. Our results demonstrate that the use of the previously determined phenotypes of heterozygous carriers in linkage analysis provides a reliable method for the investigation of simplex families in autosomal recessive traits.

  15. Map-Based Cloning of the Gene Associated With the Soybean Maturity Locus E3

    Science.gov (United States)

    Watanabe, Satoshi; Hideshima, Rumiko; Xia, Zhengjun; Tsubokura, Yasutaka; Sato, Shusei; Nakamoto, Yumi; Yamanaka, Naoki; Takahashi, Ryoji; Ishimoto, Masao; Anai, Toyoaki; Tabata, Satoshi; Harada, Kyuya

    2009-01-01

    Photosensitivity plays an essential role in the response of plants to their changing environments throughout their life cycle. In soybean [Glycine max (L.) Merrill], several associations between photosensitivity and maturity loci are known, but only limited information at the molecular level is available. The FT3 locus is one of the quantitative trait loci (QTL) for flowering time that corresponds to the maturity locus E3. To identify the gene responsible for this QTL, a map-based cloning strategy was undertaken. One phytochrome A gene (GmPhyA3) was considered a strong candidate for the FT3 locus. Allelism tests and gene sequence comparisons showed that alleles of Misuzudaizu (FT3/FT3; JP28856) and Harosoy (E3/E3; PI548573) were identical. The GmPhyA3 alleles of Moshidou Gong 503 (ft3/ft3; JP27603) and L62-667 (e3/e3; PI547716) showed weak or complete loss of function, respectively. High red/far-red (R/FR) long-day conditions enhanced the effects of the E3/FT3 alleles in various genetic backgrounds. Moreover, a mutant line harboring the nonfunctional GmPhyA3 flowered earlier than the original Bay (E3/E3; PI553043) under similar conditions. These results suggest that the variation in phytochrome A may contribute to the complex systems of soybean flowering response and geographic adaptation. PMID:19474204

  16. Mapping the Broad Structural and Mechanical Properties of Amyloid Fibrils.

    Science.gov (United States)

    Lamour, Guillaume; Nassar, Roy; Chan, Patrick H W; Bozkurt, Gunes; Li, Jixi; Bui, Jennifer M; Yip, Calvin K; Mayor, Thibault; Li, Hongbin; Wu, Hao; Gsponer, Jörg A

    2017-02-28

    Amyloids are fibrillar nanostructures of proteins that are assembled in several physiological processes in human cells (e.g., hormone storage) but also during the course of infectious (prion) and noninfectious (nonprion) diseases such as Creutzfeldt-Jakob and Alzheimer's diseases, respectively. How the amyloid state, a state accessible to all proteins and peptides, can be exploited for functional purposes but also have detrimental effects remains to be determined. Here, we measure the nanomechanical properties of different amyloids and link them to features found in their structure models. Specifically, we use shape fluctuation analysis and sonication-induced scission in combination with full-atom molecular dynamics simulations to reveal that the amyloid fibrils of the mammalian prion protein PrP are mechanically unstable, most likely due to a very low hydrogen bond density in the fibril structure. Interestingly, amyloid fibrils formed by HET-s, a fungal protein that can confer functional prion behavior, have a much higher Young's modulus and tensile strength than those of PrP, i.e., they are much stiffer and stronger due to a tighter packing in the fibril structure. By contrast, amyloids of the proteins RIP1/RIP3 that have been shown to be of functional use in human cells are significantly stiffer than PrP fibrils but have comparable tensile strength. Our study demonstrates that amyloids are biomaterials with a broad range of nanomechanical properties, and we provide further support for the strong link between nanomechanics and β-sheet characteristics in the amyloid core. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Mapping of a New Gene Wbph6(t) Resistant to the Whitebacked Planthopper, Sogatella furcifera, in Rice

    Institute of Scientific and Technical Information of China (English)

    LIXi-ming; ZHAIHu-qu; WANJian-min; MALiang-yong; ZHUANGJie-yun; LIUOuang-jie; YANGChang-deng

    2004-01-01

    A rice population consisting of 90 TN1/Gulyigu F3 lines was employed to analyze the linkage between DNA markers and a new gene Wbph6(t) conferring resistance to whitebacked planthopper, Sogatella furcifera. By using the mapping approach of bulked extremes and recessive class, Wbph6(t) was mapped onto the short arm of chromosome 11 with a genetic distance of 21.2 cM to SSLP marker RM167.

  18. Mapping of a New Gene Wbph6(t) Resistant to the Whitebacked Planthopper, Sogatella furcifera, in Rice

    Institute of Scientific and Technical Information of China (English)

    LI Xi-ming; ZHAI Hu-qu; WAN Jian-min; MA Liang-yong; ZHUANG Jie-yun; LIU Guang-jie; YANG Chang-deng

    2004-01-01

    A rice population consisting of 90 TN1/Guiyigu F3 lines was employed to analyze the linkage between DNA markers and a new gene Wbph6(t) conferring resistance to whitebacked planthopper, Sogatella furcifera. By using the mapping approach of bulked extremes and recessive class, Wbph6(t) was mapped onto the short arm of chromosome 11 with a genetic distance of 21.2 cM to SSLP marker RM167.

  19. Identification of putative candidate genes for red rot resistance in sugarcane (Saccharum species hybrid) using LD-based association mapping.

    Science.gov (United States)

    Singh, Ram K; Banerjee, Nandita; Khan, M S; Yadav, Sonia; Kumar, Sanjeev; Duttamajumder, S K; Lal, Ram Ji; Patel, Jinesh D; Guo, H; Zhang, Dong; Paterson, Andrew H

    2016-06-01

    Red rot is a serious disease of sugarcane caused by the fungus Colletotrichum falcatum that has a colossal damage potential. The fungus, prevalent mainly in the Indian sub-continent, keeps on producing new pathogenic strains leading to breakdown of resistance in newly released varieties and hence the deployment of linked markers for marker-assisted selection for resistance to this disease can fine tune the breeding programme. This study based on a panel of 119 sugarcane genotypes fingerprinted for 944 SSR alleles was undertaken with an aim to identify marker-trait associations (MTAs) for resistance to red rot. Mixed linear model containing population structure and kinship as co-factor detected four MTAs that were able to explain 10-16 % of the trait variation, individually. Among the four MTAs, EST sequences diagnostic of three could be BLAST searched to the sorghum genome with significant sequence homology. Several genes encoding important plant defence related proteins, viz., cytochrome P450, Glycerol-3-phosphate transporter-1, MAP Kinase-4, Serine/threonine-protein kinase, Ring finger domain protein and others were localized to the vicinity of these MTAs. These positional candidate genes are worth of further investigation and possibly these could contribute directly to red rot resistance, and may find a potential application in marker-assisted sugarcane breeding.

  20. Optimising parallel R correlation matrix calculations on gene expression data using MapReduce.

    Science.gov (United States)

    Wang, Shicai; Pandis, Ioannis; Johnson, David; Emam, Ibrahim; Guitton, Florian; Oehmichen, Axel; Guo, Yike

    2014-11-05

    High-throughput molecular profiling data has been used to improve clinical decision making by stratifying subjects based on their molecular profiles. Unsupervised clustering algorithms can be used for stratification purposes. However, the current speed of the clustering algorithms cannot meet the requirement of large-scale molecular data due to poor performance of the correlation matrix calculation. With high-throughput sequencing technologies promising to produce even larger datasets per subject, we expect the performance of the state-of-the-art statistical algorithms to be further impacted unless efforts towards optimisation are carried out. MapReduce is a widely used high performance parallel framework that can solve the problem. In this paper, we evaluate the current parallel modes for correlation calculation methods and introduce an efficient data distribution and parallel calculation algorithm based on MapReduce to optimise the correlation calculation. We studied the performance of our algorithm using two gene expression benchmarks. In the micro-benchmark, our implementation using MapReduce, based on the R package RHIPE, demonstrates a 3.26-5.83 fold increase compared to the default Snowfall and 1.56-1.64 fold increase compared to the basic RHIPE in the Euclidean, Pearson and Spearman correlations. Though vanilla R and the optimised Snowfall outperforms our optimised RHIPE in the micro-benchmark, they do not scale well with the macro-benchmark. In the macro-benchmark the optimised RHIPE performs 2.03-16.56 times faster than vanilla R. Benefiting from the 3.30-5.13 times faster data preparation, the optimised RHIPE performs 1.22-1.71 times faster than the optimised Snowfall. Both the optimised RHIPE and the optimised Snowfall successfully performs the Kendall correlation with TCGA dataset within 7 hours. Both of them conduct more than 30 times faster than the estimated vanilla R. The performance evaluation found that the new MapReduce algorithm and its

  1. Spin-mapping of coal structures with ESE and ENDOR

    Energy Technology Data Exchange (ETDEWEB)

    Belford, R.L.; Clarkson, R.B.

