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Sample records for cd genome allotetraploid

  1. Analysis of complete nucleotide sequences of 12 Gossypium chloroplast genomes: origin and evolution of allotetraploids.

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    Qin Xu

    Full Text Available BACKGROUND: Cotton (Gossypium spp. is a model system for the analysis of polyploidization. Although ascertaining the donor species of allotetraploid cotton has been intensively studied, sequence comparison of Gossypium chloroplast genomes is still of interest to understand the mechanisms underlining the evolution of Gossypium allotetraploids, while it is generally accepted that the parents were A- and D-genome containing species. Here we performed a comparative analysis of 13 Gossypium chloroplast genomes, twelve of which are presented here for the first time. METHODOLOGY/PRINCIPAL FINDINGS: The size of 12 chloroplast genomes under study varied from 159,959 bp to 160,433 bp. The chromosomes were highly similar having >98% sequence identity. They encoded the same set of 112 unique genes which occurred in a uniform order with only slightly different boundary junctions. Divergence due to indels as well as substitutions was examined separately for genome, coding and noncoding sequences. The genome divergence was estimated as 0.374% to 0.583% between allotetraploid species and A-genome, and 0.159% to 0.454% within allotetraploids. Forty protein-coding genes were completely identical at the protein level, and 20 intergenic sequences were completely conserved. The 9 allotetraploids shared 5 insertions and 9 deletions in whole genome, and 7-bp substitutions in protein-coding genes. The phylogenetic tree confirmed a close relationship between allotetraploids and the ancestor of A-genome, and the allotetraploids were divided into four separate groups. Progenitor allotetraploid cotton originated 0.43-0.68 million years ago (MYA. CONCLUSION: Despite high degree of conservation between the Gossypium chloroplast genomes, sequence variations among species could still be detected. Gossypium chloroplast genomes preferred for 5-bp indels and 1-3-bp indels are mainly attributed to the SSR polymorphisms. This study supports that the common ancestor of diploid A-genome

  2. Evidence of genomic exchanges between homeologous chromosomes in a cross of peanut with newly synthetized allotetraploid hybrids

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    Joel Romaric Nguepjop

    2016-11-01

    Full Text Available Cultivated peanut and synthetics are allotetraploids (2n=4x=40 with two homeologous sets of chromosomes. Meiosis in allotetraploid peanut is generally thought to show diploid-like behavior. However, a recent study pointed out the occurrence of recombination between homeologous chromosomes, especially when synthetic allotetraploids are used, challenging the view of disomic inheritance in peanut. In this study, we investigated the meiotic behavior of allotetraploid peanut using 380 SSR markers and 90 F2 progeny derived from the cross between Arachis hypogaea cv Fleur 11 (AABB and ISATGR278-18 (AAKK, a synthetic allotetraploid that harbors a K-genome that was reported to pair with the cultivated B-genome during meiosis. Segregation analysis of SSR markers showed 42 codominant SSRs with unexpected null bands among some progeny. Chi-square tests for these loci deviate from the expected 1:2:1 Mendelian ratio under disomic inheritance. A linkage map of 357 codominant loci aligned on 20 linkage groups (LGs with a total length of 1728 cM, averaging 5.1 cM between markers, was developed. Among the ten homeologous sets of LGs, one set consisted of markers that all segregated in a polysomic-like pattern, 6 in a likely disomic pattern and the 3 remaining in a mixed pattern with disomic and polysomic loci clustered on the same LG. Moreover, we reported a substitution of homeologous chromosomes in some progeny. Our results suggest that the homeologous recombination events occurred between the A and K genomes in the newly synthesized allotetraploid and have been highlighted in the progeny. Homeologous exchanges are rarely observed in tetraploid peanut and have not yet been reported for AAKK and AABB genomes. The implications of these results on peanut breeding are discussed.

  3. Evidence of Genomic Exchanges between Homeologous Chromosomes in a Cross of Peanut with Newly Synthetized Allotetraploid Hybrids

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    Nguepjop, Joel R.; Tossim, Hodo-Abalo; Bell, Joseph M.; Rami, Jean-François; Sharma, Shivali; Courtois, Brigitte; Mallikarjuna, Nalini; Sane, Djibril; Fonceka, Daniel

    2016-01-01

    Cultivated peanut and synthetics are allotetraploids (2n = 4x = 40) with two homeologous sets of chromosomes. Meiosis in allotetraploid peanut is generally thought to show diploid-like behavior. However, a recent study pointed out the occurrence of recombination between homeologous chromosomes, especially when synthetic allotetraploids are used, challenging the view of disomic inheritance in peanut. In this study, we investigated the meiotic behavior of allotetraploid peanut using 380 SSR markers and 90 F2 progeny derived from the cross between Arachis hypogaea cv Fleur 11 (AABB) and ISATGR278-18 (AAKK), a synthetic allotetraploid that harbors a K-genome that was reported to pair with the cultivated B-genome during meiosis. Segregation analysis of SSR markers showed 42 codominant SSRs with unexpected null bands among some progeny. Chi-square tests for these loci deviate from the expected 1:2:1 Mendelian ratio under disomic inheritance. A linkage map of 357 codominant loci aligned on 20 linkage groups (LGs) with a total length of 1728 cM, averaging 5.1 cM between markers, was developed. Among the 10 homeologous sets of LGs, one set consisted of markers that all segregated in a polysomic-like pattern, six in a likely disomic pattern and the three remaining in a mixed pattern with disomic and polysomic loci clustered on the same LG. Moreover, we reported a substitution of homeologous chromosomes in some progeny. Our results suggest that the homeologous recombination events occurred between the A and K genomes in the newly synthesized allotetraploid and have been highlighted in the progeny. Homeologous exchanges are rarely observed in tetraploid peanut and have not yet been reported for AAKK and AABB genomes. The implications of these results on peanut breeding are discussed. PMID:27847512

  4. BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated peanut

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    Chaine Christian

    2008-01-01

    Full Text Available Abstract Background Cultivated peanut, Arachis hypogaea is an allotetraploid of recent origin, with an AABB genome. In common with many other polyploids, it seems that a severe genetic bottle-neck was imposed at the species origin, via hybridisation of two wild species and spontaneous chromosome duplication. Therefore, the study of the genome of peanut is hampered both by the crop's low genetic diversity and its polyploidy. In contrast to cultivated peanut, most wild Arachis species are diploid with high genetic diversity. The study of diploid Arachis genomes is therefore attractive, both to simplify the construction of genetic and physical maps, and for the isolation and characterization of wild alleles. The most probable wild ancestors of cultivated peanut are A. duranensis and A. ipaënsis with genome types AA and BB respectively. Results We constructed and characterized two large-insert libraries in Bacterial Artificial Chromosome (BAC vector, one for each of the diploid ancestral species. The libraries (AA and BB are respectively c. 7.4 and c. 5.3 genome equivalents with low organelle contamination and average insert sizes of 110 and 100 kb. Both libraries were used for the isolation of clones containing genetically mapped legume anchor markers (single copy genes, and resistance gene analogues. Conclusion These diploid BAC libraries are important tools for the isolation of wild alleles conferring resistances to biotic stresses, comparisons of orthologous regions of the AA and BB genomes with each other and with other legume species, and will facilitate the construction of a physical map.

  5. Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons

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    Cotton domestication was achieved by converting perennial trees into annual crops. After ploidization, two allotetraploid species, Gossypium hirsutum and G. barbadense, were domesticated and are cultivated worldwide. However, the overall genetic diversity between and within the cultivated species is...

  6. Genetic Segregation and Genomic Hybridization Patterns Support an Allotetraploid Structure and Disomic Inheritance for Salix Species

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    Gianni Barcaccia

    2014-09-01

    Full Text Available The Salix alba L. (white willow—Salix fragilis L. (crack willow complex includes closely related polyploid species, mainly tetraploid (2n = 4x = 76, which are dioecious and hence obligate allogamous. Because little is known about the genome constitution and chromosome behavior of these pure willow trees, genetic analysis of their naturally occurring interspecific polyploid hybrids is still very difficult. A two-way pseudo-testcross strategy was exploited using single-dose AFLP markers in order to assess the main inheritance patterns of tetraploid biotypes (disomy vs. tetrasomy in segregating populations stemmed from S. alba × S. fragilis crosses and reciprocals. In addition, a genomic in situ hybridization (GISH technology was implemented in willow to shed some light on the genome structure of S. alba and S. fragilis species, and their hybrids (allopolyploidy vs. autopolyploidy. The frequency of S. alba-specific molecular markers was almost double compared to that of S. fragilis-specific ones, suggesting the phylogenetic hypothesis of S. fragilis as derivative species from S. alba-like progenitors. Cytogenetic observations at pro-metaphase revealed about half of the chromosome complements being less contracted than the remaining ones, supporting an allopolyploid origin of both S. alba and S. fragilis. Both genetic segregation and genomic hybridization data are consistent with an allotetraploid nature of the Salix species. In particular, the vast majority of the AFLP markers were inherited according to disomic patterns in S. alba × S. fragilis populations and reciprocals. Moreover, in all S. alba against S. fragilis hybridizations and reciprocals, GISH signals were observed only on the contracted chromosomes whereas the non-contracted chromosomes were never hybridized. In conclusion, half of the chromosomes of the pure species S. alba and S. fragilis are closely related and they could share a common diploid ancestor, while the rest of

  7. Genome-Wide Gene Expressions Respond Differently to A-subgenome Origins in Brassica napus Synthetic Hybrids and Natural Allotetraploid

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    Zhang, Dawei; Pan, Qi; Tan, Chen; Zhu, Bin; Ge, Xianhong; Shao, Yujiao; Li, Zaiyun

    2016-01-01

    The young allotetraploid Brassica napus (2n = 38, AACC) is one of models to study genomic responses to allopolyploidization. The extraction of AA component from natural B. napus and then restitution of progenitor B. rapa should provide a unique opportunity to reveal the genome interplay for gene expressions during the evolution. Herein, B. napus hybrids (2n = 19, AC) between the extracted and extant B. rapa (2n = 20, AA) and the same B. oleracea genotype (2n = 18, CC) were studied by RNA-seq and compared with natural B. napus donor, to reveal the gene expression changes from hybridization and domestication and the effects of A genome with different origins. Upon the initial merger of two diploid genomes, additive gene expression was prevalent in these two hybrids, for non-additively expressed genes only represented a small portion of total expressed genes. A high proportion of genes exhibited expression level dominance, with no preference to either of the parental genomes. Comparison of homoeolog expressions also showed no bias toward any genomes and the parental expression patterns were often maintained in the hybrids and natural allotetraploids. Although, the overall patterns of gene expression were highly conserved between two hybrids, the extracted B. rapa responded less and appeared more compatible for hybridization than the extant B. rapa. Our results suggested that expression level dominance and homoeolog expressions bias were balanced at the initial stage of genome merger, and such balance were largely maintained during the domestication of B. napus, despite the increased extent over time. PMID:27790227

  8. Introgression into the allotetraploid coffee ( Coffea arabica L.): segregation and recombination of the C. canephora genome in the tetraploid interspecific hybrid ( C. arabicax C. canephora).

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    Herrera, J. C.; Combes, M. C.; Anthony, F.; Charrier, A.; Lashermes, P.

    2002-03-01

    Transfer of desired characters from the diploid relative species such as Coffea canephora into the cultivated allotetraploid coffee species ( Coffea arabica L.) is essential to the continued improvement of varieties. Behaviour of the C. canephora genome and its interaction with the C. arabica genome were investigated in tetraploid interspecific hybrids ( C. arabicax C. canephora 4 x) resulting from a cross between an accession of C. arabica and a tetraploid plant of C. canephora obtained following colchicine treatment. Segregation and co-segregation of restriction fragment length polymorphism (RFLP) and microsatellite loci-markers were studied in two BC(1) populations. These two populations of 28 and 45 individuals, respectively, resulted from the backcross of two tetraploid F(1)plants to C. arabica. The presence in BC(1) plants of specific C. canephora markers was scored for 24 loci (11 RFLP and 13 microsatellites) distributed on at least 7 of the 11 linkage groups identified in C. canephora. At almost all loci analysed, the segregation of C. canephora alleles transmitted by the ( C. arabicax C. canephora 4 x) hybrids conformed to the expected ratio assuming random chromosome segregation and the absence of selection. The recombination fractions of C. canephorachromosome segments were estimated for seven marker intervals, and compared with the recombination fractions previously observed in C. canephora for the equivalent marker intervals. The recombination frequencies estimated in both plant materials were rather similar, suggesting that recombination in the ( C. arabicax C. canephora 4 x) hybrid is not significantly restricted by the genetic differentiation between chromosomes belonging to the different genomes. The hybrid ( C. arabicax C. canephora 4 x) therefore appeared particularly favourable to intergenomic recombination events and gene introgressions.

  9. Identification and Analyses of miRNA Genes in Allotetraploid Gossypium hirsutum Fiber Cells Based on the Sequenced Diploid G.raimondii Genome

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    Qin Li; Xiang Jin; Yu-Xian Zhu

    2012-01-01

    The plant genome possesses a large number of microRNAs (miRNAs) mainly 21-24 nucleotides in length.They play a vital role in regulation of target gene expression at various stages throughout the whole plant life cycle.Here we sequenced and analyzed ~ 10 million non-coding RNAs (ncRNAs) derived from fiber tissue of the allotetraploid cotton (Gossypium hirsutum) 7 days post-anthesis using ncRNA-seq technology.In terms of distinct reads,24 nt ncRNA is by far the dominant species,followed by 21 nt and 23 nt ncRNAs.Using ab initio prediction,we identified and characterized a total of 562 candidate miRNA gene loci on the recently assembled D5 genome of the diploid cotton G.raimondii.Of all the 562 predicted miRNAs,22 were previously discovered in cotton species and 187 had sequence conservation and homology to homologous miRNAs of other plant species.Nucleotide bias analysis showed that the 9th and 1st positions were significantly conserved among different types of miRNA genes.Among the 463 putative miRNA target genes,most significant up/down-regulation occurred in 10-20 days post-anthesis,indicating that miRNAs played an important role during the elongation and secondary cell wall synthesis stages of cotton fiber developmem.The discovery of new miRNA genes will help understand the mechanisms of miRNA generation and regulation in cotton.

  10. Comparative Genetics of Floral Morphology in Diploid and Allotetraploid Gossypium

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    CHEE Peng W

    2008-01-01

    @@ The cultivated Gossypium A genome diploid species G.arboreum and G.herbaceum and the allotetraploid species G.hirsutum and G.barbadense share common morphology for various floral traits,which offers an ideal system in which to investigate genetic mechanisms that differentiate diploid and tetraploid genomes.For example,knowing how a single phenotype behaves in the diploids,and comparing the same trait with different dosage effects in the tetraploids,may provide a means to study inter- and intra-genomic interactions in the polyploid genome.

  11. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

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    Cotton is the world’s most important natural textile fibre and a significant oilseed crop. Upland cotton (Gossypium hirsutum L.), an allotetraploid derived from A- and D-genome progenitors, accounts for >95% of world production. Here, we sequenced and assembled 88% of the 2.5-gigabase genome of the ...

  12. Crossovers get a boost in Brassica allotriploid and allotetraploid hybrids.

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    Leflon, Martine; Grandont, Laurie; Eber, Frédérique; Huteau, Virginie; Coriton, Olivier; Chelysheva, Liudmila; Jenczewski, Eric; Chèvre, Anne-Marie

    2010-07-01

    Meiotic crossovers are necessary to generate balanced gametes and to increase genetic diversity. Even if crossover number is usually constrained, recent results suggest that manipulating karyotype composition could be a new way to increase crossover frequency in plants. In this study, we explored this hypothesis by analyzing the extent of crossover variation in a set of related diploid AA, allotriploid AAC, and allotetraploid AACC Brassica hybrids. We first used cytogenetic methods to describe the meiotic behavior of the different hybrids. We then combined a cytogenetic estimation of class I crossovers in the entire genome by immunolocalization of a key protein, MutL Homolog1, which forms distinct foci on meiotic chromosomes, with genetic analyses to specifically compare crossover rates between one pair of chromosomes in the different hybrids. Our results showed that the number of crossovers in the allotriploid AAC hybrid was higher than in the diploid AA hybrid. Accordingly, the allotetraploid AACC hybrid showed an intermediate behavior. We demonstrated that this increase was related to hybrid karyotype composition (diploid versus allotriploid versus allotetraploid) and that interference was maintained in the AAC hybrids. These results could provide another efficient way to manipulate recombination in traditional breeding and genetic studies.

  13. Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties.

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    Yasui, Yasuo; Hirakawa, Hideki; Oikawa, Tetsuo; Toyoshima, Masami; Matsuzaki, Chiaki; Ueno, Mariko; Mizuno, Nobuyuki; Nagatoshi, Yukari; Imamura, Tomohiro; Miyago, Manami; Tanaka, Kojiro; Mise, Kazuyuki; Tanaka, Tsutomu; Mizukoshi, Hiroharu; Mori, Masashi; Fujita, Yasunari

    2016-12-01

    Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution.

  14. Evolutionary analysis of allotetraploid hybrids of red crucian carp × common carp,based on ISSR,AFLP molecular markers and cloning of cyclins genes

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    LIU LiangGuo; YAN JinPeng; LIU ShaoJun; LIU Dong; YOU CuiPing; ZHONG Huan; TAO Min; LIU Yun

    2009-01-01

    The allotetraploid hybrids of red crucian carp × common carp are the first reported artificially cultured polyploid fish with bisexual fertility and stable inheritance in vertebrate.Using ISSR and AFLP markers and the cyclins genes,the genomes and cyclin gene sequence changes were analyzed between the allotetraploid hybrids and their parents.The results indicated that the allotetraploids inherited many genetic characteristics from their parents and the genetic characteristics were stable after 15 generations.However,the allotetraploids had a closer genetic relationship with their original female parents and represented a bias toward the maternal progenitor.DNA fingerprinting analysis showed that the allotetraploids had undergone sequences deletion from their original parents and that the deleted sequences were mostly from the male parent's genome.Some non-parental bands were found in the allotetraploid hybrids.Sequences analysis of the cyclin A1 and B1 genes showed nonsynonymous substitutions of single nucleotides in codons that were different from their original parents,leading to non-parental amino acid loci.We speculate that the non-additivity in the allotetraploids,compared with their progenitors,could be an adjustment to the genomic shock from heterozygosity and polyploidy, allowing maintenance of genetic stability.

  15. Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces.

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    Alexander, William G; Peris, David; Pfannenstiel, Brandon T; Opulente, Dana A; Kuang, Meihua; Hittinger, Chris Todd

    2016-04-01

    Saccharomyces interspecies hybrids are critical biocatalysts in the fermented beverage industry, including in the production of lager beers, Belgian ales, ciders, and cold-fermented wines. Current methods for making synthetic interspecies hybrids are cumbersome and/or require genome modifications. We have developed a simple, robust, and efficient method for generating allotetraploid strains of prototrophic Saccharomyces without sporulation or nuclear genome manipulation. S. cerevisiae×S. eubayanus, S. cerevisiae×S. kudriavzevii, and S. cerevisiae×S. uvarum designer hybrid strains were created as synthetic lager, Belgian, and cider strains, respectively. The ploidy and hybrid nature of the strains were confirmed using flow cytometry and PCR-RFLP analysis, respectively. This method provides an efficient means for producing novel synthetic hybrids for beverage and biofuel production, as well as for constructing tetraploids to be used for basic research in evolutionary genetics and genome stability.

  16. Molecular and cytogenetic evidence for an allotetraploid origin of Chenopodium quinoa and C. berlandieri (Amaranthaceae).

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    Kolano, Bozena; McCann, Jamie; Orzechowska, Maja; Siwinska, Dorota; Temsch, Eva; Weiss-Schneeweiss, Hanna

    2016-07-01

    Most of the cultivated chenopods are polyploids, but their origin and evolutionary history are still poorly understood. Phylogenetic analyses of DNA sequences of four plastid regions, nrITS and nuclear 5S rDNA spacer region (NTS) of two tetraploid chenopods (2n=4x=36), Andean C. quinoa and North American C. berlandieri, and their diploid relatives allowed inferences of their origin. The phylogenetic analyses confirmed allotetraploid origin of both tetraploids involving diploids of two different genomic groups (genomes A and B) and suggested that these two might share very similar parentage. The hypotheses on the origin of the two allopolyploid species were further tested using genomic in situ hybridization (GISH). Several diploid Chenopodium species belonging to the two lineages, genome A and B, suggested by phylogenetic analyses, were tested as putative parental taxa. GISH differentiated two sets of parental chromosomes in both tetraploids and further corroborated their allotetraploid origin. Putative diploid parental taxa have been suggested by GISH for C. quinoa and C. berlandieri. Genome sizes of the analyzed allotetraploids fit nearly perfectly the expected additive values of the putative parental taxa. Directional and uniparental loss of rDNA loci of the maternal A-subgenome was revealed for both C. berlandieri and C. quinoa.

  17. Effect of ploidy increase on transgene expression: example from Citrus diploid cybrid and allotetraploid somatic hybrid expressing the EGFP gene.

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    Xu, Shi-Xiao; Cai, Xiao-Dong; Tan, Bin; Li, Ding-Li; Guo, Wen-Wu

    2011-07-01

    Polyploidization is an important speciation mechanism for all eukaryotes, and it has profound impacts on biodiversity dynamics and ecosystem functioning. Green fluorescent protein (GFP) has been used as an effective marker to visually screen somatic hybrids at an early stage in protoplast fusion. We have previously reported that the intensity of GFP fluorescence of regenerated embryoids was also an early indicator of ploidy level. However, little is known concerning the effects of ploidy increase on the GFP expression in citrus somatic hybrids at the plant level. Herein, allotetraploid and diploid cybrid plants with enhanced GFP (EGFP) expression were regenerated from the fusion of embryogenic callus protoplasts from 'Murcott' tangor (Citrus reticulata Blanco × Citrus sinensis (L.) Osbeck) and mesophyll protoplasts from transgenic 'Valencia' orange (C. sinensis (L.) Osbeck) expressing the EGFP gene, via electrofusion. Subsequent simple sequence repeat (SSR), chloroplast simple sequence repeat and cleaved amplified polymorphic sequence analysis revealed that the two regenerated tetraploid plants were true allotetraploid somatic hybrids possessing nuclear genomic DNA of both parents and cytoplasmic DNA from the callus parent, while the five regenerated diploid plants were cybrids containing nuclear DNA of the leaf parent and with complex segregation of cytoplasmic DNA. Furthermore, EGFP expression was compared in cells and protoplasts from mature leaves of these diploid cybrids and allotetraploid somatic hybrids. Results showed that the intensity of GFP fluorescence per cell or protoplast in diploid was generally brighter than in allotetraploid. Moreover, same hybridization signal was detected on allotetraploid and diploid plants by Southern blot analysis. By real-time RT-PCR and Western blot analysis, GFP expression level of the diploid cybrid was revealed significantly higher than that of the allotetraploid somatic hybrid. These results suggest that ploidy

  18. Non-additive gene regulation in a citrus allotetraploid somatic hybrid between C. reticulata Blanco and C. limon (L.) Burm.

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    Bassene, J B; Froelicher, Y; Dubois, C; Ferrer, R M; Navarro, L; Ollitrault, P; Ancillo, G

    2010-09-01

    Polyploid plants often produce new phenotypes, exceeding the range of variability existing in the diploid gene pool. Several hundred citrus allotetraploid hybrids have been created by somatic hybridization. These genotypes are interesting models to study the immediate effects of allopolyploidization on the regulation of gene expression. Here, we report genome-wide gene expression analysis in fruit pulp of a Citrus interspecific somatic allotetraploid between C. reticulata cv 'Willowleaf mandarin'+C. limon cv 'Eureka lemon', using a Citrus 20K cDNA microarray. Around 4% transcriptome divergence was observed between the two parental species, and 212 and 160 genes were more highly expressed in C. reticulata and C. limon, respectively. Differential expression of certain genes was confirmed by quantitative real-time RT-PCR. A global downregulation of the allotetraploid hybrid transcriptome was observed, as compared with a theoretical mid parent, for the genes displaying interspecific expression divergence between C. reticulata and C. limon. The genes underexpressed in mandarin, as compared with lemon, were also systematically repressed in the allotetraploid. When genes were overexpressed in C. reticulata compared with C. limon, the distribution of allotetraploid gene expression was far more balanced. Cluster analysis on the basis of gene expression clearly indicated the hybrid was much closer to C. reticulata than to C. limon. These results suggest there is a global dominance of the mandarin transcriptome, in consistence with our previous studies on aromatic compounds and proteomics. Interspecific differentiation of gene expression and non-additive gene regulation involved various biological pathways and different cellular components.

  19. Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae allotetraploids

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    Soltis Pamela S

    2010-09-01

    Full Text Available Abstract Background Tragopogon mirus and T. miscellus are allotetraploids (2n = 24 that formed repeatedly during the past 80 years in eastern Washington and adjacent Idaho (USA following the introduction of the diploids T. dubius, T. porrifolius, and T. pratensis (2n = 12 from Europe. In most natural populations of T. mirus and T. miscellus, there are far fewer 35S rRNA genes (rDNA of T. dubius than there are of the other diploid parent (T. porrifolius or T. pratensis. We studied the inheritance of parental rDNA loci in allotetraploids resynthesized from diploid accessions. We investigate the dynamics and directionality of these rDNA losses, as well as the contribution of gene copy number variation in the parental diploids to rDNA variation in the derived tetraploids. Results Using Southern blot hybridization and fluorescent in situ hybridization (FISH, we analyzed copy numbers and distribution of these highly reiterated genes in seven lines of synthetic T. mirus (110 individuals and four lines of synthetic T. miscellus (71 individuals. Variation among diploid parents accounted for most of the observed gene imbalances detected in F1 hybrids but cannot explain frequent deviations from repeat additivity seen in the allotetraploid lines. Polyploid lineages involving the same diploid parents differed in rDNA genotype, indicating that conditions immediately following genome doubling are crucial for rDNA changes. About 19% of the resynthesized allotetraploid individuals had equal rDNA contributions from the diploid parents, 74% were skewed towards either T. porrifolius or T. pratensis-type units, and only 7% had more rDNA copies of T. dubius-origin compared to the other two parents. Similar genotype frequencies were observed among natural populations. Despite directional reduction of units, the additivity of 35S rDNA locus number is maintained in 82% of the synthetic lines and in all natural allotetraploids. Conclusions Uniparental reductions of

  20. Connecting Anxiety and Genomic Copy Number Variation: A Genome-Wide Analysis in CD-1 Mice.

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    Julia Brenndörfer

    Full Text Available Genomic copy number variants (CNVs have been implicated in multiple psychiatric disorders, but not much is known about their influence on anxiety disorders specifically. Using next-generation sequencing (NGS and two additional array-based genotyping approaches, we detected CNVs in a mouse model consisting of two inbred mouse lines showing high (HAB and low (LAB anxiety-related behavior, respectively. An influence of CNVs on gene expression in the central (CeA and basolateral (BLA amygdala, paraventricular nucleus (PVN, and cingulate cortex (Cg was shown by a two-proportion Z-test (p = 1.6 x 10-31, with a positive correlation in the CeA (p = 0.0062, PVN (p = 0.0046 and Cg (p = 0.0114, indicating a contribution of CNVs to the genetic predisposition to trait anxiety in the specific context of HAB/LAB mice. In order to confirm anxiety-relevant CNVs and corresponding genes in a second mouse model, we further examined CD-1 outbred mice. We revealed the distribution of CNVs by genotyping 64 CD 1 individuals using a high-density genotyping array (Jackson Laboratory. 78 genes within those CNVs were identified to show nominally significant association (48 genes, or a statistical trend in their association (30 genes with the time animals spent on the open arms of the elevated plus-maze (EPM. Fifteen of them were considered promising candidate genes of anxiety-related behavior as we could show a significant overlap (permutation test, p = 0.0051 with genes within HAB/LAB CNVs. Thus, here we provide what is to our knowledge the first extensive catalogue of CNVs in CD-1 mice and potential corresponding candidate genes linked to anxiety-related behavior in mice.

  1. Genetic relationships between diploid and allotetraploid cherry species (Prunus avium, Prunus x gondouinii and Prunus cerasus).

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    Tavaud, M; Zanetto, A; David, J L; Laigret, F; Dirlewanger, E

    2004-12-01

    Prunus avium L. (diploid, AA, 2n=2x=16), Prunus cerasus L. (allotetraploid, AAFF, 2n=4x=32) species, and their hybrid Prunus x gondouinii Rehd., constitute the most widely cultivated cherry tree species. P. cerasus is supposed to be an hybrid species produced by the union of unreduced P. avium gametes and normal P. fruticosa gametes. A continuum of morphological traits between these three species makes their assignation difficult. The aim of this paper is to study the genetic relationships between tetraploid and diploid cherry species. In all, 114 genotypes belonging to these species were analyzed using 75 AFLP markers. The coordinates of these genotypes on the first axis of a correspondence analysis allowed us to clearly distinguish each species, to identify misclassifications and to assign unknown genotypes to one species. We showed that there are specific alleles in P. cerasus, which are not present in the A genome of P. avium and which probably come from the F genome of P. cerasus. The frequencies of each marker in the A and the F genomes were estimated in order to identify A and F specific markers. We discuss the utility of these specific markers for finding the origin of the A and F genomes in the allopolyploid species.

  2. Identification of the chromosome complement and the spontaneous 1R/1V translocations in allotetraploid Secale cereale × Dasypyrum villosum hybrids through cytogenetic approaches.

    Science.gov (United States)

    Książczyk, Tomasz; Apolinarska, Barbara; Kulak-Książczyk, Sylwia; Wiśniewska, Halina; Stojałowski, Stefan; Łapiński, Mirosław

    2011-08-01

    Genome modifications that occur at the initial interspecific hybridization event are dynamic and can be consolidated during the process of stabilization in successive generations of allopolyploids. This study identifies the number and chromosomal location of ribosomal DNA (rDNA) sites between Secale cereale, Dasypyrum villosum, and their allotetraploid S. cereale × D. villosum hybrids. For the first time, we show the advantages of FISH to reveal chromosome rearrangements in the tetraploid Secale × Dasypyrum hybrids. Based on the specific hybridization patterns of ribosomal 5S, 35S DNA and rye species-specific pSc200 DNA probes, a set of genotypes with numerous Secale/Dasypyrum translocations of 1R/1V chromosomes were identified in successive generations of allotetraploid S. cereale × D. villosum hybrids. In addition we analyse rye chromosome pairs using FISH with chromosome-specific DNA sequences on S. cereale × D. villosum hybrids.

  3. Tapping CD4 T cells for cancer immunotherapy: the choice of personalized genomics.

    Science.gov (United States)

    Zanetti, Maurizio

    2015-03-01

    Cellular immune responses that protect against tumors typically have been attributed to CD8 T cells. However, CD4 T cells also play a central role. It was shown recently that, in a patient with metastatic cholangiocarcinoma, CD4 T cells specific for a peptide from a mutated region of ERBB2IP could arrest tumor progression. This and other recent findings highlight new opportunities for CD4 T cells in cancer immunotherapy. In this article, I discuss the role and regulation of CD4 T cells in response to tumor Ags. Emphasis is placed on the types of Ags and mechanisms that elicit tumor-protective responses. I discuss the advantages and drawbacks of cancer immunotherapy through personalized genomics. These considerations should help to guide the design of next-generation therapeutic cancer vaccines.

  4. A population genetic model to infer allotetraploid speciation and long-term evolution applied to two yarrow species.

    Science.gov (United States)

    Guo, Yan-Ping; Tong, Xiao-Yuan; Wang, Lan-Wei; Vogl, Claus

    2013-07-01

    Allotetraploid speciation, that is, the generation of a hybrid tetraploid species from two diploid species, and the long-term evolution of tetraploid populations and species are important in plants. We developed a population genetic model to infer population genetic parameters of tetraploid populations from data of the progenitor and descendant species. Two yarrow species, Achillea alpina-4x and A. wilsoniana-4x, arose by allotetraploidization from the diploid progenitors, A. acuminata-2x and A. asiatica-2x. Yet, the population genetic process has not been studied in detail. We applied the model to sequences of three nuclear genes in populations of the four yarrow species and compared their pattern of variability with that in four plastid regions. The plastid data indicated that the two tetraploid species probably originated from multiple independent allopolyploidization events and have accumulated many mutations since. With the nuclear data, we found a low rate of homeologous recombination or gene conversion and a reduction in diversity relative to the level of both diploid species combined. The present analysis with a novel probabilistic model suggests a genetic bottleneck during tetraploid speciation, that the two tetraploid species have a long evolutionary history, and that they have a small amount of genetic exchange between the homeologous genomes.

  5. RAPD-based genetic analysis of offsprings from the sexual cross using allotetraploid citrus somatic hybrid as pollen parent

    Institute of Scientific and Technical Information of China (English)

    YI HuaLin; DENG XiuXin

    2007-01-01

    Huazhong Agricultural University, Wuhan 430070, ChinaThirty-one polymorphic decamer primers were selected to genotype 92 progenies from the cross between Yiben No,4, a monoembryonic diploid F1 hybrid of Citrus reticulata Blanco cv Huanongbendizao tangerine and C. ichangensis Swingle, and [Hamlin sweet orange + Rough lemon], an allotetraploid somatic hybrid of Citrus sinensis Osbeck cv. Hamlin and C. jambhiri Lush cv. Rough Lemon. x2(Chi-square) analysis of RAPD markers in the progenies indicated they were randomly transmitted from the four donor parents, without significant difference between the diploids and triploids. However,these progenies were clustered into three major groups using dendrogram constructed by UPGMA,skewed to three parents in certain degrees, 15 (13 triploids and 2 diploids) to Hamlin, 16 (9 and 7) to Yiben No. 4, and 61 (57 and 4) to [Hamlin sweet orange + Rough Lemon] from which genomic contribution was predominant in progenies, respectively.

  6. RAPD-based genetic analysis of offsprings from the sexual cross using allotetraploid citrus somatic hybrid as pollen parent

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Thirty-one polymorphic decamer primers were selected to genotype 92 progenies from the cross be- tween Yiben No.4, a monoembryonic diploid F1 hybrid of Citrus reticulata Blanco cv Huanongbendizao tangerine and C. ichangensis Swingle, and [Hamlin sweet orange + Rough lemon], an allotetraploid somatic hybrid of Citrus sinensis Osbeck cv. Hamlin and C. jambhiri Lush cv. Rough Lemon. χ2 (Chi-square) analysis of RAPD markers in the progenies indicated they were randomly transmitted from the four donor parents, without significant difference between the diploids and triploids. However, these progenies were clustered into three major groups using dendrogram constructed by UPGMA, skewed to three parents in certain degrees, 15 (13 triploids and 2 diploids) to Hamlin, 16 (9 and 7) to Yiben No. 4, and 61 (57 and 4) to [Hamlin sweet orange + Rough Lemon] from which genomic contribu- tion was predominant in progenies, respectively.