    1990-06-01

    The overall goal of this project is the development of nondestructive techniques for studying the molecular structure of coal by probing the chemical environment of naturally occurring unpaired electrons with a variety of electron magnetic resonance spectroscopies. One exceptionally promising method for investigating molecular structure in complex solids possessing unpaired electrons is Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy. Currently the aim of our S-band ESEEM work is to develop better methods for the interpretation of multifrequency ESEEM data. This problem is extremely difficult, especially for modulation resulting from quadrupolar nuclei (l > 1/2) such as {sup 33}S, {sup 14}N, and {sup 23}Na. We are pursuing two closely related paths toward this goal. One part of this effort is the development of classification system which would make ESEEM spectra more amenable to a preliminary interpretation by visual inspection. This report describes the testing of some of the capabilities of our recently constructed ESE spectrometer by carrying out a detailed investigation of the molecule DPPH, diphenylpicrylhydrazyl, a well-known stable free radical frequently used to test and tune up electron paramagnetic resonance spectrometers, but details of the nitrogen substituents on one of its aromatic rings have been uncertain and, in fact, the focus of a bit of controversy. It therefore made an excellent subject to select for this test. 14 refs., 2 figs.

  2. Synoptic Mapping of Chemical Composition, Thermal Structure, and Air Motion from UARS Observations

    Science.gov (United States)

    Salby, Murry L.

    1999-01-01

    An operational mapping algorithm was developed to process measurements of individual species observed by different satellite instruments on board UARS. Based on Fast Fourier Synoptic Mapping (FFSM), the algorithm accounts for the precessing orbit of UARS, the error of individual instruments, and gaps associated with instrument duty cycle and the satellite yaw maneuver. It provides synoptic structure and evolution on periods as short as 1 day, derived collectively from all observations of an individual species. The algorithm was applied to synoptically map temperature, thickness, and several chemical constituents observed by the instruments: MLS, CLAES, ISAMS, and HALOE. Each field variable observed by these instruments was mapped twice-daily in continuous global time series several months long. Mapped behavior produced via FFSM was compared against standard archived products generated via Kalman filtering. The standard map products reveal similar behavior, but are limited to features of larger scale. Tracer structure that develops through flow deformation and attending transport is therefore represented in those products more coarsely, eventually being sheared down to scales that are no longer represented properly. The synoptic time series also reveal a diurnal cycle for several of the constituents, one that emerges clearly in their space-time spectra. The zonal and meridional structure of diurnal variability was mapped by filtering the space-time spectrum, an intermediate product of FFSM, to those scales resolved by the UARS sampling. Geographical variations of the diurnal cycle have also been evaluated in its seasonal-mean structure by compositing distributions at individual local times. Both were compared to diurnal variations in chemical models and in dynamical models that account for transport by the diurnal tide. Diurnal variations were found to introduce spurious behavior into the archived products generated via Kalman filtering, behavior that is

  3. Information Structuring and Retrieval with Topic Maps for Medical E-Learning

    Directory of Open Access Journals (Sweden)

    STANESCU, L.

    2009-10-01

    Full Text Available The paper presents original ways of using topic maps for information structuring and retrieval in medical e-learning domain. The topic map is mainly used for graphical visualization of the MeSH thesaurus containing medical terms. The hierarchical structure of the descriptors from MeSH thesaurus that has also multiple associative and equivalence relationships between medical terms can be properly visualized in this way. The topic map is built and populated using an original algorithm, by mapping an xml file that can be downloaded for free to an xtm file that contains the topic map. The paper also presents how to use the topic map for semantic querying of a multimedia database with medical images that are accompanied by diagnosis and treatment as important information. For retrieving the interest information for student, this access path can be combined with another modern solution: the content-based visual query on the multimedia medical database using primitive features like color and texture.

  4. Molecular Tagging and Mapping of Quantitative Trait Loci for Lint Percentage and Morphological Marker Genes in Upland Cotton

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Using 219 F2 individuals developed by crossing the genetic standard line TM-1 and the multiple dominant marker line T586 in Gossypium hirsutum L., a genetic linkage map with 19 linkage groups was constructed based on simple sequence repeat (SSR) markers. Compared with our tetraploid backboned molecular genetic map from a (TM-1xHai 7124)xTM-1 BC1 population, 17 of the 19 linkage groups were combined and anchored to 12 chromosomes (sub-genomes). Of these groups, four morphological marker genes in T586 had been mapped into the molecular linkage map. Meanwhile, three quantitative trait loci for lint percentage were tagged and mapped separately on the A03 linkage group and chromosome 6.

  5. Molecular mapping of a stripe rust resistance gene in wheat line C51

    Indian Academy of Sciences (India)

    Jianmin Zheng; Zehong Yan; Li Zhao; Shizhao Li; Zengyan Zhang; Resewarne Garry; Wuyun Yang; Zongjun Pu

    2014-08-01

    Stripe rust, a major disease in areas where cool temperatures prevail, can strongly influence grain yield. To control this disease, breeders have incorporated seedling resistance genes from a variety of sources outside the primary wheat gene pool. The wheat line C51, introduced from the International Center for Agricultural Research in the Dry Areas (ICARDA), Syria, confers resistance to all races of Puccinia striiformis f. sp. tritici (PST) in China. To map the resistant gene(s) against stripe rust in wheat line C51, 212 F8 recombinant inbred lines (RILs) derived from the cross X440 × C51 were inoculated with Chinese PST race CYR33 (Chinese yellow rust, CYR) in the greenhouse. The result showed that C51 carried a single dominant gene for resistance (designated YrC51) to CYR33. Simple sequence repeat (SSR) and resistance gene-analogue polymorphism (RGAP) markers that were polymorphic between the parents were used for genotyping the 212 F8 RILs. YrC51 was closely linked to two SSR loci on chromosome 2BS with genetic distances of 5.1 cM (Xgwm429) and 7.2 cM (Xwmc770), and to three RGAP markers C51R1 (XLRR For / NLRR For), C51R2 (CLRR Rev / Cre3LR-F) and C51R3 (Pto kin4/ NLRRINV2) with genetic distances of 5.6, 1.6 and 9.2 cM, respectively. These RGAP-linked markers were then converted into STS markers.Among them, one STS marker, C51STS-4, was located at a genetic distance of 1.4 cM to YrC51 and was closely associated with resistance when validated in several populations derived from crosses between C51 and Sichuan cultivars. The results indicated that C51STS-4 can be used for marker assisted selection (MAS) and would facilitate the pyramiding of YrC51 with other genes for stripe rust resistance.

  6. Maps of sparse Markov chains efficiently reveal community structure in network flows with memory

    CERN Document Server

    Persson, Christian; Edler, Daniel; Rosvall, Martin

    2016-01-01

    To better understand the flows of ideas or information through social and biological systems, researchers develop maps that reveal important patterns in network flows. In practice, network flow models have implied memoryless first-order Markov chains, but recently researchers have introduced higher-order Markov chain models with memory to capture patterns in multi-step pathways. Higher-order models are particularly important for effectively revealing actual, overlapping community structure, but higher-order Markov chain models suffer from the curse of dimensionality: their vast parameter spaces require exponentially increasing data to avoid overfitting and therefore make mapping inefficient already for moderate-sized systems. To overcome this problem, we introduce an efficient cross-validated mapping approach based on network flows modeled by sparse Markov chains. To illustrate our approach, we present a map of citation flows in science with research fields that overlap in multidisciplinary journals. Compared...