  7. Determination and Analysis of the Putative AcaCD-Responsive Promoters of Salmonella Genomic Island 1

    Science.gov (United States)

    Olasz, Ferenc; Kiss, János

    2016-01-01

    The integrative genomic island SGI1 and its variants confer multidrug resistance in numerous Salmonella enterica serovariants and several Proteus mirabilis and Acinetobacter strains. SGI1 is mobilized by the IncA/C family plasmids. The island exploits not only the conjugation apparatus of the plasmid, but also utilizes the plasmid-encoded master regulator AcaCD to induce the excision and formation of its transfer-competent form, which is a key step in the horizontal transfer of SGI1. Triggering of SGI1 excision occurs via the AcaCD-dependent activation of xis gene expression. AcaCD binds in Pxis to an unusually long recognition sequence. Beside the Pxis promoter, upstream regions of four additional SGI1 genes, S004, S005, S012 and S018, also contain putative AcaCD-binding sites. Furthermore, SGI1 also encodes an AcaCD-related activator, FlhDCSGI1, which has no known function. Here, we have analysed the functionality of the putative AcaCD-dependent promoter regions and proved their activation by either AcaCD or FlhDCSGI1. Moreover, we provide evidence that both activators act on the same binding site in Pxis and that FlhDCSGI1 is able to complement the acaCD deletion of the IncA/C family plasmid R16a. We determined the transcription start sites for the AcaCD-responsive promoters and showed that orf S004 is expressed probably from a different start codon than predicted earlier. Additionally, expression of S003 from promoter PS004 was ruled out. Pxis and the four SGI1 promoters examined here also lack obvious -35 promoter box and their promoter profile is consistent with the class II-type activation pathway. Although the role of the four additionally analysed AcaCD/FlhDCSGI1-controlled genes in transfer and/or maintenance of SGI1 is not yet clear, the conservation of the whole region suggests the existence of some selection for their functionality. PMID:27727307

  8. Deciphering the complex leaf transcriptome of the allotetraploid species Nicotiana tabacum: a phylogenomic perspective

    Directory of Open Access Journals (Sweden)

    Bombarely Aureliano

    2012-08-01

    Full Text Available Abstract Background Polyploidization is an important mechanism in plant evolution. By analyzing the leaf transcriptomes taken from the allotetraploid Nicotiana tabacum (tobacco and parental genome donors, N. sylvesteris (S-Genome and N. tomentosiformis (T-Genome, a phylogenomic approach was taken to map the fate of homeologous gene pairs in this plant. Results A comparison between the genes present in the leaf transcriptomes of N. tabacum and modern day representatives of its progenitor species demonstrated that only 33% of assembled transcripts could be distinguished based on their sequences. A large majority of the genes (83.6% of the non parent distinguishable and 87.2% of the phylogenetic topology analyzed clusters expressed above background level (more than 5 reads showed similar overall expression levels. Homeologous sequences could be identified for 968 gene clusters, and 90% (6% of all genes of the set maintained expression of only one of the tobacco homeologs. When both homeologs were expressed, only 15% (0.5% of the total showed evidence of differential expression, providing limited evidence of subfunctionalization. Comparing the rate of synonymous nucleotide substitution (Ks and non-synonymous nucleotide substitution (Kn provided limited evidence for positive selection during the evolution of tobacco since the polyploidization event took place. Conclusions Polyploidization is a powerful mechanism for plant speciation that can occur during one generation; however millions of generations may be necessary for duplicate genes to acquire a new function. Analysis of the tobacco leaf transcriptome reveals that polyploidization, even in a young tetraploid such as tobacco, can lead to complex changes in gene expression. Gene loss and gene silencing, or subfunctionalization may explain why both homeologs are not expressed by the associated genes. With Whole Genome Duplication (WGD events, polyploid genomes usually maintain a high percentage of

  9. Phenotypic characteristics of aged CD4(+) CD28(null) T lymphocytes are determined by changes in the whole-genome DNA methylation pattern.

    Science.gov (United States)

    Suarez-Álvarez, Beatriz; Rodríguez, Ramón M; Schlangen, Karin; Raneros, Aroa Baragaño; Márquez-Kisinousky, Leonardo; Fernández, Agustín F; Díaz-Corte, Carmen; Aransay, Ana M; López-Larrea, Carlos

    2017-04-01

    Aging is associated with a progressive loss of the CD28 costimulatory molecule in CD4(+) lymphocytes (CD28(null) T cells), which is accompanied by the acquisition of new biological and functional properties that give rise to an impaired immune response. The regulatory mechanisms that govern the appearance and function of this cell subset during aging and in several associated inflammatory disorders remain controversial. Here, we present the whole-genome DNA methylation and gene expression profiles of CD28(null) T cells and its CD28(+) counterpart. A comparative analysis revealed that 296 genes are differentially methylated between the two cell subsets. A total of 160 genes associated with cytotoxicity (e.g. GRZB, TYROBP, and RUNX3) and cytokine/chemokine signaling (e.g. CX3CR1, CD27, and IL-1R) are demethylated in CD28(null) T cells, while 136 de novo-methylated genes matched defects in the TCR signaling pathway (e.g. ITK, TXK, CD3G, and LCK). TCR-landscape analysis confirmed that CD28(null) T cells have an oligo/monoclonal expansion over the polyclonal background of CD28(+) T cells, but feature a Vβ family repertoire specific to each individual. We reported that CD28(null) T cells show a preactivation state characterized by a higher level of expression of inflammasome-related genes that leads to the release of IL-1β when activated. Overall, our results demonstrate that CD28(null) T cells have a unique DNA methylation landscape, which is associated with differences in gene expression, contributing to the functionality of these cells. Understanding these epigenetic regulatory mechanisms could suggest novel therapeutic strategies to prevent the accumulation and activation of these cells during aging.

  10. Genome-wide analysis of primary CD4+ and CD8+ T cell transcriptomes shows evidence for a network of enriched pathways associated with HIV disease

    Directory of Open Access Journals (Sweden)

    Wang Bin

    2011-03-01

    Full Text Available Abstract Background HIV preferentially infects CD4+ T cells, and the functional impairment and numerical decline of CD4+ and CD8+ T cells characterize HIV disease. The numerical decline of CD4+ and CD8+ T cells affects the optimal ratio between the two cell types necessary for immune regulation. Therefore, this work aimed to define the genomic basis of HIV interactions with the cellular transcriptome of both CD4+ and CD8+ T cells. Results Genome-wide transcriptomes of primary CD4+ and CD8+ T cells from HIV+ patients were analyzed at different stages of HIV disease using Illumina microarray. For each cell subset, pairwise comparisons were performed and differentially expressed (DE genes were identified (fold change >2 and B-statistic >0 followed by quantitative PCR validation. Gene ontology (GO analysis of DE genes revealed enriched categories of complement activation, actin filament, proteasome core and proton-transporting ATPase complex. By gene set enrichment analysis (GSEA, a network of enriched pathways functionally connected by mitochondria was identified in both T cell subsets as a transcriptional signature of HIV disease progression. These pathways ranged from metabolism and energy production (TCA cycle and OXPHOS to mitochondria meditated cell apoptosis and cell cycle dysregulation. The most unique and significant feature of our work was that the non-progressing status in HIV+ long-term non-progressors was associated with MAPK, WNT, and AKT pathways contributing to cell survival and anti-viral responses. Conclusions These data offer new comparative insights into HIV disease progression from the aspect of HIV-host interactions at the transcriptomic level, which will facilitate the understanding of the genetic basis of transcriptomic interaction of HIV in vivo and how HIV subverts the human gene machinery at the individual cell type level.

  11. Two unisexual artificial polyploid clones constructed by genome addition of common carp (Cyprinus carp) and crucian carp (Carassius auratus)

    Institute of Scientific and Technical Information of China (English)

    WU; Qingjiang; (吴清江); YE; Yuzhen; (叶玉珍); DONG; Xinhong; (董新红)

    2003-01-01

    A polyploid hybrid fish with natural gynogenesis can prevent segregation and maintain their hybrid vigor in their progenies. Supposing the reproduction mode of induced polyploid fish being natural gynogenesis, allopolyploid hybrid between common carp and crucian carp into allopolyploid was performed. The purpose of this paper is to describe a lineage from sexual diploid carp transforming into allotriploid and allotetraploid unisexual clones by genome addition. The diploid hybrid between common carp and crucian carp reproduces an unreduced nucleus consisting of two parental genomes. This unreduced female pronucleus will fuse with male pronucleus and form allotriploid zygote after penetration of related species sperms. Allotriploid embryos grow normally, and part of female allotriploid can produce unreduced mature ova with three genomes. Mature ova of most allotriploid females are provided with natural gynogenetic trait and their nuclei do not fuse with any entrance sperm. All female offspring are produced by gynogenesis of allotriploid egg under activation of penetrating sperms. These offspring maintain morphological traits of their allotriploid maternal and form an allotetraploid unisexual clone by gynogenetic reproduction mode. However, female nuclei of rare allotriploid female can fuse with penetrating male pronuclei and result in the appearance of allotetraploid individuals by means of genome addition. All allotetraploid females can reproduce unreduced mature eggs containing four genomes. Therefore, mature eggs of allotetraploid maintain gynogenetic trait and allotetraploid unisexual clone is produced under activation of related species sperms.

  12. Chromosome isolation by flow sorting in Aegilops umbellulata and Ae. comosa and their allotetraploid hybrids Ae. biuncialis and Ae. geniculata.

    Directory of Open Access Journals (Sweden)

    István Molnár

    Full Text Available This study evaluates the potential of flow cytometry for chromosome sorting in two wild diploid wheats Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata. Flow karyotypes obtained after the analysis of DAPI-stained chromosomes were characterized and content of chromosome peaks was determined. Peaks of chromosome 1U could be discriminated in flow karyotypes of Ae. umbellulata and Ae. biuncialis and the chromosome could be sorted with purities exceeding 95%. The remaining chromosomes formed composite peaks and could be sorted in groups of two to four. Twenty four wheat SSR markers were tested for their position on chromosomes of Ae. umbellulata and Ae. comosa using PCR on DNA amplified from flow-sorted chromosomes and genomic DNA of wheat-Ae. geniculata addition lines, respectively. Six SSR markers were located on particular Aegilops chromosomes using sorted chromosomes, thus confirming the usefulness of this approach for physical mapping. The SSR markers are suitable for marker assisted selection of wheat-Aegilops introgression lines. The results obtained in this work provide new opportunities for dissecting genomes of wild relatives of wheat with the aim to assist in alien gene transfer and discovery of novel genes for wheat improvement.

  13. Toward Elucidating the Structure of Tetraploid Cotton Genome

    Institute of Scientific and Technical Information of China (English)

    GUO Wang-zhen

    2008-01-01

    @@ Upland cotton has the highest yield,and accounts for >95% of world cotton production.Decoding upland cotton genomes will undoubtedly provide the ultimate reference and resource for structural,functional,and evolutionary studies of the species.Here,we employed GeneTrek and BAC tagging information approaches to predict the general composition and structure of the allotetraploid cotton genome.

  14. Multiplex and genome-wide analyses reveal distinctive properties of KIR+ and CD56+ T cells in human blood.

    Science.gov (United States)

    Chan, Wing Keung; Rujkijyanont, Piya; Neale, Geoffrey; Yang, Jie; Bari, Rafijul; Das Gupta, Neha; Holladay, Martha; Rooney, Barbara; Leung, Wing

    2013-08-15

    Killer cell Ig-like receptors (KIRs) on NK cells have been linked to a wide spectrum of health conditions such as chronic infections, autoimmune diseases, pregnancy complications, cancers, and transplant failures. A small subset of effector memory T cells also expresses KIRs. In this study, we use modern analytic tools including genome-wide and multiplex molecular, phenotypic, and functional assays to characterize the KIR(+) T cells in human blood. We find that KIR(+) T cells primarily reside in the CD56(+) T population that is distinctively DNAM-1(high) with a genome-wide quiescent transcriptome, short telomere, and limited TCR excision circles. During CMV reactivation in bone marrow transplant recipients, KIR(+)CD56(+) T cells rapidly expanded in real-time but not KIR(+)CD56(-) T cells or KIR(+) NK cells. In CMV(+) asymptomatic donors, as much as 50% of CD56(+) T cells are KIR(+), and most are distinguishably KIR2DL2/3(+)NKG2C(+)CD57(+). Functionally, the KIR(+)CD56(+) T cell subset lyses cancer cells and CMVpp65-pulsed target cells in a dual KIR-dependent and TCR-dependent manner. Analysis of metabolic transcriptome confirms the immunological memory status of KIR(+)CD56(+) T cells in contrast to KIR(-)CD56(+) T cells that are more active in energy metabolism and effector differentiation. KIR(-)CD56(+) T cells have >25-fold higher level of expression of RORC than the KIR(+) counterpart and are a previously unknown producer of IL-13 rather than IL-17 in multiplex cytokine arrays. Our data provide fundamental insights into KIR(+) T cells biologically and clinically.

  15. The ultrastructure of pollen grain surface in allotetraploid petunia (Petunia hybrida hort. superbissima as revealed by scanning electron microscopy

    Directory of Open Access Journals (Sweden)

    S. Muszyński

    2015-05-01

    Full Text Available The ultrastructure of pollen grain surface in allotetraploid petunias was analyzed by scanning electron microscopy. The pollen grain wall is developed into characteristic pattern of convulations.

  16. Genetic mapping of wild introgressions into cultivated peanut: a way toward enlarging the genetic basis of a recent allotetraploid

    Directory of Open Access Journals (Sweden)

    Glaszmann Jean-Christophe

    2009-08-01

    Full Text Available Abstract Background Peanut (Arachis hypogaea L. is widely used as a food and cash crop around the world. It is considered to be an allotetraploid (2n = 4x = 40 originated from a single hybridization event between two wild diploids. The most probable hypothesis gave A. duranensis as the wild donor of the A genome and A. ipaënsis as the wild donor of the B genome. A low level of molecular polymorphism is found in cultivated germplasm and up to date few genetic linkage maps have been published. The utilization of wild germplasm in breeding programs has received little attention due to the reproductive barriers between wild and cultivated species and to the technical difficulties encountered in making large number of crosses. We report here the development of a SSR based genetic map and the analysis of genome-wide segment introgressions into the background of a cultivated variety through the utilization of a synthetic amphidiploid between A. duranensis and A. ipaënsis. Results Two hundred ninety eight (298 loci were mapped in 21 linkage groups (LGs, spanning a total map distance of 1843.7 cM with an average distance of 6.1 cM between adjacent markers. The level of polymorphism observed between the parent of the amphidiploid and the cultivated variety is consistent with A. duranensis and A. ipaënsis being the most probable donor of the A and B genomes respectively. The synteny analysis between the A and B genomes revealed an overall good collinearity of the homeologous LGs. The comparison with the diploid and tetraploid maps shed new light on the evolutionary forces that contributed to the divergence of the A and B genome species and raised the question of the classification of the B genome species. Structural modifications such as chromosomal segment inversions and a major translocation event prior to the tetraploidisation of the cultivated species were revealed. Marker assisted selection of BC1F1 and then BC2F1 lines carrying the desirable donor

  17. BioSMACK: a linux live CD for genome-wide association analyses.

    Science.gov (United States)

    Hong, Chang Bum; Kim, Young Jin; Moon, Sanghoon; Shin, Young-Ah; Go, Min Jin; Kim, Dong-Joon; Lee, Jong-Young; Cho, Yoon Shin

    2012-01-01

    Recent advances in high-throughput genotyping technologies have enabled us to conduct a genome-wide association study (GWAS) on a large cohort. However, analyzing millions of single nucleotide polymorphisms (SNPs) is still a difficult task for researchers conducting a GWAS. Several difficulties such as compatibilities and dependencies are often encountered by researchers using analytical tools, during the installation of software. This is a huge obstacle to any research institute without computing facilities and specialists. Therefore, a proper research environment is an urgent need for researchers working on GWAS. We developed BioSMACK to provide a research environment for GWAS that requires no configuration and is easy to use. BioSMACK is based on the Ubuntu Live CD that offers a complete Linux-based operating system environment without installation. Moreover, we provide users with a GWAS manual consisting of a series of guidelines for GWAS and useful examples. BioSMACK is freely available at http://ksnp.cdc. go.kr/biosmack.

  18. Genome-wide association study of systemic sclerosis identifies CD247 as a novel susceptibility locus

    Science.gov (United States)

    Radstake, Timothy R.D.J.; Gorlova, Olga; Rueda, Blanca; Martin, Jose-Ezequiel; Alizadeh, Behrooz Z.; Palomino-Morales, Rogelio; Coenen, Marieke J.; Vonk, Madelon C.; Voskuyl, Alexandre E.; Scheurwegh, Annemie J.; Broen, Jasper C.; van Riel, Piet L.C.M.; van ‘t Slot, Ruben; Italiaander, Annet; Ophoff, Roel A.; Riemekasten, Gabriela; Hunzelmann, Nico; Simeon, Carmen P.; Ortego-Centeno, Norberto; González-Gay, Miguel A.; González-Escribano, María F.; Airo, Paolo; van Laar, Jaap; Herrick, Ariane; Worthington, Jane; Hesselstrand, Roger; Smith, Vanessa; de Keyser, Filip; Houssiau, Fredric; Chee, Meng May; Madhok, R; Shiels, Paul; Westhovens, Rene; Kreuter, Alexander; Kiener, Hans; de Baere, Elfride; Witte, Torsten; Padykov, Leonid; Klareskog, Lars; Beretta, Lorenzo; Scorza, Rafaella; Lie, Benedicte A.; Hoffman-Vold, Anna-Maria; Carreira, P; Varga, J.; Hinchcliff, M.; Gregersen, Peter; Lee, Annette T.; Ying, Jun; Han, Younghun; Weng, Shih-Feng; Amos, Christopher I.; Wigley, Fredrick M.; Hummers, Laura; Nelson, J. Lee; Agarwal, Sandeep K.; Assassi, Shervin; Gourh, Pravitt; Tan, Filemon K.; Koeleman, Bobby P.C.; Arnett, Frank C; Martin, Javier; Mayes, Maureen D.

    2010-01-01

    Systemic sclerosis (SSc) is an autoimmune disease characterized by fibrosis of the skin and internal organs that leads to profound disability and premature death. To identify novel SSc susceptibility loci we conducted the first genome wide association study (GWAS) in a population of Caucasian ancestry including a total of 2296 SSc patients and 5171 controls. Analysis of 279,621 autosomal single nucleotide polymorphisms (SNPs) followed by replication testing in an independent case-control set of European ancestry (2,753 SSc patients / 4,569 controls) identified a new susceptibility locus for systemic sclerosis at CD247 (1q22-23; rs2056626, P = 2.09 × 10−7 in the discovery samples, P = 3.39 × 10−9 in the combined analysis). Additionally, we confirm and firmly establish the role of MHC (2.31 × 10−18), IRF5 (P =1.86 × 10−13) and STAT4 (P =3.37 × 10−9) gene regions as SSc genetic risk factors. PMID:20383147

  19. Differential regulation of gene products in newly synthesized Brassica napus allotetraploids is not related to protein function nor subcellular localization

    Directory of Open Access Journals (Sweden)

    Valot Benoît

    2007-02-01

    Full Text Available Abstract Background Allopolyploidy is a preeminent process in plant evolution that results from the merger of distinct genomes in a common nucleus via inter-specific hybridization. Allopolyploid formation is usually related to genome-wide structural and functional changes though the underlying mechanisms operating during this "genomic shock" still remain poorly known. The aim of the present study was to investigate the modifications occurring at the proteomic level following an allopolyploidization event and to determine whether these changes are related to functional properties of the proteins. In a previous report, we applied comparative proteomics to synthetic amphiploids of Brassica napus and to its diploid progenitors B. rapa and B. oleracea. Although several hundred polypeptides displayed additivity (i.e. mid-parent values in the amphiploids, many of them showed non-additivity. Here, we report the in silico functional characterization of the "non-additive" proteins (the ones with a non-additive pattern of regulation in synthetic B. napus. Results The complete set of non-additive proteins (335 in the stem and 205 in the root, as well as a subset of additive polypeptides (200 per organ, was identified by mass spectrometry. Several protein isoforms were found, and most of them (~55% displayed "different" or "opposite" patterns of regulation in the amphiploids, i.e. isoforms of the same protein showing both up-regulation and down-regulation in the synthetic B. napus compared to the mid-parent value. Components of protein complexes were identified of which ~50% also displayed "different" or "opposite" patterns of regulation in the allotetraploids. In silico functional categorization of the identified proteins was carried out, and showed that neither functional category nor metabolic pathway were systematically affected by non-additivity in the synthetic amphiploids. In addition, no subcellular compartment was found to be over- or under

  20. Experimental evidence for the ancestry of allotetraploid Trifolium repens and creation of synthetic forms with value for plant breeding

    Directory of Open Access Journals (Sweden)

    Williams Warren M

    2012-04-01

    Full Text Available Abstract Background White clover (Trifolium repens is a ubiquitous weed of the temperate world that through use of improved cultivars has also become the most important legume of grazed pastures world-wide. It has long been suspected to be allotetraploid, but the diploid ancestral species have remained elusive. Putative diploid ancestors were indicated by DNA sequence phylogeny to be T. pallescens and T. occidentale. Here, we use further DNA evidence as well as a combination of molecular cytogenetics (FISH and GISH and experimental hybridization to test the hypothesis that white clover originated as a hybrid between T. pallescens and T. occidentale. Results T. pallescens plants were identified with chloroplast trnL intron DNA sequences identical to those of white clover. Similarly, T. occidentale plants with nuclear ITS sequences identical to white clover were also identified. Reciprocal GISH experiments, alternately using labeled genomic DNA probes from each of the putative ancestral species on the same white clover cells, showed that half of the chromosomes hybridized with each probe. F1 hybrids were generated by embryo rescue and these showed strong interspecific chromosome pairing and produced a significant frequency of unreduced gametes, indicating the likely mode of polyploidization. The F1 hybrids are inter-fertile with white clover and function as synthetic white clovers, a valuable new resource for the re-incorporation of ancestral genomes into modern white clover for future plant breeding. Conclusions Evidence from DNA sequence analyses, molecular cytogenetics, interspecific hybridization and breeding experiments supports the hypothesis that a diploid alpine species (T. pallescens hybridized with a diploid coastal species (T. occidentale to generate tetraploid T. repens. The coming together of these two narrowly adapted species (one alpine and the other maritime, along with allotetraploidy, has led to a transgressive hybrid with a

  1. Sequencing of the Cultivated Tetraploid CottonGenome-Gossypium hirsutum

    Institute of Scientific and Technical Information of China (English)

    YU Shu-xun; WANG Kun-bo; LI Fu-guang; KOHEL Russell J; PERCY Richard G; YU John Z

    2008-01-01

    @@ Cotton is an important cash crop in the world,and it plays an irreplaceable role in China's nationaleconomy.Cultivated upland cotton (Gossypium hirsutum L.) represents 95% of the world's cottonproduction,but it has a complex allotetraploid genome that contains at least 30000 genes in 2500 MbDNA.

  2. Sequencing of the Cultivated Tetraploid Cotton Genome-Gossypium hirsutum

    Institute of Scientific and Technical Information of China (English)

    KOHEL; Russell; J; PERCY; Richard; G; YU; John; Z

    2008-01-01

    Cotton is an important cash crop in the world,and it plays an irreplaceable role in China's national economy.Cultivated upland cotton(Gossypium hirsutum L.) represents 95% of the world's cotton production,but it has a complex allotetraploid genome that contains at least 30000 genes in 2500 Mb

  3. Homeolog loss and expression changes in natural populations of the recently and repeatedly formed allotetraploid Tragopogon mirus (Asteraceae

    Directory of Open Access Journals (Sweden)

    Soltis Pamela S

    2010-02-01

    additivity. These results suggest that loss of homeologs and changes in gene expression are not the immediate result of hybridization, but are processes that occur following polyploidization, occurring during the early (T. mirus and a second recently formed allopolyploid, T. miscellus, exhibit more homeolog losses than gene silencing events. Furthermore, both allotetraploids undergo biased loss of homeologs contributed by their shared diploid parent, T. dubius. Further studies are required to assess whether the results for the 30 genes so far examined are representative of the entire genome.

  4. A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B

    DEFF Research Database (Denmark)

    Yamauchi, Toshimasa; Hara, Kazuo; Maeda, Shiro;

    2010-01-01

    We conducted a genome-wide association study of type 2 diabetes (T2D) using 459,359 SNPs in a Japanese population with a three-stage study design (stage 1, 4,470 cases and 3,071 controls; stage 2, 2,886 cases and 3,087 controls; stage 3, 3,622 cases and 2,356 controls). We identified new...... associations in UBE2E2 on chromosome 3 and in C2CD4A-C2CD4B on chromosome 15 at genome-wide significant levels (rs7612463 in UBE2E2, combined P = 2.27 × 10¿¿; rs7172432 in C2CD4A-C2CD4B, combined P = 3.66 × 10¿¿). The association of these two loci with T2D was replicated in other east Asian populations....... In the European populations, the C2CD4A-C2CD4B locus was significantly associated with T2D, and a combined analysis of all populations gave P = 8.78 × 10¿¹4, whereas the UBE2E2 locus did not show association to T2D. In conclusion, we identified two new loci at UBE2E2 and C2CD4A-C2CD4B associated...

  5. Genome Insight and Comparative Pathogenomic Analysis of Nesterenkonia jeotgali Strain CD08_7 Isolated from Duodenal Mucosa of Celiac Disease Patient

    Science.gov (United States)

    Chander, Atul M.; Nair, Ramesan G.; Kaur, Gurwinder; Kochhar, Rakesh; Dhawan, Devinder K.; Bhadada, Sanjay K.; Mayilraj, Shanmugam

    2017-01-01

    Species of the genus Nesterenkonia have been isolated from different ecological niches, especially from saline habitats and reported as weak human pathogens causing asymptomatic bacteraemia. Here, for the first time we are reporting the genome sequence and pathogenomic analysis of a strain designated as CD08_7 isolated from the duodenal mucosa of a celiac disease patient, identified as Nesterenkonia jeotgali. To date, only five strains of the genus Nesterenkonia (N. massiliensis strain NP1T, Nesterenkonia sp. strain JCM 19054, Nesterenkonia sp. strain F and Nesterenkonia sp. strain AN1) have been whole genome sequenced and annotated. In the present study we have mapped and compared the virulence profile of N. jeotgali strain CD08_7 along with other reference genomes which showed some characteristic features that could contribute to pathogenicity. The RAST (Rapid Annotation using Subsystem Technology) based genome mining revealed more genes responsible for pathogenicity in strain CD08_7 when compared with the other four sequenced strains. The studied categories were resistance to antibiotic and toxic compounds, invasion and intracellular resistance, membrane transport, stress response, osmotic stress, oxidative stress, phages and prophages and iron acquisition. A total of 1431 protein-encoding genes were identified in the genome of strain CD08_7 among which 163 were predicted to contribute for pathogenicity. Out of 163 genes only 59 were common to other genome, which shows the higher levels of genetic richness in strain CD08_7 that may contribute to its functional versatility. This study provides a comprehensive analysis on genome of N. jeotgali strain CD08_7 and possibly indicates its importance as a clinical pathogen. PMID:28210247

  6. Genome-wide identification of Fas/CD95 alternative splicing regulators reveals links with iron homeostasis.

    Science.gov (United States)

    Tejedor, J Ramón; Papasaikas, Panagiotis; Valcárcel, Juan

    2015-01-08

    Alternative splicing of Fas/CD95 exon 6 generates either a membrane-bound receptor that promotes, or a soluble isoform that inhibits, apoptosis. Using an automatized genome-wide siRNA screening for alternative splicing regulators of endogenous transcripts in mammalian cells, we identified 200 genes whose knockdown modulates the ratio between Fas/CD95 isoforms. These include classical splicing regulators; core spliceosome components; and factors implicated in transcription and chromatin remodeling, RNA transport, intracellular signaling, and metabolic control. Coherent effects of genes involved in iron homeostasis and pharmacological modulation of iron levels revealed a link between intracellular iron and Fas/CD95 exon 6 inclusion. A splicing regulatory network linked iron levels with reduced activity of the Zinc-finger-containing splicing regulator SRSF7, and in vivo and in vitro assays revealed that iron inhibits SRSF7 RNA binding. Our results uncover numerous links between cellular pathways and RNA processing and a mechanism by which iron homeostasis can influence alternative splicing.

  7. Whole-genome approach implicates CD44 in cellular resistance to carboplatin

    Directory of Open Access Journals (Sweden)

    Shukla Sunita J

    2009-01-01

    Full Text Available Abstract Carboplatin is a chemotherapeutic agent used in the management of many cancers, yet treatment is limited by resistance and toxicities. To achieve a better understanding of the genetic contribution to carboplatin resistance or toxicities, lymphoblastoid cell lines from 34 large Centre d'Etude du Polymorphisme Humain pedigrees were utilised to evaluate interindividual variation in carboplatin cytotoxicity. Significant heritability, ranging from 0.17-0.36 (p = 1 × 10-7 to 9 × 10-4, was found for cell growth inhibition following 72-hour treatment at each carboplatin concentration (10, 20, 40 and 80 μM and IC50 (concentration for 50 per cent cell growth inhibition. Linkage analysis revealed 11 regions with logarithm of odds (LOD scores greater than 1.5. The highest LOD score on chromosome 11 (LOD = 3.36, p = 4.2 × 10-5 encompasses 65 genes within the 1 LOD confidence interval for the carboplatin IC50. We further analysed the IC50 phenotype with a linkage-directed association analysis using 71 unrelated HapMap and Perlegen cell lines and identified 18 single nucleotide polymorphisms within eight genes that were significantly associated with the carboplatin IC50 (p -5; false discovery rate 50 values of the eight associated genes, which identified the most significant correlation between CD44 expression and IC50 (r2 = 0.20; p = 6 × 10-4. The quantitative real-time polymerase chain reaction further confirmed a statistically significant difference in CD44 expression levels between carboplatin-resistant and -sensitive cell lines (p = 5.9 × 10-3. Knockdown of CD44 expression through small interfering RNA resulted in increased cellular sensitivity to carboplatin (p CD44 as being important in conferring cellular resistance to carboplatin.

  8. Transmission of clonal hepatitis C virus genomes reveals the dominant but transitory role of CD8¿ T cells in early viral evolution

    DEFF Research Database (Denmark)

    Callendret, Benoît; Bukh, Jens; Eccleston, Heather B;

    2011-01-01

    The RNA genome of the hepatitis C virus (HCV) diversifies rapidly during the acute phase of infection, but the selective forces that drive this process remain poorly defined. Here we examined whether Darwinian selection pressure imposed by CD8(+) T cells is a dominant force driving early amino acid...... occurred slowly over several years of chronic infection. Together these observations indicate that during acute hepatitis C, virus evolution was driven primarily by positive selection pressure exerted by CD8(+) T cells. This influence of immune pressure on viral evolution appears to subside as chronic...... replacement in HCV viral populations. This question was addressed in two chimpanzees followed for 8 to 10 years after infection with a well-defined inoculum composed of a clonal genotype 1a (isolate H77C) HCV genome. Detailed characterization of CD8(+) T cell responses combined with sequencing of recovered...

  9. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry

    Science.gov (United States)

    High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium) and allotetraploid sour cherry (P. cerasus). This effort was led by RosBREED, a commun...

  10. Functional genomics analysis of vitamin D effects on CD4+ T cells in vivo in experimental autoimmune encephalomyelitis ‬

    KAUST Repository

    Zeitelhofer, Manuel

    2017-02-15

    Vitamin D exerts multiple immunomodulatory functions and has been implicated in the etiology and treatment of several autoimmune diseases, including multiple sclerosis (MS). We have previously reported that in juvenile/adolescent rats, vitamin D supplementation protects from experimental autoimmune encephalomyelitis (EAE), a model of MS. Here we demonstrate that this protective effect associates with decreased proliferation of CD4+ T cells and lower frequency of pathogenic T helper (Th) 17 cells. Using transcriptome, methylome, and pathway analyses in CD4+ T cells, we show that vitamin D affects multiple signaling and metabolic pathways critical for T-cell activation and differentiation into Th1 and Th17 subsets in vivo. Namely, Jak/Stat, Erk/Mapk, and Pi3K/Akt/mTor signaling pathway genes were down-regulated upon vitamin D supplementation. The protective effect associated with epigenetic mechanisms, such as (i) changed levels of enzymes involved in establishment and maintenance of epigenetic marks, i.e., DNA methylation and histone modifications; (ii) genome-wide reduction of DNA methylation, and (iii) up-regulation of noncoding RNAs, including microRNAs, with concomitant down-regulation of their protein-coding target RNAs involved in T-cell activation and differentiation. We further demonstrate that treatment of myelin-specific T cells with vitamin D reduces frequency of Th1 and Th17 cells, down-regulates genes in key signaling pathways and epigenetic machinery, and impairs their ability to transfer EAE. Finally, orthologs of nearly 50% of candidate MS risk genes and 40% of signature genes of myelin-reactive T cells in MS changed their expression in vivo in EAE upon supplementation, supporting the hypothesis that vitamin D may modulate risk for developing MS.

  11. Linkage mapping in tetraploid willows: segregation of molecular markers and estimation of linkage phases support an allotetraploid structure for Salix alba x Salix fragilis interspecific hybrids.

    Science.gov (United States)

    Barcaccia, G; Meneghetti, S; Albertini, E; Triest, L; Lucchin, M

    2003-02-01

    Salix alba-Salix fragilis complex includes closely related dioecious polyploid species, which are obligate outcrossers. Natural populations of these willows and their hybrids are represented by a mixture of highly heterozygous genotypes sharing a common gene pool. Since nothing is known about their genomic constitution, tetraploidy (2n=4x=76) in willow species makes basic and applied genetic studies difficult. We have used a two-way pseudotestcross strategy and single-dose markers (SDMs) to construct the first linkage maps for both pistillate and staminate willows. A total of 242 amplified fragment length polymorphisms (AFLPs) and 50 selective amplifications of microsatellite polymorphic loci (SAMPL) markers, which showed 1:1 segregation in the F(1) mapping populations, were used in linkage analysis. In S. alba, 73 maternal and 48 paternal SDMs were mapped to 19 and 16 linkage groups covering 708 and 339 cM, respectively. In S. fragilis, 13 maternal and 33 paternal SDMs were mapped in six and 14 linkage groups covering 98 and 321 cM, respectively. For most cosegregation groups, a comparable number of markers linked in coupling and repulsion was identified. This finding suggests that most of chromosomes pair preferentially as occurs in allotetraploid species exhibiting disomic inheritance. The detection of 10 pairs of marker alleles from single parents showing codominant inheritance strengthens this hypothesis. The fact that, of the 1122 marker loci identified in the two male and female parents, the vast majority (77.5%) were polymorphic and as few as 22.5% were shared between parental species highlight that S. alba and S. fragilis genotypes are differentiated. The highly difference between S. alba- and S. fragilis-specific markers found in both parental combinations (on average, 65.3 vs 34.7%, respectively) supports the (phylogenetic) hypothesis that S. fragilis is derived from S. alba-like progenitors.

  12. Conditions in home and transplant soils have differential effects on the performance of diploid and allotetraploid anthericum species.

    Directory of Open Access Journals (Sweden)

    Lucie Černá

    Full Text Available Due to increased levels of heterozygosity, polyploids are expected to have a greater ability to adapt to different environments than their diploid ancestors. While this theoretical pattern has been suggested repeatedly, studies comparing adaptability to changing conditions in diploids and polyploids are rare. The aim of the study was to determine the importance of environmental conditions of origin as well as target conditions on performance of two Anthericum species, allotetraploid A. liliago and diploid A. ramosum and to explore whether the two species differ in the ability to adapt to these environmental conditions. Specifically, we performed a common garden experiment using soil from 6 localities within the species' natural range, and we simulated the forest and open environments in which they might occur. We compared the performance of diploid A. ramosum and allotetraploid A. liliago originating from different locations in the different soils. The performance of the two species was not affected by simulated shading but differed strongly between the different target soils. Growth of the tetraploids was not affected by the origin of the plants. In contrast, diploids from the most nutrient poor soil performed best in the richest soil, indicating that diploids from deprived environments have an increased ability to acquire nutrients when available. They are thus able to profit from transfer to novel nutrient rich environments. Therefore, the results of the study did not support the general expectation that the polyploids should have a greater ability than the diploids to adapt to a wide range of conditions. In contrast, the results are in line with the observation that diploids occupy a wider range of environments than the allotetraploids in our system.

  13. [Genome Rearrangements in Azospirillum brasilense Sp7 with the Involvement of the Plasmid pRhico and the Prophage phiAb-Cd].