  7. CFHTLenS: Mapping the Large Scale Structure with Gravitational Lensing

    CERN Document Server

    Van Waerbeke, Ludovic; Erben, Thomas; Heymans, Catherine; Hildebrandt, Hendrik; Hoekstra, Henk; Kitching, Thomas D; Mellier, Yannick; Miller, Lance; Coupon, Jean; Harnois-Déraps, Joachim; Fu, Liping; Hudson, Michael J; Kilbinger, Martin; Kuijken, Konrad; Rowe, Barnaby T P; Schrabback, Tim; Semboloni, Elisabetta; Vafaei, Sanaz; van Uitert, Edo; Velander, Malin

    2013-01-01

    We present a quantitative analysis of the largest contiguous maps of projected mass density obtained from gravitational lensing shear. We use data from the 154 deg2 covered by the Canada France Hawaii Telescope Lensing Survey. Our study is the first attempt to quantitatively characterize the scientific value of lensing maps, which could serve in the future as a complementary approach to the study of the dark universe with gravitational lensing. We show that mass maps contain unique cosmological information beyond that of traditional two-points statistical analysis techniques. Using a series of numerical simulations, we first show that gravitational lensing inversion provides a reliable probe of the projected matter distribution of large scale structure. We validate our analysis by quantifying the robustness of the maps with various statistical estimators. The same process is then applied to the CFHTLenS data. It is found that the statistical properties of the projected mass are fully consistent with the cosmo...

  8. Gene-Environment Interactions Target Mitogen-activated Protein 3 Kinase 1 (MAP3K1) Signaling in Eyelid Morphogenesis*

    Science.gov (United States)

    Mongan, Maureen; Meng, Qinghang; Wang, Jingjing; Kao, Winston W.-Y.; Puga, Alvaro; Xia, Ying

    2015-01-01

    Gene-environment interactions determine the biological outcomes through mechanisms that are poorly understood. Mouse embryonic eyelid closure is a well defined model to study the genetic control of developmental programs. Using this model, we investigated how exposure to dioxin-like environmental pollutants modifies the genetic risk of developmental abnormalities. Our studies reveal that mitogen-activated protein 3 kinase 1 (MAP3K1) signaling is a focal point of gene-environment cross-talk. Dioxin exposure, acting through the aryl hydrocarbon receptor (AHR), blocked eyelid closure in genetic mutants in which MAP3K1 signaling was attenuated but did not disturb this developmental program in either wild type or mutant mice with attenuated epidermal growth factor receptor or WNT signaling. Exposure also markedly inhibited c-Jun phosphorylation in Map3k1+/− embryonic eyelid epithelium, suggesting that dioxin-induced AHR pathways can synergize with gene mutations to inhibit MAP3K1 signaling. Our studies uncover a novel mechanism through which the dioxin-AHR axis interacts with the MAP3K1 signaling pathways during fetal development and provide strong empirical evidence that specific gene alterations can increase the risk of developmental abnormalities driven by environmental pollutant exposure. PMID:26109068

  9. Gene for the catalytic subunit of mouse DNA-dependent protein kinase maps to the scid locus.

    Science.gov (United States)

    Miller, R D; Hogg, J; Ozaki, J H; Gell, D; Jackson, S P; Riblet, R

    1995-01-01

    The gene encoding the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) has been proposed recently as a candidate gene for the mouse severe combined immune deficiency (scid) locus. We have used a partial cDNA clone for human DNA-PKcs to map the mouse homologue using a large interspecific backcross panel. We found that the mouse gene for DNA-PKcs does not recombine with scid, consistent with the hypothesis that scid is a mutation in the mouse gene for DNA-PKcs. Images Fig. 3 PMID:7479885

  10. Genetic analysis and SSR mapping of stem rust resistance gene from wheat mutant D51

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Wheat (Triticum aestivum L.) stem rust caused by Puccinia graminis f.sp.tritici is one of the main diseases of wheat worldwide.Wheat mutant line D51,which forms a highly susceptive cultivar 'L6239' to the three races notated and cultured with immature embryos,shows resistance to prevailing races 21C3CPH,21C3CKH,and 21C3CTR of P.graminis f.sp.tritici in China.In this study,the number and the expression stages of the resistance genes in mutant D51 were studied using inoculation identification and microsatellite (SSR) marker analysis.Two F1 populations from the crosses of D51×L6239 (60 individuals) and D51 × Chinese Spring (60 individuals),their F2 populations (185 and 175 individuals respectively) at the seedling stage,and one F2 population derived from the cross of D51×L6239 (194 individuals) at the adult stage were inoculated with pathogen race 21C3CPH to test for resistance.All F1 individuals of the two crosses were immune to stem rust at both seedling and adult stages.The response pattern of the three F2 populations showed that the R:S segregation ratio was 3:1,suggesting that the stem rust resistance of D51 is controlled by a single dominant gene,and is expressed during the entire growth period.The identification of the stem rust resistance by the F3 progeny test confirmed the credibility of the F2 population test.Segregating populations and small population analyses were used to identify chromosomal regions and molecular markers linked to the gene by the SSR marker method.A total of 675 SSR markers and 185 individuals of the D51 x L6239 F2 population were used to search genetically linked markers to the target gene.Using Mapmaker 3.0 and Map-draw with Kosambi's function and other options set at default values,molecular mapping revealed that the gene was located on chromosome 5DS,linked with and flanked by two SSR markers,Xgwml90 and Xwmc150,at 18.58 and 21.33 cM,respectively.It has been reported that only one stem rust resistant gene,Sr30,is located on the

  11. A susceptibility gene for premature ovarian failure (POF) maps to proximal Xq28.

    Science.gov (United States)

    Rossetti, Francesca; Rizzolio, Flavio; Pramparo, Tiziano; Sala, Cinzia; Bione, Silvia; Bernardi, Franca; Goegan, Mara; Zuffardi, Orsetta; Toniolo, Daniela

    2004-10-01

    Terminal deletions of the long arm of the human X chromosome have been described in women with premature ovarian failure (POF). We report here the molecular characterization of an inherited deletion in two affected women and in their mother. The two daughters presented secondary amenorrhea at 17 or 22 years respectively, while the mother was fertile. She had four children, but she eventually had premature menopause at 43 years of age. The fine molecular analysis of the deletion showed that the three women carried an identical deletion. We conclude that the phenotypic difference within the family must be attributed to genetic or environmental factors and not to the presence of different extent deletions. By comparison with other deletions in the region, we map a susceptibility gene for POF to 4.5 Mb, in the distal part of Xq.

  12. PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps.

    Science.gov (United States)

    Corrado, Gianluca; Tebaldi, Toma; Bertamini, Giulio; Costa, Fabrizio; Quattrone, Alessandro; Viero, Gabriella; Passerini, Andrea

    2014-04-23

    The progress in mapping RNA-protein and RNA-RNA interactions at the transcriptome-wide level paves the way to decipher possible combinatorial patterns embedded in post-transcriptional regulation of gene expression. Here we propose an innovative computational tool to extract clusters of mRNA trans-acting co-regulators (RNA binding proteins and non-coding RNAs) from pairwise interaction annotations. In addition the tool allows to analyze the binding site similarity of co-regulators belonging to the same cluster, given their positional binding information. The tool has been tested on experimental collections of human and yeast interactions, identifying modules that coordinate functionally related messages. This tool is an original attempt to uncover combinatorial patterns using all the post-transcriptional interaction data available so far. PTRcombiner is available at http://disi.unitn.it/~passerini/software/PTRcombiner/.