    Science.gov (United States)

    Katsy, E I; Petrova, L P

    2015-12-01

    Alphaproteobacteria of the species Azospirillum brasilense have a multicomponent genome that undergoes frequent spontaneous rearrangements, yielding changes in the plasmid profiles of strains. Specifically, variants (Cd, Sp7.K2, Sp7.1, Sp7.4, Sp7.8, etc.) of the type strainA. brasilense Sp7 that had lost a 115-MDa plasmid were previously selected. In many of them, the molecular weight of a 90-MDa plasmid (p90 or pRhico), which is a kind of "depot" for glycopolymer biosynthesis genes, increased. In this study, a collection of primers was designed to the plasmid pRhico and to the DNA of prophage phiAb-Cd integrated in it. The use ofthese primers in polymerase chain reactions allowed the detection of the probable excision of phiAb-Cd phage from the DNA of A. brasilense variants Sp7.4 and Sp7.8 and other alterations of the pRhico structure in A. brasilense strains Cd, Sp7.K2, and Sp7.8. The developed primers and PCR conditions may be recoin mended for primary analysis of spontaneous plasmid rearrangements in A. brasilense Sp7 and related strains.

  14. Analysis of intron sequence variability of the conservative HMG-box of Sox9 genes in allotetraploids and their original parents

    Institute of Scientific and Technical Information of China (English)

    Liu Jifang; Liu Shaojun; Tao Min; Li Wei; Liu Yun

    2007-01-01

    The Sox genes of allotetraploids and their original maternal red crucian carp ( Carassius caassius red var. ) and original paternal common carp ( Cyprinus carpio L. ) were detected by PCR with the designed primers based on the conserved HMG-box sequence in different species. Sequencing of Sox genes indicated that two Sox9 genes (Atsox9a and Atsox9b ) existed in allotetraploids, while only one Sox9 gene existed in red crucian carp ( Rcsox9a ) and common carp ( Ccsox9b ). All of the four Sox9 genes contained an intron in the HMG-box, with the sizes of 413 bp, 703 bp, 401 bp and 714 bp, respectively. Moreover, the introns obeyed the rule of "GT-AG". A high similarity was observed between introns of Atsox9a and Rcsox9a (94.4 % ), Atsox9b and Ccsox9b (97.8 % ). Interestingly, the deduced amino acid sequences of their corresponding exons all shared 100 % identity. Thus, introns of the HMG-domain of Sox9s in allotetraploids and their original parents have not only the length polymorphism but also intron variability. Our results provide significant molecular evidence for the origin and evolution of allotetraploids.

  15. Genome-Based In Silico Identification of New Mycobacterium tuberculosis Antigens Activating Polyfunctional CD8+ T Cells in Human Tuberculosis

    DEFF Research Database (Denmark)

    Tang, Sheila Tuyet; van Meijgaarden, Krista E.; Caccamo, Nadia

    2011-01-01

    was validated for all 18 epitopes. Intracellular cytokine staining for IFN-gamma, IL-2, and TNF-alpha revealed mono-, dual-, as well as triple-positive CD8(+) T cells, indicating these M. tuberculosis peptide-specific CD8(+) T cells were (poly) functional. Moreover, these T cells were primed during natural...... infection, because they were absent from M. tuberculosis-noninfected individuals. Control CMV peptide/HLA-A*0201 tetramers stained CD8(+) T cells in M. tuberculosis-infected and noninfected individuals equally, whereas Ebola peptide/HLA-A*0201 tetramers were negative. In conclusion, the M. tuberculosis...

  16. High-density Linkage Map of Cultivated Allotetraploid Cotton Based on SSR, TRAP, SRAP and AFLP Markers

    Institute of Scientific and Technical Information of China (English)

    Jiwen Yu; Shuxun Yu; Cairui Lu; Wu Wang; Shuli Fan; Meizhen Song; Zhongxu Lin; Xianlong Zhang; Jinfa Zhang

    2007-01-01

    A high-density linkage map was constructed for an F2 population derived from an interspecific cross of cultivated allotetraploid species between Gossyplum hirsutum L. and G. barbadense L. A total of 186 F2 individuals from the interspecific cross of "CRI 36 × Hai 7124" were genotyped at 1 252 polymorphic loci including a novel marker system,target region amplification polymorphism (TRAP). The map consists of 1 097 markers, including 697 simple sequence repeats (SSRs), 171 TRAPs, 129 sequence-related amplified polymorphisms, 98 amplified fragment length polymorphisms, and two morphological markers, and spanned 4 536.7 cM with an average genetic distance of 4.1 cM per marker. Using 45 duplicated SSR loci among chromosomes, 11 of the 13 pairs of homologous chromosomes were identified in tetraplold cotton. This map will provide an essential resource for high resolution mapping of quantitative trait loci and molecular breeding in cotton.

  17. Comparative genomics analysis of rice and pineapple contributes to understand the chromosome number reduction and genomic changes in grasses

    Directory of Open Access Journals (Sweden)

    Jinpeng Wang

    2016-10-01

    Full Text Available Rice is one of the most researched model plant, and has a genome structure most resembling that of the grass common ancestor after a grass common tetraploidization ~100 million years ago. There has been a standing controversy whether there had been 5 or 7 basic chromosomes, before the tetraploidization, which were tackled but could not be well solved for the lacking of a sequenced and assembled outgroup plant to have a conservative genome structure. Recently, the availability of pineapple genome, which has not been subjected to the grass-common tetraploidization, provides a precious opportunity to solve the above controversy and to research into genome changes of rice and other grasses. Here, we performed a comparative genomics analysis of pineapple and rice, and found solid evidence that grass-common ancestor had 2n =2x =14 basic chromosomes before the tetraploidization and duplicated to 2n = 4x = 28 after the event. Moreover, we proposed that enormous gene missing from duplicated regions in rice should be explained by an allotetraploid produced by prominently divergent parental lines, rather than gene losses after their divergence. This means that genome fractionation might have occurred before the formation of the allotetraploid grass ancestor.

  18. Genome-wide association study and gene expression analysis identifies CD84 as a predictor of response to etanercept therapy in rheumatoid arthritis.

    Directory of Open Access Journals (Sweden)

    Jing Cui

    2013-03-01

    Full Text Available Anti-tumor necrosis factor alpha (anti-TNF biologic therapy is a widely used treatment for rheumatoid arthritis (RA. It is unknown why some RA patients fail to respond adequately to anti-TNF therapy, which limits the development of clinical biomarkers to predict response or new drugs to target refractory cases. To understand the biological basis of response to anti-TNF therapy, we conducted a genome-wide association study (GWAS meta-analysis of more than 2 million common variants in 2,706 RA patients from 13 different collections. Patients were treated with one of three anti-TNF medications: etanercept (n = 733, infliximab (n = 894, or adalimumab (n = 1,071. We identified a SNP (rs6427528 at the 1q23 locus that was associated with change in disease activity score (ΔDAS in the etanercept subset of patients (P = 8 × 10(-8, but not in the infliximab or adalimumab subsets (P>0.05. The SNP is predicted to disrupt transcription factor binding site motifs in the 3' UTR of an immune-related gene, CD84, and the allele associated with better response to etanercept was associated with higher CD84 gene expression in peripheral blood mononuclear cells (P = 1 × 10(-11 in 228 non-RA patients and P = 0.004 in 132 RA patients. Consistent with the genetic findings, higher CD84 gene expression correlated with lower cross-sectional DAS (P = 0.02, n = 210 and showed a non-significant trend for better ΔDAS in a subset of RA patients with gene expression data (n = 31, etanercept-treated. A small, multi-ethnic replication showed a non-significant trend towards an association among etanercept-treated RA patients of Portuguese ancestry (n = 139, P = 0.4, but no association among patients of Japanese ancestry (n = 151, P = 0.8. Our study demonstrates that an allele associated with response to etanercept therapy is also associated with CD84 gene expression, and further that CD84 expression correlates with disease activity. These findings support a model in which CD84

  19. 转青鱼生长激素基因异源四倍体鲫鲤%Black Carp GH Gene Transgenic Allotetraploid Hybrids of Carassius auratus red var.(♀) × Cyprinus carpio (♂)

    Institute of Scientific and Technical Information of China (English)

    冯浩; 傅永明; 骆剑; 吴慧; 刘筠; 刘少军

    2011-01-01

    The ecological risk is the “bottleneck” for commercialization of transgenic fish. The sterile transgenic triploid fish derived from hydrating the transgenic tetraploid fish and transgenic diploid fish is one of the keys to solve this problem.The “all fish” gene construct (pbcAbcGHc) containing Black Carp B-actin gene promoter and cDNA of growth hormone (GH) gene from the same species was introduced into the fertilized eggs of the allotetroploid fish through microinjection. The contrast cultivation results show that the weight and body length of PO of the transgenic allotetraploid fish of 150 days were much larger than those of the controls. PCR assay was applied among 60 transgenic allotetraploid fish of 150 days and the integration ratio of the exogenous transplant gene in the genome of the caudal fin is 90%. The transplant gene could be detected in 13 of 20 samples from the sperm of the male transgenic tetraploid fish.The RT-PCR result demonstrates that the transcription of exogenous GH gene could be found in the muscle, liver,kidney and oval of the biggest transgenic allotetraploid fish. This study has developed PO of the Black Carp GH gene transgenic tetraploid fish with outstanding growth rate, which made the solid foundation for the pure line establishment of the transgenic tetraploid fish and for developing the sterile transgenic triploid fish.%生态安全性是转基因鱼走向市场的瓶颈,通过转基因四倍体鱼同转基因二倍体鱼杂交获得不育的转基因三倍体鱼是解决该问题的有效途径之一.本研究构建了青鱼β-actin基因启动子和青鱼生长激素(GH)基因精确连接的"金鱼"基因pbcAbcGHc;并采用显微注射法将pbcAbcGHc 导入异源四倍体鲫鲤受精卵.对照养殖结果表明,150日龄的转基因异源四倍体鲫鲤原代(P0)的体重及体长明显大于对照组.选择60尾P0代转基因异源四倍体鲫鲤,采用PCR方法检测出外源青鱼GH基因在P0代转基因四倍体尾

  20. Multiplex and genome-wide analyses reveal distinctive properties of KIR+ and CD56+ T cells in human blood

    OpenAIRE

    Chan, Wing Keung; Rujkijyanont, Piya; Neale, Geoffrey; Jie YANG; Bari, Rafijul; Gupta, Neha Das; Holladay, Martha; Rooney, Barbara; Leung, Wing

    2013-01-01

    Killer-cell immunoglobulin-like receptors (KIRs) on natural killer (NK) cells have been linked to a wide spectrum of health conditions such as chronic infections, autoimmune diseases, pregnancy complications, cancers, and transplant failures. A small subset of effector memory T cells also expresses KIRs. Here, we use modern analytic tools including genome-wide and multiplex molecular, phenotypic, and functional assays to characterize the KIR+ T cells in human blood. We find that KIR+ T cells ...

  1. Genomic and Immunological Tumor Profiling Identifies Targetable Pathways and Extensive CD8+/PDL1+ Immune Infiltration in Inflammatory Breast Cancer Tumors.

    Science.gov (United States)

    Hamm, Christopher A; Moran, Diarmuid; Rao, Kakuturu; Trusk, Patricia B; Pry, Karen; Sausen, Mark; Jones, Siân; Velculescu, Victor E; Cristofanilli, Massimo; Bacus, Sarah

    2016-07-01

    Inflammatory breast cancer (IBC) is a rare and aggressive form of breast cancer that remains poorly understood at the molecular level. Comprehensive tumor profiling was performed to understand clinically actionable alterations in IBC. Targeted next-generation sequencing (NGS) and IHC were performed to identify activated pathways in IBC tumor tissues. siRNA studies examined the impact of IBC genomic variants in cellular models. IBC tumor tissues were further characterized for immune infiltration and immune checkpoint expression by IHC. Genomic analysis identified recurrent alterations in core biologic pathways, including activating and targetable variants in HER/PI3K/mTOR signaling. High rates of activating HER3 point mutations were discovered in IBC tumors. Cell line studies confirmed a role for mutant HER3 in IBC cell proliferation. Immunologic analysis revealed a subset of IBC tumors associated with high CD8(+)/PD-L1(+) lymphocyte infiltration. Immune infiltration positively correlated with an NGS-based estimate of neoantigen exposure derived from the somatic mutation rate and mutant allele frequency, iScore. Additionally, DNA mismatch repair alterations, which may contribute to higher iScores, occurred at greater frequency in tumors with higher immune infiltration. Our study identifies genomic alterations that mechanistically contribute to oncogenic signaling in IBC and provides a genetic basis for the selection of clinically relevant targeted and combination therapeutic strategies. Furthermore, an NGS-based estimate of neoantigen exposure developed in this study (iScore) may be a useful biomarker to predict immune infiltration in IBC and other cancers. The iScore may be associated with greater levels of response to immunotherapies, such as PD-L1/PD-1-targeted therapies. Mol Cancer Ther; 15(7); 1746-56. ©2016 AACR.

  2. Isolation and genome-wide expression and methylation characterization of CD31+ cells from normal and malignant human prostate tissue

    Science.gov (United States)

    Luo, Wei; Hu, Qiang; Wang, Dan; Deeb, Kristin K.; Ma, Yingyu; Morrison, Carl D.; Liu, Song; Johnson, Candace S.; Trump, Donald L.

    2013-01-01

    Endothelial cells (ECs) are an important component involved in the angiogenesis. Little is known about the global gene expression and epigenetic regulation in tumor endothelial cells. The identification of gene expression and epigenetic difference between human prostate tumor-derived endothelial cells (TdECs) and those in normal tissues may uncover unique biological features of TdEC and facilitate the discovery of new anti-angiogenic targets. We established a method for isolation of CD31+ endothelial cells from malignant and normal prostate tissues obtained at prostatectomy. TdECs and normal-derived ECs (NdECs) showed >90% enrichment in primary culture and demonstrated microvascular endothelial cell characteristics such as cobblestone morphology in monolayer culture, diI-acetyl-LDL uptake and capillary-tube like formation in Matrigel®. In vitro primary cultures of ECs maintained expression of endothelial markers such as CD31, von Willebrand factor, intercellular adhesion molecule, vascular endothelial growth factor receptor 1, and vascular endothelial growth factor receptor 2. We then conducted a pilot study of transcriptome and methylome analysis of TdECs and matched NdECs from patients with prostate cancer. We observed a wide spectrum of differences in gene expression and methylation patterns in endothelial cells, between malignant and normal prostate tissues. Array-based expression and methylation data were validated by qRT-PCR and bisulfite DNA pyrosequencing. Further analysis of transcriptome and methylome data revealed a number of differentially expressed genes with loci whose methylation change is accompanied by an inverse change in gene expression. Our study demonstrates the feasibility of isolation of ECs from histologically normal prostate and prostate cancer via CD31+ selection. The data, although preliminary, indicates that there exist widespread differences in methylation and transcription between TdECs and NdECs. Interestingly, only a small

  3. The genome of Chenopodium quinoa.

    Science.gov (United States)

    Jarvis, David E; Ho, Yung Shwen; Lightfoot, Damien J; Schmöckel, Sandra M; Li, Bo; Borm, Theo J A; Ohyanagi, Hajime; Mineta, Katsuhiko; Michell, Craig T; Saber, Noha; Kharbatia, Najeh M; Rupper, Ryan R; Sharp, Aaron R; Dally, Nadine; Boughton, Berin A; Woo, Yong H; Gao, Ge; Schijlen, Elio G W M; Guo, Xiujie; Momin, Afaque A; Negrão, Sónia; Al-Babili, Salim; Gehring, Christoph; Roessner, Ute; Jung, Christian; Murphy, Kevin; Arold, Stefan T; Gojobori, Takashi; Linden, C Gerard van der; van Loo, Eibertus N; Jellen, Eric N; Maughan, Peter J; Tester, Mark

    2017-02-16

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  4. The genome of Chenopodium quinoa

    KAUST Repository

    Jarvis, David E.

    2017-02-08

    Chenopodium quinoa (quinoa) is a highly nutritious grain identified as an important crop to improve world food security. Unfortunately, few resources are available to facilitate its genetic improvement. Here we report the assembly of a high-quality, chromosome-scale reference genome sequence for quinoa, which was produced using single-molecule real-time sequencing in combination with optical, chromosome-contact and genetic maps. We also report the sequencing of two diploids from the ancestral gene pools of quinoa, which enables the identification of sub-genomes in quinoa, and reduced-coverage genome sequences for 22 other samples of the allotetraploid goosefoot complex. The genome sequence facilitated the identification of the transcription factor likely to control the production of anti-nutritional triterpenoid saponins found in quinoa seeds, including a mutation that appears to cause alternative splicing and a premature stop codon in sweet quinoa strains. These genomic resources are an important first step towards the genetic improvement of quinoa.