  13. Genetic mapping of the alpha-galactosidase MEL gene family on right and left telomeres of Saccharomyces cerevisiae.

    Science.gov (United States)

    Naumov, G I; Naumova, E S; Louis, E J

    1995-04-30

    The alpha-galactosidase MEL2-MEL10 genes have been genetically mapped to right and left telomere regions of the following chromosomes of Saccharomyces cerevisiae: MEL2 at VII L, MEL3 at XVI L, MEL4 at XI L, MEL5 at IV L, MEL6 at XIII R, MEL7 at VI R, MEL8 at XV R, MEL9 at X R and MEL10 at XII R. A set of tester strains with URA3 inserted into individual telomeres and no MEL genes was used for mapping.

  14. Structural basis of eukaryotic gene transcription.

    Science.gov (United States)

    Boeger, Hinrich; Bushnell, David A; Davis, Ralph; Griesenbeck, Joachim; Lorch, Yahli; Strattan, J Seth; Westover, Kenneth D; Kornberg, Roger D

    2005-02-07

    An RNA polymerase II promoter has been isolated in transcriptionally activated and repressed states. Topological and nuclease digestion analyses have revealed a dynamic equilibrium between nucleosome removal and reassembly upon transcriptional activation, and have further shown that nucleosomes are removed by eviction of histone octamers rather than by sliding. The promoter, once exposed, assembles with RNA polymerase II, general transcription factors, and Mediator in a approximately 3 MDa transcription initiation complex. X-ray crystallography has revealed the structure of RNA polymerase II, in the act of transcription, at atomic resolution. Extension of this analysis has shown how nucleotides undergo selection, polymerization, and eventual release from the transcribing complex. X-ray and electron crystallography have led to a picture of the entire transcription initiation complex, elucidating the mechanisms of promoter recognition, DNA unwinding, abortive initiation, and promoter escape.

  15. Maps of Evolving Cloud Structures in Luhman 16AB from HST Time-resolved Spectroscopy

    Science.gov (United States)

    Karalidi, Theodora; Apai, Dániel; Marley, Mark S.; Buenzli, Esther

    2016-07-01

    WISE J104915.57-531906.1 is the nearest brown dwarf binary to our solar system, consisting of two brown dwarfs in the L/T transition: Luhman 16A and B. In this paper, we present the first map of Luhman 16A, and maps of Luhman 16B for two epochs. Our maps were created by applying Aeolus, a Markov-Chain Monte Carlo code that maps the top-of-the-atmosphere (TOA) structure of brown dwarf and other ultracool atmospheres, to light curves of Luhman 16A and B using the Hubble Space Telescope’s G141 and G102 grisms. Aeolus retrieved three or four spots in the TOA of Luhman 16A and B, with a surface coverage of 19%-32% (depending on an assumed rotational period of 5 hr or 8 hr) or 21%-38.5% (depending on the observational epoch), respectively. The brightness temperature of the spots of the best-fit models was ˜200 K hotter than the background TOA. We compared our Luhman 16B map with the only previously published map. Interestingly, our map contained a large TOA spot that was cooler (ΔT ˜ 51 K) than the background, which lay at low latitudes, in agreement with the previous Luhman 16B map. Finally, we report the detection of a feature reappearing in Luhman 16B light curves that are separated by tens of hundreds of rotations from each other. We speculate that this feature is related to TOA structures of Luhman 16B.

  16. Molecular Mapping of a Gene for Resistance to Stripe Rust in Wheat Variety PIW138

    Institute of Scientific and Technical Information of China (English)

    YUE Yan-li; YAO Zhan-jun; REN Xin-xin; WANG Li

    2010-01-01

    Stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is one of the most damaging diseases of common wheat(Triticum aestivum L.).Wheat variety PIW138 introduced from Pakistan is resistant to the currently prevailing Pst race CYR32 in China.In this study,the bulked segregant analysis(BSA)method and simple sequence repeat(SSR)markers were used to map the stripe rust resistance gene in PIW138.The resistant and susceptible DNA bulks were prepared from the segregating F2 population of the cross between Thatcher,a susceptible variety as the female parent,and PIW138 as the male parent.The segregation of resistant and susceptible F2 plants inoculated with CYR32 indicated that single dominant gene determined the reactions of PIW138 line and temporarily designated as YrP138.Total 200 SSR primers were screened,and 4 SSR markers,Xwmc52,Xbarc61,Xgwm268,and Xgwm153,on chromosome 1B were found to be polymorphic between the resistant and the susceptible DNA bulks as well as their parents.Genetic linkage was tested on the segregating F2 population with 259 plants,including 196 resistant and 63 susceptible plants.All 4 SSR markers were linked to the stripe rust resistance gene in PIW138.The genetic distances of Xwmc52,Xbarc61,Xgwm268,and Xgwm153to the resistance gene were 29.8,6.2,6.8,and 8.2 cM,respectively.

  17. Integrating QTL mapping and transcriptomics identifies candidate genes underlying QTLs associated with soybean tolerance to low-phosphorus stress.

    Science.gov (United States)

    Zhang, Dan; Zhang, Hengyou; Chu, Shanshan; Li, Hongyan; Chi, Yingjun; Triebwasser-Freese, Daniella; Lv, Haiyan; Yu, Deyue

    2017-01-01

    Soybean is a high phosphorus (P) demand species that is sensitive to low-P stress. Although many quantitative trait loci (QTL) for P efficiency have been identified in soybean, but few of these have been cloned and agriculturally applied mainly due to various limitations on identifying suitable P efficiency candidate genes. Here, we combined QTL mapping, transcriptome profiling, and plant transformation to identify candidate genes underlying QTLs associated with low-P tolerance and response mechanisms to low-P stress in soybean. By performing QTL linkage mapping using 152 recombinant inbred lines (RILs) that were derived from a cross between a P-efficient variety, Nannong 94-156, and P-sensitive Bogao, we identified four major QTLs underlying P efficiency. Within these four QTL regions, 34/81 candidate genes in roots/leaves were identified using comparative transcriptome analysis between two transgressive RILs, low-P tolerant genotype B20 and sensitive B18. A total of 22 phosphatase family genes were up-regulated significantly under low-P condition in B20. Overexpression of an acid phosphatase candidate gene, GmACP2, in soybean hairy roots increased P efficiency by 15.43-24.54 % compared with that in controls. Our results suggest that integrating QTL mapping and transcriptome profiling could be useful for rapidly identifying candidate genes underlying complex traits, and phosphatase-encoding genes, such as GmACP2, play important roles involving in low-P stress tolerance in soybean.

  18. Assembly of the Genome of the Disease Vector Aedes aegypti onto a Genetic Linkage Map Allows Mapping of Genes Affecting Disease Transmission

    KAUST Repository

    Juneja, Punita

    2014-01-30

    The mosquito Aedes aegypti transmits some of the most important human arboviruses, including dengue, yellow fever and chikungunya viruses. It has a large genome containing many repetitive sequences, which has resulted in the genome being poorly assembled - there are 4,758 scaffolds, few of which have been assigned to a chromosome. To allow the mapping of genes affecting disease transmission, we have improved the genome assembly by scoring a large number of SNPs in recombinant progeny from a cross between two strains of Ae. aegypti, and used these to generate a genetic map. This revealed a high rate of misassemblies in the current genome, where, for example, sequences from different chromosomes were found on the same scaffold. Once these were corrected, we were able to assign 60% of the genome sequence to chromosomes and approximately order the scaffolds along the chromosome. We found that there are very large regions of suppressed recombination around the centromeres, which can extend to as much as 47% of the chromosome. To illustrate the utility of this new genome assembly, we mapped a gene that makes Ae. aegypti resistant to the human parasite Brugia malayi, and generated a list of candidate genes that could be affecting the trait. © 2014 Juneja et al.

  19. FREQUENT STRUCTURE ALTERATIONS OF p53 GENE IN NASOPHARYNGEAL CARCINOMA

    Institute of Scientific and Technical Information of China (English)

    龙江斌; 区宝祥; 梁启万; 李辉梅

    1998-01-01

    By southern hybridization with 1.8 kb cDNA probe,a high freqnency (40.5%) of structural abnormality of p 53 gene was observed in primary nasopharyngeal carcinoma (NPC) biopsies. The regioas of exons 1 to 4 of the gene were examined by poiymerase chain reaction-single strand conformation polymorphism, no point nmtation was found. Because very low rate of point mutation had been reported in exons 5 to 8,we considered that structural ahnormality in the region of exons 1 to 8 of the gene might be uncommon in NPC. The speetrophotometer scaaning analysis of outoradiograms and rehybridization investigation of nitrocellulose filter with exon 11 probe indicated that most of structure aberrations we observed might be rearrangement occurring in exon ll.