  5. n-TiO{sub 2} and CdCl{sub 2} co-exposure to titanium dioxide nanoparticles and cadmium: Genomic, DNA and chromosomal damage evaluation in the marine fish European sea bass (Dicentrarchus labrax)

    Energy Technology Data Exchange (ETDEWEB)

    Nigro, M.; Bernardeschi, M. [Department of Clinical and Experimental Medicine, Pisa University, Pisa (Italy); Costagliola, D. [Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta (Italy); Della Torre, C. [Department of Physical, Earth and Environmental Sciences, University of Siena, Siena (Italy); Frenzilli, G., E-mail: giada@biomed.unipi.it [Department of Clinical and Experimental Medicine, Pisa University, Pisa (Italy); Guidi, P.; Lucchesi, P. [Department of Clinical and Experimental Medicine, Pisa University, Pisa (Italy); Mottola, F.; Santonastaso, M. [Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta (Italy); Scarcelli, V. [Department of Clinical and Experimental Medicine, Pisa University, Pisa (Italy); Monaci, F.; Corsi, I. [Department of Physical, Earth and Environmental Sciences, University of Siena, Siena (Italy); Stingo, V.; Rocco, L. [Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Second University of Naples, Caserta (Italy)

    2015-11-15

    Highlights: • European sea bass was exposed to CdCl{sub 2} and n-TiO{sub 2} alone and in combination. • Genotoxicity was evaluated by RAPD-assay, comet assay and cytome assay. • CdCl{sub 2} induced DNA primary damage but not chromosomal damage. • n-TiO{sub 2} induced chromosomal damage but not DNA primary damage. • Co-exposure effects depend on the biomarker used. - Abstract: Due to the large production and growing use of titanium dioxide nanoparticles (n-TiO{sub 2}), their release in the marine environment and their potential interaction with existing toxic contaminants represent a growing concern for biota. Different end-points of genotoxicity were investigated in the European sea bass Dicentrarchus labrax exposed to n-TiO{sub 2} (1 mg L{sup −1}) either alone and combined with CdCl{sub 2} (0.1 mg L{sup −1}) for 7 days. DNA primary damage (comet assay), apoptotic cells (diffusion assay), occurrence of micronuclei and nuclear abnormalities (cytome assay) were assessed in peripheral erythrocytes and genomic stability (random amplified polymorphism DNA-PCR, RAPD assay) in muscle tissue. Results showed that genome template stability was reduced after CdCl{sub 2} and n-TiO{sub 2} exposure. Exposure to n-TiO{sub 2} alone was responsible for chromosomal alteration but ineffective in terms of DNA damage; while the opposite was observed in CdCl{sub 2} exposed specimens. Co-exposure apparently prevents the chromosomal damage and leads to a partial recovery of the genome template stability.

  6. Comparative Proteomic, Physiological, Morphological, and Biochemical Analyses Reveal the Characteristics of the Diploid Spermatozoa of Allotetraploid Hybrids of Red Crucian Carp (Carassius auratus) and Common Carp (Cyprinus carpio).

    Science.gov (United States)

    Duan, Wei; Xu, Kang; Hu, Fangzhou; Zhang, Yi; Wen, Ming; Wang, Jing; Tao, Min; Luo, Kaikun; Zhao, Rurong; Qin, Qinbo; Zhang, Chun; Liu, Jinhui; Liu, Yun; Liu, Shaojun

    2016-02-01

    The generation of diploid spermatozoa is essential for the continuity of tetraploid lineages. The DNA content of diploid spermatozoa from allotetraploid hybrids of red crucian carp and common carp was nearly twice as great as that of haploid spermatozoa from common carp, and the durations of rapid and slow progressive motility were longer. We performed comparative proteomic analyses to measure variations in protein composition between diploid and haploid spermatozoa. Using two-dimensional electrophoresis followed by liquid chromatography tandem mass spectrometry, 21 protein spots that changed in abundance were analyzed. As the common carp and the allotetraploid hybrids are not fully sequenced organisms, we identified proteins by Mascot searching against the National Center for Biotechnology Information non-redundant (NR) protein database for the zebrafish (Danio rerio), and verified them against predicted homologous proteins derived from transcriptomes of the testis. Twenty protein spots were identified successfully, belonging to four gene ontogeny categories: cytoskeleton, energy metabolism, the ubiquitin-proteasome system, and other functions, indicating that these might be associated with the variation in diploid spermatozoa. This categorization of variations in protein composition in diploid spermatozoa will provide new perspectives on male polyploidy. Moreover, our approach indicates that transcriptome data are useful for proteomic analyses in organisms lacking full protein sequences.

  7. The B73 maize genome: complexity, diversity, and dynamics.

    Science.gov (United States)

    Schnable, Patrick S; Ware, Doreen; Fulton, Robert S; Stein, Joshua C; Wei, Fusheng; Pasternak, Shiran; Liang, Chengzhi; Zhang, Jianwei; Fulton, Lucinda; Graves, Tina A; Minx, Patrick; Reily, Amy Denise; Courtney, Laura; Kruchowski, Scott S; Tomlinson, Chad; Strong, Cindy; Delehaunty, Kim; Fronick, Catrina; Courtney, Bill; Rock, Susan M; Belter, Eddie; Du, Feiyu; Kim, Kyung; Abbott, Rachel M; Cotton, Marc; Levy, Andy; Marchetto, Pamela; Ochoa, Kerri; Jackson, Stephanie M; Gillam, Barbara; Chen, Weizu; Yan, Le; Higginbotham, Jamey; Cardenas, Marco; Waligorski, Jason; Applebaum, Elizabeth; Phelps, Lindsey; Falcone, Jason; Kanchi, Krishna; Thane, Thynn; Scimone, Adam; Thane, Nay; Henke, Jessica; Wang, Tom; Ruppert, Jessica; Shah, Neha; Rotter, Kelsi; Hodges, Jennifer; Ingenthron, Elizabeth; Cordes, Matt; Kohlberg, Sara; Sgro, Jennifer; Delgado, Brandon; Mead, Kelly; Chinwalla, Asif; Leonard, Shawn; Crouse, Kevin; Collura, Kristi; Kudrna, Dave; Currie, Jennifer; He, Ruifeng; Angelova, Angelina; Rajasekar, Shanmugam; Mueller, Teri; Lomeli, Rene; Scara, Gabriel; Ko, Ara; Delaney, Krista; Wissotski, Marina; Lopez, Georgina; Campos, David; Braidotti, Michele; Ashley, Elizabeth; Golser, Wolfgang; Kim, HyeRan; Lee, Seunghee; Lin, Jinke; Dujmic, Zeljko; Kim, Woojin; Talag, Jayson; Zuccolo, Andrea; Fan, Chuanzhu; Sebastian, Aswathy; Kramer, Melissa; Spiegel, Lori; Nascimento, Lidia; Zutavern, Theresa; Miller, Beth; Ambroise, Claude; Muller, Stephanie; Spooner, Will; Narechania, Apurva; Ren, Liya; Wei, Sharon; Kumari, Sunita; Faga, Ben; Levy, Michael J; McMahan, Linda; Van Buren, Peter; Vaughn, Matthew W; Ying, Kai; Yeh, Cheng-Ting; Emrich, Scott J; Jia, Yi; Kalyanaraman, Ananth; Hsia, An-Ping; Barbazuk, W Brad; Baucom, Regina S; Brutnell, Thomas P; Carpita, Nicholas C; Chaparro, Cristian; Chia, Jer-Ming; Deragon, Jean-Marc; Estill, James C; Fu, Yan; Jeddeloh, Jeffrey A; Han, Yujun; Lee, Hyeran; Li, Pinghua; Lisch, Damon R; Liu, Sanzhen; Liu, Zhijie; Nagel, Dawn Holligan; McCann, Maureen C; SanMiguel, Phillip; Myers, Alan M; Nettleton, Dan; Nguyen, John; Penning, Bryan W; Ponnala, Lalit; Schneider, Kevin L; Schwartz, David C; Sharma, Anupma; Soderlund, Carol; Springer, Nathan M; Sun, Qi; Wang, Hao; Waterman, Michael; Westerman, Richard; Wolfgruber, Thomas K; Yang, Lixing; Yu, Yeisoo; Zhang, Lifang; Zhou, Shiguo; Zhu, Qihui; Bennetzen, Jeffrey L; Dawe, R Kelly; Jiang, Jiming; Jiang, Ning; Presting, Gernot G; Wessler, Susan R; Aluru, Srinivas; Martienssen, Robert A; Clifton, Sandra W; McCombie, W Richard; Wing, Rod A; Wilson, Richard K

    2009-11-20

    We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

  8. Expression of lactate/H⁺ symporters MCT1 and MCT4 and their chaperone CD147 predicts tumor progression in clear cell renal cell carcinoma: immunohistochemical and The Cancer Genome Atlas data analyses.

    Science.gov (United States)

    Kim, Younghye; Choi, Jung-Woo; Lee, Ju-Han; Kim, Young-Sik

    2015-01-01

    Clear cell renal cell carcinomas (ccRCCs) have inactivation of the von Hippel-Lindau protein, leading to the accumulation of hypoxia-inducible factor-α (HIF-α). HIF-1α induces aerobic glycolysis, the Warburg effect, whereas HIF-2α functions as an oncoprotein. Lactate transport through monocarboxylate transporters (MCTs) and the chaperone CD147 is essential for high glycolytic cancer cell survival. To elucidate the clinical significance of MCT1, MCT4, and CD147 expression, we investigated their expressions by immunohistochemistry in ccRCC specimens and validated the results by an open-access The Cancer Genome Atlas data analysis. Overexpression of MCT1, MCT4, and CD147 was observed in 49.4% (89/180), 39.4% (71/180), and 79.4% (143/180) of ccRCC patients, respectively. High MCT1 expression was associated with older age (P = .017), larger tumor size (P = .015), and advanced TNM stage (P = .012). However, MCT4 overexpression was not related to any variables. CD147 overexpression correlated with high grade (P = .005), tumor necrosis (P = .016), and larger tumor size (P = .038). In univariate analysis, high expression of MCT1 (P CD147 (P = .02) was linked to short progression-free survival. In multivariate analysis, high MCT1 expression was associated with worse progression-free survival (P = .001). In conclusion, high expression of MCT1 and CD147 is associated with poor prognostic factors. Overexpression of MCT1, MCT4, and CD147 predicts tumor progression. Reversing the Warburg effect by targeting the lactate transporters may be a useful strategy to prevent ccRCC progression.

  9. Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication.

    Science.gov (United States)

    Uno, Y; Nishida, C; Takagi, C; Ueno, N; Matsuda, Y

    2013-11-01

    It has been suggested that whole-genome duplication (WGD) occurred twice during the evolutionary process of vertebrates around 450 and 500 million years ago, which contributed to an increase in the genomic and phenotypic complexities of vertebrates. However, little is still known about the evolutionary process of homoeologous chromosomes after WGD because many duplicate genes have been lost. Therefore, Xenopus laevis (2n=36) and Xenopus (Silurana) tropicalis (2n=20) are good animal models for studying the process of genomic and chromosomal reorganization after WGD because X. laevis is an allotetraploid species that resulted from WGD after the interspecific hybridization of diploid species closely related to X. tropicalis. We constructed a comparative cytogenetic map of X. laevis using 60 complimentary DNA clones that covered the entire chromosomal regions of 10 pairs of X. tropicalis chromosomes. We consequently identified all nine homoeologous chromosome groups of X. laevis. Hybridization signals on two pairs of X. laevis homoeologous chromosomes were detected for 50 of 60 (83%) genes, and the genetic linkage is highly conserved between X. tropicalis and X. laevis chromosomes except for one fusion and one inversion and also between X. laevis homoeologous chromosomes except for two inversions. These results indicate that the loss of duplicated genes and inter- and/or intrachromosomal rearrangements occurred much less frequently in this lineage, suggesting that these events were not essential for diploidization of the allotetraploid genome in X. laevis after WGD.

  10. Molecular pathway profiling of T lymphocyte signal transduction pathways; Th1 and Th2 genomic fingerprints are defined by TCR and CD28-mediated signaling

    Directory of Open Access Journals (Sweden)

    Smeets Ruben L

    2012-03-01

    Full Text Available Abstract Background T lymphocytes are orchestrators of adaptive immunity. Naïve T cells may differentiate into Th1, Th2, Th17 or iTreg phenotypes, depending on environmental co-stimulatory signals. To identify genes and pathways involved in differentiation of Jurkat T cells towards Th1 and Th2 subtypes we performed comprehensive transcriptome analyses of Jurkat T cells stimulated with various stimuli and pathway inhibitors. Results from these experiments were validated in a human experimental setting using whole blood and purified CD4+ Tcells. Results Calcium-dependent activation of T cells using CD3/CD28 and PMA/CD3 stimulation induced a Th1 expression profile reflected by increased expression of T-bet, RUNX3, IL-2, and IFNγ, whereas calcium-independent activation via PMA/CD28 induced a Th2 expression profile which included GATA3, RXRA, CCL1 and Itk. Knock down with siRNA and gene expression profiling in the presence of selective kinase inhibitors showed that proximal kinases Lck and PKCθ are crucial signaling hubs during T helper cell activation, revealing a clear role for Lck in Th1 development and for PKCθ in both Th1 and Th2 development. Medial signaling via MAPkinases appeared to be less important in these pathways, since specific inhibitors of these kinases displayed a minor effect on gene expression. Translation towards a primary, whole blood setting and purified human CD4+ T cells revealed that PMA/CD3 stimulation induced a more pronounced Th1 specific, Lck and PKCθ dependent IFNγ production, whereas PMA/CD28 induced Th2 specific IL-5 and IL-13 production, independent of Lck activation. PMA/CD3-mediated skewing towards a Th1 phenotype was also reflected in mRNA expression of the master transcription factor Tbet, whereas PMA/CD28-mediated stimulation enhanced GATA3 mRNA expression in primary human CD4+ Tcells. Conclusions This study identifies stimulatory pathways and gene expression profiles for in vitro skewing of T helper cell

  11. Genome Sizes in Hepatica Mill: (Ranunculaceae Show a Loss of DNA, Not a Gain, in Polyploids

    Directory of Open Access Journals (Sweden)

    B. J. M. Zonneveld

    2010-01-01

    , and a possible pentaploid. The somatic nuclear DNA contents (2C-value, as measured by flow cytometry with propidium iodide, were shown to range from 33 to 80 pg. The Asiatic and American species, often considered subspecies of H. nobilis, could be clearly distinguished from European H. nobilis. DNA content confirmed the close relationships in the Asiatic species, and these are here considered as subspecies of H. asiatica. Parents for the allotetraploid species could be suggested based on their nuclear DNA content. Contrary to the increase in genome size suggested earlier for Hepatica, a significant (6%–14% loss of nuclear DNA in the natural allopolyploids was found.

  12. Genome-wide Profiling Reveals Remarkable Parallels Between Insertion Site Selection Properties of the MLV Retrovirus and the piggyBac Transposon in Primary Human CD4+ T Cells

    Science.gov (United States)

    Gogol-Döring, Andreas; Ammar, Ismahen; Gupta, Saumyashree; Bunse, Mario; Miskey, Csaba; Chen, Wei; Uckert, Wolfgang; Schulz, Thomas F; Izsvák, Zsuzsanna; Ivics, Zoltán

    2016-01-01

    The inherent risks associated with vector insertion in gene therapy need to be carefully assessed. We analyzed the genome-wide distributions of Sleeping Beauty (SB) and piggyBac (PB) transposon insertions as well as MLV retrovirus and HIV lentivirus insertions in human CD4+ T cells with respect to a panel of 40 chromatin states. The distribution of SB transposon insertions displayed the least deviation from random, while the PB transposon and the MLV retrovirus showed unexpected parallels across all chromatin states. Both MLV and PB insertions are enriched at transcriptional start sites (TSSs) and co-localize with BRD4-associated sites. We demonstrate physical interaction between the PB transposase and bromodomain and extraterminal domain proteins (including BRD4), suggesting convergent evolution of a tethering mechanism that directs integrating genetic elements into TSSs. We detect unequal biases across the four systems with respect to targeting genes whose deregulation has been previously linked to serious adverse events in gene therapy clinical trials. The SB transposon has the highest theoretical chance of targeting a safe harbor locus in the human genome. The data underscore the significance of vector choice to reduce the mutagenic load on cells in clinical applications. PMID:26755332

  13. Allogamy-Autogamy Switch Enhance Assortative Mating in the Allotetraploid Centaurea seridis L. Coexisting with the Diploid Centaurea aspera L. and Triggers the Asymmetrical Formation of Triploid Hybrids

    Science.gov (United States)

    Ferriol, María; Garmendia, Alfonso; Gonzalez, Ana; Merle, Hugo

    2015-01-01

    Hybridization between tetraploids and their related diploids is generally unsuccessful in Centaurea, hence natural formation of triploid hybrids is rare. In contrast, the diploid Centaurea aspera and the allotetraploid C. seridis coexist in several contact zones where a high frequency of triploid hybrids is found. We analyzed the floral biology of the three taxa to identify reproductive isolation mechanisms that allow their coexistence. Flowering phenology was recorded, and controlled pollinations within and between the three taxa were performed in the field. Ploidy level and germination of progeny were also assessed. There was a 50% flowering overlap which indicated a phenological shift. Diploids were strictly allogamous and did not display mentor effects, while tetraploids were found to be highly autogamous. This breakdown of self-incompatibility by polyploids is first described in Centaurea. The asymmetrical formation of the hybrid was also found: all the triploid intact cypselae came from the diploid mothers pollinated by the pollen of tetraploids. Pollen and eggs from triploids were totally sterile, acting as a strong triploid block. These prezygotic isolation mechanisms ensured higher assortative mating in tetraploids than in diploids, improving their persistence in the contact zones. However these mechanisms can also be the cause of the low genetic diversity and high genetic structure observed in C. seridis. PMID:26469271

  14. Genome-wide nucleosome positioning mode and relationship with TFBS dis-tribution in human CD4 +T cell%人类CD4+T细胞核小体定位模式及其与TFBS分布特征关系研究

    Institute of Scientific and Technical Information of China (English)

    蓝贤梅; 黄艳; 崔颖

    2014-01-01

    目的:研究人类CD4+T细胞全基因组核小体抑制和激活状态下的定位模式,转录因子结合位点( Transcription factor binding site , TFBS)分布特征以及两者之间的关系。方法采用生物信息学软件R、Java等通过编写比对算法进行统计学分析。结果人类CD4+T细胞中核小体定位在染色质上的分布比例为0.6,从休眠到激活状态核小体定位发生位置改变,呈现稳定定位模式和动态定位模式,且比例分别为2%和98%,核小体定位具有较大的动态变化性;核小体定位与TFBS位置关系研究中,发现分布在核小体内的TFBS数目较大,但总体长度较短;而分布在连接DNA上的TFBS数目相对较少,但总体长度较长。结论人类CD4+T细胞休眠和激活状态下全基因组的核小体定位模式基本一致,核小体定位与TFBS关系有明显特征。%Objective To study the human genome-wide nucleosome positioning mode from CD4 +T cell under inhibition and activation status , TFBS distribution characteristics as well as the relationship between them .Methods Using bioinformatics software R , Java to write align-ment algorithms to perform statistical analysis .Results The nucleosomes positioning rate on the chromatin in human CD 4 +T cell was about 60%.Nucleosome positioning lacation came to change when condition of cell was from rest condition to activity condition , both stable positio-ning mode and dynamic positioning mode , and the proportion of them in all of nucleosome posi-tioning were 2%and 98%respectively .Nucleosome positioning appeared larger dynamic varia-bility.Studying the position relationship between nucleosome positioning and TFBS , found that the distribution number of TFBS in nucleosome positioning sequences was bigger , but the over-all length was shorter .And distribution number in the linker was relatively small , but the over-all length was longer than the other .Conclusion The distribution

  15. TU-CD-BRB-07: Identification of Associations Between Radiologist-Annotated Imaging Features and Genomic Alterations in Breast Invasive Carcinoma, a TCGA Phenotype Research Group Study

    Energy Technology Data Exchange (ETDEWEB)

    Rao, A; Net, J [University of Miami, Miami, Florida (United States); Brandt, K [Mayo Clinic, Rochester, Minnesota (United States); Huang, E [National Cancer Institute, NIH, Bethesda, MD (United States); Freymann, J; Kirby, J [Leidos Biomedical Research Inc., Frederick, MD (United States); Burnside, E [University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin (United States); Morris, E; Sutton, E [Memorial Sloan Kettering Cancer Center, New York, NY (United States); Bonaccio, E [Roswell Park Cancer Institute, Buffalo, NY (United States); Giger, M; Jaffe, C [Univ Chicago, Chicago, IL (United States); Ganott, M; Zuley, M [University of Pittsburgh Medical Center - Magee Womens Hospital, Pittsburgh, Pennsylvania (United States); Le-Petross, H [MD Anderson Cancer Center, Houston, TX (United States); Dogan, B [UT MDACC, Houston, TX (United States); Whitman, G [UTMDACC, Houston, TX (United States)

    2015-06-15

    Purpose: To determine associations between radiologist-annotated MRI features and genomic measurements in breast invasive carcinoma (BRCA) from the Cancer Genome Atlas (TCGA). Methods: 98 TCGA patients with BRCA were assessed by a panel of radiologists (TCGA Breast Phenotype Research Group) based on a variety of mass and non-mass features according to the Breast Imaging Reporting and Data System (BI-RADS). Batch corrected gene expression data was obtained from the TCGA Data Portal. The Kruskal-Wallis test was used to assess correlations between categorical image features and tumor-derived genomic features (such as gene pathway activity, copy number and mutation characteristics). Image-derived features were also correlated with estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2/neu) status. Multiple hypothesis correction was done using Benjamini-Hochberg FDR. Associations at an FDR of 0.1 were selected for interpretation. Results: ER status was associated with rim enhancement and peritumoral edema. PR status was associated with internal enhancement. Several components of the PI3K/Akt pathway were associated with rim enhancement as well as heterogeneity. In addition, several components of cell cycle regulation and cell division were associated with imaging characteristics.TP53 and GATA3 mutations were associated with lesion size. MRI features associated with TP53 mutation status were rim enhancement and peritumoral edema. Rim enhancement was associated with activity of RB1, PIK3R1, MAP3K1, AKT1,PI3K, and PIK3CA. Margin status was associated with HIF1A/ARNT, Ras/ GTP/PI3K, KRAS, and GADD45A. Axillary lymphadenopathy was associated with RB1 and BCL2L1. Peritumoral edema was associated with Aurora A/GADD45A, BCL2L1, CCNE1, and FOXA1. Heterogeneous internal nonmass enhancement was associated with EGFR, PI3K, AKT1, HF/MET, and EGFR/Erbb4/neuregulin 1. Diffuse nonmass enhancement was associated with HGF/MET/MUC20/SHIP

  16. Distinct origin of the Y and St genome in Elymus species: evidence from the analysis of a large sample of St genome species using two nuclear genes.

    Directory of Open Access Journals (Sweden)

    Chi Yan

    Full Text Available BACKGROUND: Previous cytological and single copy nuclear genes data suggested the St and Y genome in the StY-genomic Elymus species originated from different donors: the St from a diploid species in Pseudoroegneria and the Y from an unknown diploid species, which are now extinct or undiscovered. However, ITS data suggested that the Y and St genome shared the same progenitor although rather few St genome species were studied. In a recent analysis of many samples of St genome species Pseudoroegneria spicata (Pursh À. Löve suggested that one accession of P. spicata species was the most likely donor of the Y genome. The present study tested whether intraspecific variation during sampling could affect the outcome of analyses to determining the origin of Y genome in allotetraploid StY species. We also explored the evolutionary dynamics of these species. METHODOLOGY/PRINCIPAL FINDINGS: Two single copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2 and the translation elongation factor G (EF-G sequences from 58 accessions of Pseudoroegneria and Elymus species, together with those from Hordeum (H, Agropyron (P, Australopyrum (W, Lophopyrum (E(e, Thinopyrum (E(a, Thinopyrum (E(b, and Dasypyrum (V were analyzed using maximum parsimony, maximum likelihood and Bayesian methods. Sequence comparisons among all these genomes revealed that the St and Y genomes are relatively dissimilar. Extensive sequence variations have been detected not only between the sequences from St and Y genome, but also among the sequences from diploid St genome species. Phylogenetic analyses separated the Y sequences from the St sequences. CONCLUSIONS/SIGNIFICANCE: Our results confirmed that St and Y genome in Elymus species have originated from different donors, and demonstrated that intraspecific variation does not affect the identification of genome origin in polyploids. Moreover, sequence data showed evidence to support the suggestion of the genome

  17. CD163

    DEFF Research Database (Denmark)

    Moestrup, Søren K; Møller, Holger J

    2004-01-01

    CD163 is a hemoglobin scavenger receptor exclusively expressed in the monocyte-macrophage system. A particularly high expression is seen in macrophages of the 'alternative activation' phenotype playing a major role in dampening the inflammatory response and in scavenging components of damaged cells....... CD163-mediated endocytosis of haptoglobin-hemoglobin complexes formed upon red blood cell hemolysis leads to lysosomal degradation of the ligand protein and metabolism of heme by cytosolic heme oxygenase. In accordance with a stimulated expression of haptoglobin, CD163 and heme oxygenase-1 during...... the acute phase response, there is evidence that this metabolic pathway regulates inflammation by at least two ways. First, CD163 is reported to directly induce intracellular signaling leading to secretion of anti-inflammatory cytokines. Second and perhaps even more important, the CD163-mediated delivery...

  18. 基于短序列测序数据的四倍体拟南芥转录组研究%De Novo Assembly of Allotetraploid Arabidopsis suecica Transcriptome using Short Reads for Gene Discovery and Marker Identification

    Institute of Scientific and Technical Information of China (English)

    刘新星; 陈超

    2011-01-01

    为了促进对四倍体拟南芥(A.suecica)的研究,阐明多倍体植物在染色体加倍过程中遗传物质的变化,从而在分子层面上解释多倍体植物的环境适应和进化机制,描述了一套基于第二代测序技术的转录组短序列组装和生物信息学分析方法.通过对23 000 000条来至于Illumina测序平台的序列数据进行SOAPdenovo组装,以及后续的TGICL聚类和Phrap拼接,共得到125 953条非冗余的转录本序列,其N50和平均长度分别为550bp和331bp.通过BLASTX比对,共有96 057(76.3%)条转录本序列与Nr数据库中的植物蛋白序列具有高度同源性(e-value<10-5),对转录本序列的GO(gene ontology)要的蛋白功能.另外,将A.suecica转录组的GC含量与其相邻物种进行了比较分析,并对简单重复序列(SSRs)进行了鉴定.研究结果表明基于短序列测序数据的多重kmer组装对于转录组分析的可行性,并且为其他相关物种的转录组组装和基因表达分析提供了重要的参考价值.%To facilitate the research on Arabidopsis suecica (A. suecica), a method was presented for de novo assembly of A. suecica transcriptome using short reads produced by Illumina sequencing platform. 23 million sequencing reads were assembled into 125 953 unique sequences with the N50 length of 550 bp and mean size of 331 bp. At the protein level, a total of 96 057 (76. 3% ) A. suecica transcripts showed significant similarity with transcripts proteins from the other plants in the Nr database. Functional categorization revealed the conservation of genes involved in various biological processes in A. suecica. In addition, simple sequence repeats (SSRs) motifs in the A. suecica transcriptome was identified. The data provides a comprehensive sequence resource available for A. suecica study and demonstrates that the short pair-end reads sequencing allows de novo transcriptome assembly in a allotetraploid species lacking genome information. It is anticipated that

  19. TU-CD-BRB-02: BEST IN PHYSICS (JOINT IMAGING-THERAPY): Identification of Molecular Phenotypes by Integrating Radiomics and Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Grossmann, P; Velazquez, E Rios; Parmar, C; Aerts, H [Dana-Farber Cancer Institute/Harvard Medical School, Boston, MA (United States); Grove, O; Gillies, R [H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida (United States); El-Hachem, N [Institut de Recherches Cliniques de Montreal, Montreal, Quebec (Canada); Leijenaar, R [Research Institute GROW, Maastricht (Netherlands); Haibe-Kains, B [University Health Network, Toronto, Ontario (Canada); Lambin, P

    2015-06-15

    Purpose: To uncover the mechanistic connections between radiomic features, molecular pathways, and clinical outcomes, to develop radiomic based predictors of pathway activation states in individual patients, and to assess whether combining radiomic with clinical and genomic data improves prognostication. Methods: We analyzed two independent lung cancer cohorts totaling 351 patients, for whom diagnostic computed tomography (CT) scans, gene-expression profiles, and clinical outcomes were available. The tumor phenotype was characterized based on 636 radiomic features describing tumor intensity, texture, shape and size. We performed an integrative analysis by developing and independently validating association modules of coherently expressed radiomic features and molecular pathways. These modules were statistically tested for significant associations to overall survival (OS), TNM stage, and pathologic histology. Results: We identified thirteen radiomic-pathway association modules (p < 0.05), the most prominent of which were associated with the immune system, p53 pathway, and other pathways involved in cell cycle regulation. Eleven modules were significantly associated with clinical outcomes (p < 0.05). Strong predictive power for pathway activation states in individual patients was observed using radiomics; the strongest per module predictions ranged from an intra-tumor heterogeneity feature predicting RNA III polymerase transcription (AUC 0.62, p = 0.03), to a tumor intensity dispersion feature predicting pyruvate metabolism and citric acid TCA cycle (AUC 0.72, p < 10−{sup 6}). Stepwise combinations of radiomic data with clinical outcomes and gene expression profiles resulted in consistent increases of prognostic power to predict OS (concordance index max = 0.73, p < 10−{sup 9}). Conclusion: This study demonstrates that radiomic approaches permit a non-invasive assessment of molecular and clinical characteristics of tumors, and therefore have the unprecedented

  20. Evolutionary biology of CD1.

    Science.gov (United States)

    Dascher, C C

    2007-01-01

    The recognition more than a decade ago that lipids presented by CD1 could function as T cell antigens revealed a startling and previously unappreciated complexity to the adaptive immune system. The initial novelty of lipid antigen presentation by CD1 has since given way to a broader perspective of the immune system's capacity to sense and respond to a diverse array of macromolecules. Some immune recognition systems such as Toll-like receptors can trace their origins back into the deep history of sea urchins and arthropods. Others such as the major histocompatibility complex (MHC) appear relatively recently and interestingly, only in animals that also possess a jaw. The natural history of CD1 is thus part of the wider story of immune system evolution and should be considered in this context. Most evidence indicates that CD1 probably evolved from a classical MHC class I (MHC I) gene at some point during vertebrate evolution. This chapter reviews the evidence for this phylogenetic relationship and attempts to connect CD1 to existing models of MHC evolution. This endeavor is facilitated today by the recent availability of whole genome sequence data from a variety of species. Investigators have used these data to trace the ultimate origin of the MHC to a series of whole genome duplications that occurred roughly 500 million years ago. Sequence data have also revealed homologs of the mammalian MHC I and MHC II gene families in virtually all jawed vertebrates including sharks, bony fishes, reptiles, and birds. In contrast, CD1 genes have thus far been found only in a subset of these animal groups. This pattern of CD1 occurrence in the genomes of living species suggests the emergence of CD 1 in an early terrestrial vertebrate.

  1. 棉花功能基因组研究用的突变体库构建%Establishment of Mutated Gene Bank for Cotton Functional Genomic Research

    Institute of Scientific and Technical Information of China (English)

    Ye-hua YANG; Xue-kui WANG; Zhen-bin WU; Hai-yan LIU

    2002-01-01

    @@ Upland cotton is one of the important cultivated allotetraploid species. From the point of functional genomic research, it is hard to obtain homozygous recessive mutants by applying of traditional mutagensis methods in this crop as its many traits are controlled by more than two pairs of alleles. Adopting of specific transposon tagging strategy which is widely used to induce and isolate mutated genes in various plant species can avoid isolating recessive mutants and is easy to find and characterize the mutated genes in the tetraploid cotton species.

  2. Comparative analysis of A, B,C and D genomes in the genus Oryza with C0t-1 DNA of C genome

    Institute of Scientific and Technical Information of China (English)

    LAN Weizhen; QIN Rui; LI Gang; HE Guangcun

    2006-01-01

    Fluorescence in situ hybridization (FISH)was applied to somatic chromosomes preparations of Oryza officinalis Wall. (CC), O. sativa L. (AA)×O. officinalis F1 hybrid (AC), backcross progenies BC1 (AAC and ACC), O. latifolia Desv. (CCDD), O. alta Swallen (CCDD) and O. punctata Kotschy (BBCC)with a labelled probe of Cot-1 DNA from O. officinalis.In O. officinalis, the homologous chromosomes showed similar signal bands probed by C0t-1 DNA and karyotype analysis was conducted based on the band patterns. Using no blocking DNA, the probe identified the chromosomes of C genome clearly, but detected few signals on chromosomes of A genome in the F1 hybrid and two backcross progenies of BC1.It is obvious that the highly and moderately repetitive DNA sequences were considerably different between C and A genomes. The chromosomes of C genome were also discriminated from the chromosomes of D-and B-genome in the tetraploid species O. latifolia, O.alta and O. punctata by C0t-1 DNA-FISH. Comparison of the fluorescence intensity on the chromosomes of B, C and D genomes in O. latifolia, O. alta,and O. punctata indicated that the differentiations between C and D genomes are less than that between C and B genomes. The relationship between C and D genomes in O. alta is closer than that of C and D genomes in O. latifolia. This would be one of the causes for the fact that both the genomes are of the same karyotype (CCDD) but belong to different species. The above results showed that the C0t-1 DNA had a high specificity of genome and species. In this paper, the origin of allotetraploid in genus Oryza is also discussed.

  3. Physiological, genomic and transcriptional diversity in responses to boron deficiency in rapeseed genotypes

    Science.gov (United States)

    Hua, Yingpeng; Zhou, Ting; Ding, Guangda; Yang, Qingyong; Shi, Lei; Xu, Fangsen

    2016-01-01

    Allotetraploid rapeseed (Brassica napus L. AnAnCnCn, 2n=4x=38) is highly susceptible to boron (B) deficiency, a widespread limiting factor that causes severe losses in seed yield. The genetic variation in the sensitivity to B deficiency found in rapeseed genotypes emphasizes the complex response architecture. In this research, a B-inefficient genotype, ‘Westar 10’ (‘W10’), responded to B deficiencies during vegetative and reproductive development with an over-accumulation of reactive oxygen species, severe lipid peroxidation, evident plasmolysis, abnormal floral organogenesis, and widespread sterility compared to a B-efficient genotype, ‘Qingyou 10’ (‘QY10’). Whole-genome re-sequencing (WGS) of ‘QY10’ and ‘W10’ revealed a total of 1 605 747 single nucleotide polymorphisms and 218 755 insertions/deletions unevenly distributed across the allotetraploid rapeseed genome (~1130Mb). Digital gene expression (DGE) profiling identified more genes related to B transporters, antioxidant enzymes, and the maintenance of cell walls and membranes with higher transcript levels in the roots of ‘QY10’ than in ‘W10’ under B deficiency. Furthermore, based on WGS and bulked segregant analysis of the doubled haploid (DH) line pools derived from ‘QY10’ and ‘W10’, two significant quantitative trait loci (QTLs) for B efficiency were characterized on chromosome C2, and DGE-assisted QTL-seq analyses then identified a nodulin 26-like intrinsic protein gene and an ATP-binding cassette (ABC) transporter gene as the corresponding candidates regulating B efficiency. This research facilitates a more comprehensive understanding of the differential physiological and transcriptional responses to B deficiency and abundant genetic diversity in rapeseed genotypes, and the DGE-assisted QTL-seq analyses provide novel insights regarding the rapid dissection of quantitative trait genes in plant species with complex genomes. PMID:27639094

  4. A new synthetic allotetraploid (A1A1G2G2 between Gossypium herbaceum and G. australe: bridging for simultaneously transferring favorable genes from these two diploid species into upland cotton.

    Directory of Open Access Journals (Sweden)

    Quan Liu

    Full Text Available Gossypium herbaceum, a cultivated diploid cotton species (2n = 2x = 26, A1A1, has favorable traits such as excellent drought tolerance and resistance to sucking insects and leaf curl virus. G. australe, a wild diploid cotton species (2n = 2x = 26, G2G2, possesses numerous economically valuable characteristics such as delayed pigment gland morphogenesis (which is conducive to the production of seeds with very low levels of gossypol as a potential food source for humans and animals and resistance to insects, wilt diseases and abiotic stress. Creating synthetic allotetraploid cotton from these two species would lay the foundation for simultaneously transferring favorable genes into cultivated tetraploid cotton. Here, we crossed G. herbaceum (as the maternal parent with G. australe to produce an F1 interspecific hybrid and doubled its chromosome complement with colchicine, successfully generating a synthetic tetraploid. The obtained tetraploid was confirmed by morphology, cytology and molecular markers and then self-pollinated. The S1 seedlings derived from this tetraploid gradually became flavescent after emergence of the fifth true leaf, but they were rescued by grafting and produced S2 seeds. The rescued S1 plants were partially fertile due to the existence of univalents at Metaphase I of meiosis, leading to the formation of unbalanced, nonviable gametes lacking complete sets of chromosomes. The S2 plants grew well and no flavescence was observed, implying that interspecific incompatibility, to some extent, had been alleviated in the S2 generation. The synthetic allotetraploid will be quite useful for polyploidy evolutionary studies and as a bridge for transferring favorable genes from these two diploid species into Upland cotton through hybridization.