  20. Di-hadron fragmentation and mapping of the nucleon structure

    CERN Document Server

    Pisano, Silvia

    2015-01-01

    The fragmentation of a colored parton directly into a pair of colorless hadrons is a non-perturbative mechanism that offers important insights into the nucleon structure. Di-hadron fragmentation functions can be extracted from semi-inclusive electron-positron annihilation data. They also appear in observables describing the semi-inclusive production of two hadrons in deep-inelastic scattering of leptons off nucleons or in hadron-hadron collisions. When a target nucleon is transversely polarized, a specific chiral-odd di-hadron fragmentation function can be used as the analyzer of the net density of transversely polarized quarks in a transversely polarized nucleon, the so-called transversity distribution. The latter can be extracted through suitable single-spin asymmetries in the framework of collinear factorization, thus in a much simpler framework with respect to the traditional one in single-hadron fragmentation. At subleading twist, the same chiral-odd di-hadron fragmentation function provides the cleanest...

  1. Spin-mapping of Coal Structures with ESE and ENDOR

    Science.gov (United States)

    Belford, R. L.; Clarkson, R. B.

    1989-12-01

    The broad goals of this project are to determine by nondestructive magnetic resonance methods chemical and physical structural characteristics of organic parts of native and treated coals. In this project period, we have begun to explore a technique which promises to enable us to follow to course of coal cleaning processes with microscopic spatial resolution. For the past five years, our laboratory has worked on extensions of the EPR technique as applied to coal to address these analytical problems. In this report we (1) describe the world's first nuclear magnetic resonance imaging results from an Illinois {number sign}6 coal and (2) transmit a manuscript describing how organic sulfur affect the very-high-frequency EPR spectra of coals. Magnetic resonance imaging (MRI) is a non-destructive technique that has found wide medical application as a means of visualizing the interior of human bodies. We have used MRI techniques to study the diffusion of an organic solvent (DMSO) into the pores of Illinois {number sign}6 coal. Proton MRI images reveal that this solvent at room temperature does not penetrate approximately 30% of the coal volume. Regions of the coal that exclude solvent could be related to inertinite and mineral components. A multi-technique imaging program is contemplated.

  2. Fine genetic map of mouse chromosome 10 around the polycystic kidney disease gene, jcpk, and ankyrin 3

    Energy Technology Data Exchange (ETDEWEB)

    Bryda, E.C.; Ling, H.; Rathbun, D.E. [New York State Department of Health, Albany, NY (United States)] [and others

    1996-08-01

    A chlorambucil (CHL)-induced mutation of the jcpk (juvenile congenital polycystic kidney disease) gene causes a severe early onset polycystic kidney disease. In an intercross involving Mus musculus castaneus, jcpk was precisely mapped 0.2 cM distal to D10Mit115 and 0.8 cM proximal to D10Mit173. In addition, five genes, Cdc2a, Col6al, Col6a2, Bcr, and Ank3 were mapped in both this jcpk intercross and a (BALB/c X CAST/Ei)F{sub 1} x BALB/c backcross. All five genes were eliminated as possible candidates for jcpk based on the mapping data. The jcpk intercross allowed the orientation of the Ank3 gene relative to the centromere to be determined. D10Mit115, D10Mit173, D10Mit199, and D10Mit200 were separated genetically in this cross. The order and genetic distances of all markers and gene loci mapped in the jcpk intercross were consistent with those derived from the BALB/c backcross, indicating that the CHL-induced lesion has not generated any gross chromosomal abnormalities detectable in these studies. 39 refs., 3 figs.

  3. Structure of the human G gamma-A gamma-delta-beta-globin gene locus

    NARCIS (Netherlands)

    Bernards, R.A.; Little, P.F.R.; Annison, F.; Williamson, R.; Flavell, R.A.

    1979-01-01

    We have constructed a physical map of the human G gamma-, A gamma-, delta-, and beta-globin genes. The previously described maps of the fetal and adult beta-like globin genes have been linked to one another by identification of a DNA fragment, generated by BamHI, that contains part of each of the A

  4. Mapping Milky Way Halo Structure with Blue Horizontal Branch Stars

    Science.gov (United States)

    Martin, Charles; Newberg, Heidi Jo; Carlin, Jeffrey L.

    2017-01-01

    The use of blue horizontal brach (BHB) and red giant branch stars as tracers of stellar debris streams is a common practice and has been useful in the confirmation of kinematic properties of previously identified streams. This work explores less common ways of untangling the velocity signatures of streams traveling radially to our line of sight, and to peer toward the higher density region of the Galactic Center using data from the Sloan Digital Sky Survey (SDSS). Using spectra of BHB stars, we are able to kinematically distinguish moving groups in the Milky Way halo. The results of this thesis advance our knowledge of the following stellar halo substructures: the Pisces Stellar Stream, the Hercules-Aquila Cloud, the Hercules Halo Stream, and the Hermus Stream. A study of red giant stars led to the kinematic discovery of the Pisces Stellar Stream. Red giant stars were also examined to determine that the previously identified velocity signature that was suggested for the Hercules-Aquila Cloud was due to disk star contamination and errors in preliminary SDSS velocities. The Hercules Halo Stream is a previously unidentified structure that could be related to the Hercules-Aquila Cloud, and was discovered as a velocity excess of SDSS BHB stars. We identify a group of 10 stars with similar velocities that are spatially coincident with the Hermus Stream. An orbit is fit to the Hermus Stream that rules out a connection with the Phoenix Stream.This work was supported by NSF grants AST 09-37523, 14-09421, 16-15688, the NASA/NY Space Grant fellowship, and contributions made by The Marvin Clan, Babette Josephs, Manit Limlamai, and the 2015 Crowd Funding Campaign to Support Milky Way Research.

  5. Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep

    Directory of Open Access Journals (Sweden)

    Miller Joshua M

    2010-09-01

    Full Text Available Abstract Background The construction of genetic linkage maps in free-living populations is a promising tool for the study of evolution. However, such maps are rare because it is difficult to develop both wild pedigrees and corresponding sets of molecular markers that are sufficiently large. We took advantage of two long-term field studies of pedigreed individuals and genomic resources originally developed for domestic sheep (Ovis aries to construct a linkage map for bighorn sheep, Ovis canadensis. We then assessed variability in genomic structure and recombination rates between bighorn sheep populations and sheep species. Results Bighorn sheep population-specific maps differed slightly in contiguity but were otherwise very similar in terms of genomic structure and recombination rates. The joint analysis of the two pedigrees resulted in a highly contiguous map composed of 247 microsatellite markers distributed along all 26 autosomes and the X chromosome. The map is estimated to cover about 84% of the bighorn sheep genome and contains 240 unique positions spanning a sex-averaged distance of 3051 cM with an average inter-marker distance of 14.3 cM. Marker synteny, order, sex-averaged interval lengths and sex-averaged total map lengths were all very similar between sheep species. However, in contrast to domestic sheep, but consistent with the usual pattern for a placental mammal, recombination rates in bighorn sheep were significantly greater in females than in males (~12% difference, resulting in an autosomal female map of 3166 cM and an autosomal male map of 2831 cM. Despite differing genome-wide patterns of heterochiasmy between the sheep species, sexual dimorphism in recombination rates was correlated between orthologous intervals. Conclusions We have developed a first-generation bighorn sheep linkage map that will facilitate future studies of the genetic architecture of trait variation in this species. While domestication has been hypothesized

  6. Fine mapping of the dominant glandless Gene Gle2 in Sea-island cotton (Gossypium barbadense L.)

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Gle2 is a mutant gene that controls glandless trait in cotton plants and seeds. It is an important gene resource to gossypol-free cottonseed breeding. The objective of this research was to develop SSR markers tightly linked with Gle2 by using the F2 segregating population containing 1599 plants derived from the cross of G. hirsutum genetic standard line TM-1 and G. barbadense glandless mutant line Hai-1. Genetic analysis suggested that the Gle2 was an incomplete dominant gene. Based on the backbone of genetic linkage map from G. hirsutum × G. barbadense BC1 published by our laboratory, Gle2 was located between CIR362 and NAU2251b, NAU3860b, STV033, with a genetic distance 9.27 and 0.96 cM, respectively. This result is useful for cloning Gle2 gene by map-based cloning method.

  7. Identification of candidate genes for drought stress tolerance in rice by the integration of a genetic (QTL) map with the rice genome physical map

    Institute of Scientific and Technical Information of China (English)

    WANG Xu-sheng; ZHU Jun; MANSUETO Locedie; BRUSKIEWICH Richard

    2005-01-01

    Genetic improvement for drought stress tolerance in rice involves the quantitative nature of the trait, which reflects the additive effects of several genetic loci throughout the genome. Yield components and related traits under stressed and well-water conditions were assayed in mapping populations derived from crosses of Azucena×IR64 and Azucena×Bala. To find the candidate rice genes underlying Quantitative Trait Loci (QTL) in these populations, we conducted in silico analysis of a candidate region flanked by the genetic markers RM212 and RM319on chromosome 1, proximal to the semi-dwarf (sd1) locus. A total of 175annotated genes were identified from this region. These included 48 genes annotated by functional homology to known genes, 23pseudogenes, 24 ab initio predicted genes supported by an alignment match to an EST (Expressed sequence tag) of unknown function, and 80 hypothetical genes predicted solely by ab initio means. Among these, 16 candidate genes could potentially be involved in drought stress response.

  8. Over half of breakpoints in gene pairs involved in cancer-specific recurrent translocations are mapped to human chromosomal fragile sites

    Directory of Open Access Journals (Sweden)

    Pierce Levi CT

    2009-01-01

    Full Text Available Abstract Background Gene rearrangements such as chromosomal translocations have been shown to contribute to cancer development. Human chromosomal fragile sites are regions of the genome especially prone to breakage, and have been implicated in various chromosome abnormalities found in cancer. However, there has been no comprehensive and quantitative examination of the location of fragile sites in relation to all chromosomal aberrations. Results Using up-to-date databases containing all cancer-specific recurrent translocations, we have examined 444 unique pairs of genes involved in these translocations to determine the correlation of translocation breakpoints and fragile sites in the gene pairs. We found that over half (52% of translocation breakpoints in at least one gene of these gene pairs are mapped to fragile sites. Among these, we examined the DNA sequences within and flanking three randomly selected pairs of translocation-prone genes, and found that they exhibit characteristic features of fragile DNA, with frequent AT-rich flexibility islands and the potential of forming highly stable secondary structures. Conclusion Our study is the first to examine gene pairs involved in all recurrent chromosomal translocations observed in tumor cells, and to correlate the location of more than half of breakpoints to positions of known fragile sites. These results provide strong evidence to support a causative role for fragile sites in the generation of cancer-specific chromosomal rearrangements.

  9. Expression Profiling Coupled with In-silico Mapping Identifies Candidate Genes for Reducing Aflatoxin Accumulation in Maize

    Science.gov (United States)

    Dhakal, Ramesh; Chai, Chenglin; Karan, Ratna; Windham, Gary L.; Williams, William P.; Subudhi, Prasanta K.

    2017-01-01

    Aflatoxin, produced by Aspergillus flavus, is hazardous to health of humans and livestock. The lack of information about large effect QTL for resistance to aflatoxin accumulation is a major obstacle to employ marker-assisted selection for maize improvement. The understanding of resistance mechanisms of the host plant and the associated genes is necessary for improving resistance to A. flavus infection. A suppression subtraction hybridization (SSH) cDNA library was made using the developing kernels of Mp715 (resistant inbred) and B73 (susceptible inbred) and 480 randomly selected cDNA clones were sequenced to identify differentially expressed genes (DEGs) in response to A. flavus infection and map these clones onto the corn genome by in-silico mapping. A total of 267 unigenes were identified and majority of genes were related to metabolism, stress response, and disease resistance. Based on the reverse northern hybridization experiment, 26 DEGs were selected for semi-quantitative RT-PCR analysis in seven inbreds with variable resistance to aflatoxin accumulation at two time points after A. flavus inoculation. Most of these genes were highly expressed in resistant inbreds. Quantitative RT-PCR analysis validated upregulation of PR-4, DEAD-box RNA helicase, and leucine rich repeat family protein in resistant inbreds. Fifty-six unigenes, which were placed on linkage map through in-silico mapping, overlapped the QTL regions for resistance to aflatoxin accumulation identified in a mapping population derived from the cross between B73 and Mp715. Since majority of these mapped genes were related to disease resistance, stress response, and metabolism, these should be ideal candidates to investigate host pathogen interaction and to reduce aflatoxin accumulation in maize. PMID:28428796

  10. Effects of Prior Knowledge and Concept-Map Structure on Disorientation, Cognitive Load, and Learning

    Science.gov (United States)

    Amadieu, Franck; van Gog, Tamara; Paas, Fred; Tricot, Andre; Marine, Claudette

    2009-01-01

    This study explored the effects of prior knowledge (high vs. low; HPK and LPK) and concept-map structure (hierarchical vs. network; HS and NS) on disorientation, cognitive load, and learning from non-linear documents on "the infection process of a retrograde virus (HIV)". Participants in the study were 24 adults. Overall subjective ratings of…

  11. Constructivist-Visual Mind Map Teaching Approach and the Quality of Students' Cognitive Structures

    Science.gov (United States)

    Dhindsa, Harkirat S.; Makarimi-Kasim; Anderson, O. Roger

    2011-01-01

    This study compared the effects of a constructivist-visual mind map teaching approach (CMA) and of a traditional teaching approach (TTA) on (a) the quality and richness of students' knowledge structures and (b) TTA and CMA students' perceptions of the extent that a constructivist learning environment (CLE) was created in their classes. The sample…

  12. Mapping the Structure of Knowledge for Teaching Nominal Categorical Data Analysis

    Science.gov (United States)

    Groth, Randall E.; Bergner, Jennifer A.

    2013-01-01

    This report describes a model for mapping cognitive structures related to content knowledge for teaching. The model consists of knowledge elements pertinent to teaching a content domain, the nature of the connections among them, and a means for representing the elements and connections visually. The model is illustrated through empirical data…

  13. The Structure of the MAP2K MEK6 Reveals an Autoinhibitory Dimer

    Energy Technology Data Exchange (ETDEWEB)

    Min, Xiaoshan; Akella, Radha; He, Haixia; Humphreys, John M.; Tsutakawa, Susan E.; Lee, Seung-Jae; Tainer, John A.; Cobb, Melanie H.; Goldsmith, Elizabeth J.

    2009-07-13

    MAP2Ks are dual-specificity protein kinases functioning at the center of three-tiered MAP kinase modules. The structure of the kinase domain of the MAP2K MEK6 with phosphorylation site mimetic aspartic acid mutations (MEK6/{Delta}N/DD) has been solved at 2.3 {angstrom} resolution. The structure reveals an autoinhibited elongated ellipsoidal dimer. The enzyme adopts an inactive conformation, based upon structural queues, despite the phosphomimetic mutations. Gel filtration and small-angle X-ray scattering analysis confirm that the crystallographically observed ellipsoidal dimer is a feature of MEK6/{Delta}N/DD and full-length unphosphorylated wild-type MEK6 in solution. The interface includes the phosphate binding ribbon of each subunit, part of the activation loop, and a rare 'arginine stack' between symmetry-related arginine residues in the N-terminal lobe. The autoinhibited structure likely confers specificity on active MAP2Ks. The dimer may also serve the function in unphosphorylated MEK6 of preventing activation loop phosphorylation by inappropriate kinases.

  14. Mapping the Structure of Knowledge for Teaching Nominal Categorical Data Analysis

    Science.gov (United States)

    Groth, Randall E.; Bergner, Jennifer A.

    2013-01-01

    This report describes a model for mapping cognitive structures related to content knowledge for teaching. The model consists of knowledge elements pertinent to teaching a content domain, the nature of the connections among them, and a means for representing the elements and connections visually. The model is illustrated through empirical data…

  15. Genetic mapping of the gene for Usher syndrome: Linkage analysis in a large Samaritan kindred

    Energy Technology Data Exchange (ETDEWEB)

    Bonne-Tamir, B.; Korostishevsky, M.; Kalinsky, H.; Seroussi, E.; Beker, R.; Weiss, S. (Sackler Faculty of Medicine, Ramat-Aviv (Israel)); Godel, V. (Ichilov Hospital, Tel-Aviv (Israel))

    1994-03-01

    Usher syndrome is a group of autosomal recessive disorders associated with congenital sensorineural deafness and progressive visual loss due to retinitis pigmentosa. Sixteen members of the small inbred Samaritan isolate with autosomal recessive deafness from 59 individuals including parents and affected and nonaffected sibs were typed for markers on chromosomes 1q and 11q for which linkage has recently been established for Usher syndrome types II and I. Statistically significant linkage was observed with four markers on 11q (D11S533, D11S527, OMP, and INT2) with a maximum six-point location score of 11.61 at the D11S533 locus. Analysis of haplotypes supports the notion that the mutation arose only once in an ancestral chromosome carrying a specific haplotype. The availability of markers closely linked to the disease locus allows indirect genotype analysis and identifies all carriers of the gene within the community. Furthermore, the detection of complete linkage disequilibrium between the D11S533 marker and the Usher gene suggests that these loci are either identical or adjacent and narrows the critical region to which physical mapping efforts are currently directed. 35 refs., 2 figs., 6 tabs.

  16. Gene-based mapping and pathway analysis of metabolic traits in dairy cows.

    Directory of Open Access Journals (Sweden)

    Ngoc-Thuy Ha

    Full Text Available The metabolic adaptation of dairy cows during the transition period has been studied intensively in the last decades. However, until now, only few studies have paid attention to the genetic aspects of this process. Here, we present the results of a gene-based mapping and pathway analysis with the measurements of three key metabolites, (1 non-esterified fatty acids (NEFA, (2 beta-hydroxybutyrate (BHBA and (3 glucose, characterizing the metabolic adaptability of dairy cows before and after calving. In contrast to the conventional single-marker approach, we identify 99 significant and biologically sensible genes associated with at least one of the considered phenotypes and thus giving evidence for a genetic basis of the metabolic adaptability. Moreover, our results strongly suggest three pathways involved in the metabolism of steroids and lipids are potential candidates for the adaptive regulation of dairy cows in their early lactation. From our perspective, a closer investigation of our findings will lead to a step forward in understanding the variability in the metabolic adaptability of dairy cows in their early lactation.

  17. Analysis of the Mitogen-activated protein kinase kinase 4 (MAP2K4 tumor suppressor gene in ovarian cancer

    Directory of Open Access Journals (Sweden)

    Ryland Georgina L

    2011-05-01

    Full Text Available Abstract Background MAP2K4 is a putative tumor and metastasis suppressor gene frequently found to be deleted in various cancer types. We aimed to conduct a comprehensive analysis of this gene to assess its involvement in ovarian cancer. Methods We screened for mutations in MAP2K4 using High Resolution Melt analysis of 149 primary ovarian tumors and methylation at the promoter using Methylation-Specific Single-Stranded Conformation Polymorphism analysis of 39 tumors. We also considered the clinical impact of changes in MAP2K4 using publicly available expression and copy number array data. Finally, we used siRNA to measure the effect of reducing MAP2K4 expression in cell lines. Results In addition to 4 previously detected homozygous deletions, we identified a homozygous 16 bp truncating deletion and a heterozygous 4 bp deletion, each in one ovarian tumor. No promoter methylation was detected. The frequency of MAP2K4 homozygous inactivation was 5.6% overall, and 9.8% in high-grade serous cases. Hemizygous deletion of MAP2K4 was observed in 38% of samples. There were significant correlations of copy number and expression in three microarray data sets. There was a significant correlation between MAP2K4 expression and overall survival in one expression array data set, but this was not confirmed in an independent set. Treatment of JAM and HOSE6.3 cell lines with MAP2K4 siRNA showed some reduction in proliferation. Conclusions MAP2K4 is targeted by genetic inactivation in ovarian cancer and restricted to high grade serous and endometrioid carcinomas in our cohort.

  18. Genetic mapping, marker assisted selection and allelic relationships for the Pu 6 gene conferring rust resistance in sunflower.

    Science.gov (United States)

    Bulos, Mariano; Vergani, Pablo Nicolas; Altieri, Emiliano

    2014-09-01

    Rust resistance in the sunflower line P386 is controlled by Pu 6 , a gene which was reported to segregate independently from other rust resistant genes, such as R 4 . The objectives of this work were to map Pu 6 , to provide and validate molecular tools for its identification, and to determine the linkage relationship of Pu 6 and R 4 . Genetic mapping of Pu 6 with six markers covered 24.8 cM of genetic distance on the lower end of linkage Group 13 of the sunflower consensus map. The marker most closely linked to Pu 6 was ORS316 at 2.5 cM in the distal position. ORS316 presented five alleles when was assayed with a representative set of resistant and susceptible lines. Allelism test between Pu 6 and R 4 indicated that both genes are linked at a genetic distance of 6.25 cM. This is the first confirmation based on an allelism test that at least two members of the R adv /R 4 /R 11 / R 13a /R 13b /Pu 6 cluster of genes are at different loci. A fine elucidation of the architecture of this complex locus will allow designing and constructing completely new genomic regions combining genes from different resistant sources and the elimination of the linkage drag around each resistant gene.

  19. Facet Theory and the Mapping Sentence as Hermeneutically Consistent Structured Meta-Ontology and Structured Meta-Mereology

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    Paul M W Hackett

    2016-03-01

    Full Text Available When behaviour is interpreted in a reliable manner (i.e., robustly across different situations and times its explained meaning may be seen to possess hermeneutic consistency. In this essay I present an evaluation of the hermeneutic consistency that I propose may be present when the research tool know as the mapping sentence is used to create generic structural ontologies. I also claim that theoretical and empirical validity is a likely result of employing the mapping sentence in research design and interpretation. These claims are non-contentious within the realm of quantitative psychological and behavioural research. However, I extend the scope of both facet theory based research and claims for its structural utility, reliability and validity to philosophical and qualitative investigations. I assert that the hermeneutic consistency of a structural ontology is a product of a structural representation’s ontological components and the mereological relationships between these ontological sub-units: the mapping sentence seminally allows for the depiction of such structure.

  20. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon.

    Directory of Open Access Journals (Sweden)

    Yu Cui

    Full Text Available The ND18 strain of Barley stripe mosaic virus (BSMV infects several lines of Brachypodium distachyon, a recently developed model system for genomics research in cereals. Among the inbred lines tested, Bd3-1 is highly resistant at 20 to 25 °C, whereas Bd21 is susceptible and infection results in an intense mosaic phenotype accompanied by high levels of replicating virus. We generated an F(6:7 recombinant inbred line (RIL population from a cross between Bd3-1 and Bd21 and used the RILs, and an F(2 population of a second Bd21 × Bd3-1 cross to evaluate the inheritance of resistance. The results indicate that resistance segregates as expected for a single dominant gene, which we have designated Barley stripe mosaic virus resistance 1 (Bsr1. We constructed a genetic linkage map of the RIL population using SNP markers to map this gene to within 705 Kb of the distal end of the top of chromosome 3. Additional CAPS and Indel markers were used to fine map Bsr1 to a 23 Kb interval containing five putative genes. Our study demonstrates the power of using RILs to rapidly map the genetic determinants of BSMV resistance in Brachypodium. Moreover, the RILs and their associated genetic map, when combined with the complete genomic sequence of Brachypodium, provide new resources for genetic analyses of many other traits.

  1. Co-mapping studies of QTLs for fruit acidity and candidate genes of organic acid metabolism and proton transport in sweet melon (Cucumis melo L.).

    Science.gov (United States)

    Cohen, S; Tzuri, G; Harel-Beja, R; Itkin, M; Portnoy, V; Sa'ar, U; Lev, S; Yeselson, L; Petrikov, M; Rogachev, I; Aharoni, A; Ophir, R; Tadmor, Y; Lewinsohn, E; Burger, Y; Katzir, N; Schaffer, A A

    2012-07-01

    Sweet melon cultivars contain a low level of organic acids and, therefore, the quality and flavor of sweet melon fruit is determined almost exclusively by fruit sugar content. However, genetic variability for fruit acid levels in the Cucumis melo species exists and sour fruit accessions are characterized by acidic fruit pH of 6. In this paper, we report results from a mapping population based on recombinant inbred lines (RILs) derived from the cross between the non-sour 'Dulce' variety and the sour PI 414323 accession. Results show that a single major QTL for pH co-localizes with major QTLs for the two predominant organic acids in melon fruit, citric and malic, together with an additional metabolite which we identified as uridine. While the acidic recombinants were characterized by higher citric and malic acid levels, the non-acidic recombinants had a higher uridine content than did the acidic recombinants. Additional minor QTLs for pH, citric acid and malic acid were also identified and for these the increased acidity was unexpectedly contributed by the non-sour parent. To test for co-localization of these QTLs with genes encoding organic acid metabolism and transport, we mapped the genes encoding structural enzymes and proteins involved in organic acid metabolism, transport and vacuolar H+ pumps. None of these genes co-localized with the major pH QTL, indicating that the gene determining melon fruit pH is not one of the candidate genes encoding this primary metabolic pathway. Linked markers were tested in two additional inter-varietal populations and shown to be linked to the pH trait. The presence of the same QTL in such diverse segregating populations suggests that the trait is determined throughout the species by variability in the same gene and is indicative of a major role of the evolution of this gene in determining the important domestication trait of fruit acidity within the species.

  2. A gene for nystagmus-associated episodic ataxia maps to chromosome 19p

    Energy Technology Data Exchange (ETDEWEB)

    Kramer, P.L.; Root, D.; Gancher, S. [and others

    1994-09-01

    Episodic ataxia (EA) is a rare, autosomal dominant disorder, characterized by attacks of generalized ataxia and relatively normal neurological function between attacks. Onset occurs in childhood or adolescence and persists through adulthood. Penetrance is nearly complete. EA is clinically heterogeneous, including at least two distinct entities: (1) episodes of ataxia and dysarthria lasting hours to days, generally with interictal nystagmus (MIM 108500); (2) episodes of ataxia and dysarthria lasting only minutes, with interictal myokymia (MMM 160120). The EA/nystagmus patients sometimes develop persistent ataxia and cerebellar atrophy. Previously we reported linkage in four EA/myokymia families to a K{sup +} channel gene on chromosome 12p. We excluded this region in a large family with EA/nystagmus. We now report evidence for linkage to chromosome 19p in this and in one other EA/nystagmus family, based on eight microsatellite markers which span approximately 30 cM. The region is flanked distally by D19S209 and proximally by D19S226. All six markers within this region gave positive evidence for linkage; the highest total two-point lod scores occurred wtih D19S221 (3.98 at theta = 0.10) and D19S413 (3.37 at theta = 0.05). Interestingly, Joutel et al. (1993) mapped a gene for familial hemiplegic migraine (FHM) to the region around D19S221. Some individuals in these families have ataxia, cerebellar atrophy and interictal nystagmus, but no episodic ataxia. These results demonstrate that the clinical heterogeneity in EA reflects underlying genetic hetreogeneity. In addition, they suggest that EA/nystagmus and some FHM may represent different mutations in the same gene locus on chromosome 19p.

  3. Damage mapping in structural health monitoring using a multi-grid architecture

    Energy Technology Data Exchange (ETDEWEB)

    Mathews, V. John [Dept. of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT 84112 (United States)

    2015-03-31

    This paper presents a multi-grid architecture for tomography-based damage mapping of composite aerospace structures. The system employs an array of piezo-electric transducers bonded on the structure. Each transducer may be used as an actuator as well as a sensor. The structure is excited sequentially using the actuators and the guided waves arriving at the sensors in response to the excitations are recorded for further analysis. The sensor signals are compared to their baseline counterparts and a damage index is computed for each actuator-sensor pair. These damage indices are then used as inputs to the tomographic reconstruction system. Preliminary damage maps are reconstructed on multiple coordinate grids defined on the structure. These grids are shifted versions of each other where the shift is a fraction of the spatial sampling interval associated with each grid. These preliminary damage maps are then combined to provide a reconstruction that is more robust to measurement noise in the sensor signals and the ill-conditioned problem formulation for single-grid algorithms. Experimental results on a composite structure with complexity that is representative of aerospace structures included in the paper demonstrate that for sufficiently high sensor densities, the algorithm of this paper is capable of providing damage detection and characterization with accuracy comparable to traditional C-scan and A-scan-based ultrasound non-destructive inspection systems quickly and without human supervision.

  4. The human met-ase gene (GZMM): Structure, sequence, and close physical linkage to the serine protease gene cluster on 19p13.3

    Energy Technology Data Exchange (ETDEWEB)

    Pilat, D.; Zimmer, M.; Wekerle, H. [Max-Planck-Institut fuer Psychiatrie, Martinsried (Germany)] [and others

    1994-12-01

    Cosmid clones containing the genes for the human and murine natural killer cell serine protease Met-ase (gene symbol GZMM; granzyme M) were identified by screening human and murine cosmid libraries with rat Met-ase (RNIK-Met-1) cDNA. The human gene has a size of 7.5 kb and an exon-intron structure identical to that of serine protease genes located on human chromosomes 5q11-q12, 14q11.2, and 19p13.3 that are expressed by lymphocytes, mast cells, or myelomonocyte precursors. Using cosmid DNA as a probe for fluorescence in situ hybridization, we identified the chromosomal position of human Met-ase as 19p13.3. Interphase studies with two differentially labeled probes for Met-ase and the azurocidin (AZU1), proteinase 3 (PRTN3), and neutrophil elastase (ELA2) gene cluster revealed that the distance of Met-ase from this gene cluster is in the range of 200 to 500 kb. Using differentially labeled mouse cosmid probes, we also mapped the murine gene for Met-ase to chromosomal band 10C, close to the gene for lamin B2. Thus, the Met-ase, AZU1, PRTN3, and ELA2 genes fall into an established region of homology between mouse chromosomal band 10C and human 19p13.3. 35 refs., 4 figs.

  5. BATTEN-DISEASE GENE, CLN3 - LINKAGE DISEQUILIBRIUM MAPPING IN THE FINNISH POPULATION, AND ANALYSIS OF EUROPEAN HAPLOTYPES

    NARCIS (Netherlands)

    MITCHISON, HM; ORAWE, AM; TASCHNER, PEM; SANDKUIJL, LA; SANTAVUORI, P; DEVOS, N; BREUNING, MH; MOLE, SE; GARDINER, RM; JARVELA, IE

    The gene for Batten disease (juvenile-onset neuronal ceroid lipofuscinosis, or Spielmeyer-Sjogren disease), CLN3, maps to 16p11.2-12.1. Four microsatellite markers-D16S288, D16S299, D16S298, and SPN-are in strong linkage disequilibrium with CLN3 in 142 families from 16 different countries. These

  6. SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

    Directory of Open Access Journals (Sweden)

    Parida Swarup K

    2012-08-01

    Full Text Available Abstract Background Single nucleotide polymorphism (SNP validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. Results Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%. Of these 325 (84.6% showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. Conclusions SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice.

  7. Epigenome mapping highlights chromatin-mediated gene regulation in the protozoan parasite Trichomonas vagi