  5. Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes.

    Science.gov (United States)

    Wang, Xuewen; Bennetzen, Jeffrey L

    2015-02-01

    Nicotiana, a member of the Solanaceae family, is one of the most important research model plants, and of high agricultural and economic value worldwide. To better understand the substantial and rapid research progress with Nicotiana in recent years, its genomics, genetics, and nicotine gene studies are summarized, with useful web links. Several important genetic maps, including a high-density map of N. tabacum consisting of ~2,000 markers published in 2012, provide tools for genetics research. Four whole genome sequences are from allotetraploid species, including N. benthamiana in 2012, and three N. tabacum cultivars (TN90, K326, and BX) in 2014. Three whole genome sequences are from diploids, including progenitors N. sylvestris and N. tomentosiformis in 2013 and N. otophora in 2014. These and additional studies provide numerous insights into genome evolution after polyploidization, including changes in gene composition and transcriptome expression in N. tabacum. The major genes involved in the nicotine biosynthetic pathway have been identified and the genetic basis of the differences in nicotine levels among Nicotiana species has been revealed. In addition, other progress on chloroplast, mitochondrial, and NCBI-registered projects on Nicotiana are discussed. The challenges and prospects for genomic, genetic and application research are addressed. Hence, this review provides important resources and guidance for current and future research and application in Nicotiana.

  6. BAC-end sequence-based SNP mining in Allotetraploid Cotton (Gossypium) utilizing re-sequencing data, phylogenetic inferences and perspectives for genetic mapping

    Science.gov (United States)

    A bacterial artificial chromosome (BAC) library and BAC-end sequences for Gossypium hirsutum L. have recently been developed. Here we report on genomic-based genome-wide SNP mining utilizing re-sequencing data with a BAC-end sequence reference for twelve G. hirsutum L. lines, one G. barbadense L. li...

  7. 异源四倍体棉花栽培品种分子连锁遗传图谱的构建%Construction of Molecular Linkage Map of Cultivated Allotetraploid Cotton (Gossypium hirsutum L.×G. Barbadense L. )with SSR and RAPD Markers

    Institute of Scientific and Technical Information of China (English)

    Jun ZHANG; Wang-zhen GUO; Tian-zhen ZHANG

    2002-01-01

      A permanent doubled haploid population from the crossing of G. hirsutum × G. barbadense were developed by means of Vsg, virescently marked semigamy line in sea island cotton,which was characterized by a cytological mechanism for developing haploids with certain convenience, and thus constructed an allotetraploid cotton molecular genetic linkage map with the high level polymorphic SSR and RAPD markers.……

  8. Soluble CD163

    DEFF Research Database (Denmark)

    Parkner, Tina; Sørensen, L P; Nielsen, A R;

    2012-01-01

    Soluble CD163 (sCD163) was recently identified as a strong risk marker for developing type 2 diabetes. We hypothesised that sCD163 independently associates with insulin resistance.......Soluble CD163 (sCD163) was recently identified as a strong risk marker for developing type 2 diabetes. We hypothesised that sCD163 independently associates with insulin resistance....

  9. Cancer Genome Anatomy Project | Office of Cancer Genomics

    Science.gov (United States)

    The National Cancer Institute (NCI) Cancer Genome Anatomy Project (CGAP) is an online resource designed to provide the research community access to biological tissue characterization data. Request a free copy of the CGAP Website Virtual Tour CD from ocg@mail.nih.gov.

  10. Cancer Genome Anatomy Project (CGAP) | Office of Cancer Genomics

    Science.gov (United States)

    CGAP generated a wide range of genomics data on cancerous cells that are accessible through easy-to-use online tools. Researchers, educators, and students can find "in silico" answers to biological questions through the CGAP website. Request a free copy of the CGAP Website Virtual Tour CD from ocg@mail.nih.gov to learn how to navigate the website.

  11. Study on the Morphological Characteristics of the Allotetraploid of Red Crucian Carp(♀) × Common Carp(♂)%异源四倍体鲫鲤的形态特征研究

    Institute of Scientific and Technical Information of China (English)

    李建中; 张轩杰; 刘少军; 周工健; 刘筠

    2001-01-01

    The morphological characteristics of the allotetraploid fi sh were studied by ordinary regulations and were compared with those of Red crucia n Carp (Carassius auratus red var.) and Common Carp (Cyprinus carpio L.). The results were as follows: D.3,16~19; A.3,5~7; scalles in lateral line 30 ~34,scalles above lateral line 5~7,scalles below lateral line 5~8; gill raker 32 ~35; pharyngeal tooth 2, 1.4~4.1; vertebrae, 31~33; body length/body height = 2.33~3.33, body length/head length =2.73~4.60; head length / Lip length =2.67 ~4.01, head length /eye diameter =3.33~5.13; caudal peduncel length/caudal ped uncel height =0.83~1.32. The results indicated that the morphological character istics of the allotetraploid fish were steady.%按常规标准测定了异源四倍体鲫鲤的形态特征,并与二倍体的红鲫和湘江野鲤进行了比较.主要结果如下:异源四倍体鲫鲤的背鳍条Ⅲ,16~19;臀鳍条Ⅲ,5~7;侧线鳞30~34,侧线上鳞为5~7,侧线下鳞为5~8;鳃耙数32~35;下咽齿2行,1.4~4.1;脊椎骨31~33;口须2对;体长为体高的2.23~3.33倍,为头长的2.73~4.60倍;头长为吻长的2.67~4.01倍,为眼径的3.33~5.13倍;尾柄长为尾柄高的0.83~1.32倍.研究表明,异源四倍体鲫鲤形态性状稳定,已形成了一个新的四倍体鱼种群.

  12. Producing CD-ROMs.

    Science.gov (United States)

    Hyams, Peter, Ed.

    1992-01-01

    This issue presents 11 articles that address issues relating to the production of CD-ROMs. Highlights include current uses of CD-ROM; standards; steps involved in producing CD-ROMs, including data capture, conversion, and tagging, product design, and indexing; authoring; selecting indexing and retrieval software; costs; multimedia CD-ROMs; and…

  13. Functional receptor molecules CD300lf and CD300ld within the CD300 family enable murine noroviruses to infect cells

    Science.gov (United States)

    Haga, Kei; Fujimoto, Akira; Takai-Todaka, Reiko; Miki, Motohiro; Doan, Yen Hai; Murakami, Kosuke; Yokoyama, Masaru; Murata, Kazuyoshi; Nakanishi, Akira; Katayama, Kazuhiko

    2016-01-01

    Norovirus is the leading cause of acute gastroenteritis worldwide. Since the discovery of human norovirus (HuNoV), an efficient and reproducible norovirus replication system has not been established in cultured cells. Although limited amounts of virus particles can be produced when the HuNoV genome is directly transfected into cells, the HuNoV cycle of infection has not been successfully reproduced in any currently available cell-culture system. Those results imply that the identification of a functional cell-surface receptor for norovirus might be the key to establishing a norovirus culture system. Using a genome-wide CRISPR/Cas9 guide RNA library, we identified murine CD300lf and CD300ld as functional receptors for murine norovirus (MNV). The treatment of susceptible cells with polyclonal antibody against CD300lf significantly reduced the production of viral progeny. Additionally, ectopic CD300lf expression in nonsusceptible cell lines derived from other animal species enabled MNV infection and progeny production, suggesting that CD300lf has potential for dictating MNV host tropism. Furthermore, CD300ld, which has an amino acid sequence in the N-terminal region of its extracellular domain that is highly homologous to that of CD300lf, also functions as a receptor for MNV. Our results indicate that direct interaction of MNV with two cell-surface molecules, CD300lf and CD300ld, dictates permissive noroviral infection. PMID:27681626

  14. 四倍体鲫鲤、三倍体湘云鲫染色体减数分裂观察%Chromosome pairing in meiosis Ⅰ in allotetraploid hybrids and allotriploid crucian carp

    Institute of Scientific and Technical Information of China (English)

    张纯; 何晓晓; 刘少军; 孙远东; 刘筠

    2005-01-01

    In the present paper, the chromosome pairing during meiosis Ⅰ(MⅠ)of spermatocytes in allotetraploid hybrids of the red crucian carp (Carassius auratus, red var.)(♀)×common carp Cyprinus carpio (♂), allotriploid crucian carp, diploid red crucian carp and common carp was investigated. As the control groups, their chromosome number in metaphase of mitosis was also examined. During MⅠ, the homologous chromosomes of allotetraploid hybrids were paired, showing 100 bivalents, no univalent, trivalent and quadrivalent being found. The chromosome spreads of the allotriploid in MⅠconsisted of 50 bivalents and 50 unsynapsed univalent. Both in diploid red crucian carp and diploid common carp, only 50 bivalents were observed respectively. In the control groups, the metaphase spreads of chromosomes in mitosis in allotetraploid hybrids, allotriploids, diploid red crucian carp and common carp were 4n=200, 3n=150, and 2n=100, respectively. In all the different species, the bivalent number in MⅠ agreed with the chromosome number in mitosis. The 200 chromosomes the allotetraploids possessed only formed 100 bivalents during MⅠ, indicating that they were able to produce stably diploid gametes, maintaining the tetraploidy from one generation to the next one. The coexistence of bivalents and univalent in MⅠin triploid crucian carp resulted in the failure to form the normal mature gametes, providing the evidence on the chromosome level for the sterility of the triploids[Acta Zoologica Sinica 51(1):89-94,2005].%用精巢细胞直接制片法观察了异源四倍体鲫鲤、三倍体湘云鲫和二倍体红鲫、湘江野鲤精母细胞染色体第一次减数分裂中期配对情况;作为对照,观察了上述四种鱼肾细胞的有丝分裂中期染色体.在精母细胞第一次减数分裂中,异源四倍体鲫鲤同源染色体两两配对,形成100个二价体,没有观察到单价体、三价体和四价体;三倍体湘云鲫精母细胞形成50个二价体和50

  15. Precision engineering for PRRSV resistance in pigs: Macrophages from genome edited pigs lacking CD163 SRCR5 domain are fully resistant to both PRRSV genotypes while maintaining biological function

    Science.gov (United States)

    Jackson, Ben; Mileham, Alan J.; Ait-Ali, Tahar; Whitelaw, C. Bruce A.

    2017-01-01

    Porcine Reproductive and Respiratory Syndrome (PRRS) is a panzootic infectious disease of pigs, causing major economic losses to the world-wide pig industry. PRRS manifests differently in pigs of all ages but primarily causes late-term abortions and stillbirths in sows and respiratory disease in piglets. The causative agent of the disease is the positive-strand RNA PRRS virus (PRRSV). PRRSV has a narrow host cell tropism, limited to cells of the monocyte/macrophage lineage. CD163 has been described as a fusion receptor for PRRSV, whereby the scavenger receptor cysteine-rich domain 5 (SRCR5) region was shown to be an interaction site for the virus in vitro. CD163 is expressed at high levels on the surface of macrophages, particularly in the respiratory system. Here we describe the application of CRISPR/Cas9 to pig zygotes, resulting in the generation of pigs with a deletion of Exon 7 of the CD163 gene, encoding SRCR5. Deletion of SRCR5 showed no adverse effects in pigs maintained under standard husbandry conditions with normal growth rates and complete blood counts observed. Pulmonary alveolar macrophages (PAMs) and peripheral blood monocytes (PBMCs) were isolated from the animals and assessed in vitro. Both PAMs and macrophages obtained from PBMCs by CSF1 stimulation (PMMs) show the characteristic differentiation and cell surface marker expression of macrophages of the respective origin. Expression and correct folding of the SRCR5 deletion CD163 on the surface of macrophages and biological activity of the protein as hemoglobin-haptoglobin scavenger was confirmed. Challenge of both PAMs and PMMs with PRRSV genotype 1, subtypes 1, 2, and 3 and PMMs with PRRSV genotype 2 showed complete resistance to viral infections assessed by replication. Confocal microscopy revealed the absence of replication structures in the SRCR5 CD163 deletion macrophages, indicating an inhibition of infection prior to gene expression, i.e. at entry/fusion or unpacking stages. PMID:28231264

  16. Cancer genomics

    DEFF Research Database (Denmark)

    Norrild, Bodil; Guldberg, Per; Ralfkiær, Elisabeth Methner

    2007-01-01

    Almost all cells in the human body contain a complete copy of the genome with an estimated number of 25,000 genes. The sequences of these genes make up about three percent of the genome and comprise the inherited set of genetic information. The genome also contains information that determines whe...

  17. CD4+/CD8+ double-positive T cells

    DEFF Research Database (Denmark)

    Overgaard, Nana H; Jung, Ji-Won; Steptoe, Raymond J

    2015-01-01

    CD4(+)/CD8(+) DP thymocytes are a well-described T cell developmental stage within the thymus. However, once differentiated, the CD4(+) lineage or the CD8(+) lineage is generally considered to be fixed. Nevertheless, mature CD4(+)/CD8(+) DP T cells have been described in the blood and peripheral...... lymphoid tissues of numerous species, as well as in numerous disease settings, including cancer. The expression of CD4 and CD8 is regulated by a very strict transcriptional program involving the transcription factors Runx3 and ThPOK. Initially thought to be mutually exclusive within CD4(+) and CD8(+) T...... cells, CD4(+)/CD8(+) T cell populations, outside of the thymus, have recently been described to express concurrently ThPOK and Runx3. Considerable heterogeneity exists within the CD4(+)/CD8(+) DP T cell pool, and the function of CD4(+)/CD8(+) T cell populations remains controversial, with conflicting...

  18. Sequencing and expression analysis of CD3γ/δ and CD3εchains in mandarin fish, Siniperca chuatsi

    Institute of Scientific and Technical Information of China (English)

    GUO Zheng; NIE Pin

    2013-01-01

    The genomic and cDNA sequences of the CD3γ/δ and CD3ε homologues in the mandarin fish,Siniperca chuatsi,were determined.As in other vertebrate CD3 molecules,the deduced amino acid sequences of mandarin fish CD3γ/δ and CD3ε contained conserved residues and motifs,such as cysteine residues and CXXC and immunoreceptor tyrosine-based activation motifs.However,mandarin fish CD3γ/δ and CD3ε showed some differences to their mammalian counterparts,specifically the absence of a negatively charged residue in the transmembrane region of CD3γ/δ.Additionally,while an N-glycosylation site was present in CD3ε,the site was not observed in CD3γ/δ.The CD3γ/δ and CD3ε subunit sequences contain six and five exons,respectively,consistent with homologues from Atlantic salmon,Salmo salar.Phylogenetic analysis also revealed that CD3γ/δ and CD3ε in mandarin fish are closely related to their counterparts in Acanthopterygian fish.Real-time PCR showed CD3γ/δ and CD3ε were expressed mainly in the thymus and spleen in normal healthy fish and,to a lesser extent,in mucosal-associated lymphoid tissues,such as the intestine and gills.When lymphocytes isolated from head kidney were treated with the mitogens phytohemagglutinin,concanavalin,and polyriboinosinic polyribocytidylic acid,mRNA expression levels of CD3γ/δ and CD3ε were significantly elevated within 12 h of treatment.This indicated the presence of T lymphocytes in the head kidney of teleost fish,and also the recognition of mitogens by the lymphocytes.Mandarin fish infected with the bacterial pathogen Flavobacterium columnare also showed an increase in the expression of CD3γ/δ and CD3ε mRNA,indicating that CD3γ/δ and CD3ε lymphocytes are involved in the immune response of this species.

  19. Sequencing and expression analysis of CD3γ/δ and CD3ɛ chains in mandarin fish, Siniperca chuatsi

    Science.gov (United States)

    Guo, Zheng; Nie, Pin

    2013-01-01

    The genomic and cDNA sequences of the CD3γ/δ and CD3ɛ homologues in the mandarin fish, Siniperca chuats i, were determined. As in other vertebrate CD3 molecules, the deduced amino acid sequences of mandarin fish CD3γ/δ and CD3ɛ contained conserved residues and motifs, such as cysteine residues and CXXC and immunoreceptor tyrosine-based activation motifs. However, mandarin fish CD3γ/δ and CD3ɛ showed some differences to their mammalian counterparts, specifically the absence of a negatively charged residue in the transmembrane region of CD3γ/δ. Additionally, while an N -glycosylation site was present in CD3ɛ, the site was not observed in CD3γ/δ. The CD3γ/δ and CD3ɛ subunit sequences contain six and five exons, respectively, consistent with homologues from Atlantic salmon, Salmo salar. Phylogenetic analysis also revealed that CD3γ/δ and CD3ɛ in mandarin fish are closely related to their counterparts in Acanthopterygian fish. Real-time PCR showed CD3γ/δ and CD3ɛ were expressed mainly in the thymus and spleen in normal healthy fish and, to a lesser extent, in mucosal-associated lymphoid tissues, such as the intestine and gills. When lymphocytes isolated from head kidney were treated with the mitogens phytohemagglutinin, concanavalin, and polyriboinosinic polyribocytidylic acid, mRNA expression levels of CD3γ/δ and CD3ɛ were significantly elevated within 12 h of treatment. This indicated the presence of T lymphocytes in the head kidney of teleost fish, and also the recognition of mitogens by the lymphocytes. Mandarin fish infected with the bacterial pathogen Flavobacterium columnare also showed an increase in the expression of CD3γ/δ and CD3ɛ mRNA, indicating that CD3γ/δ and CD3ɛ lymphocytes are involved in the immune response of this species.

  20. Soluble CD163

    DEFF Research Database (Denmark)

    Møller, Holger J

    2012-01-01

    of sCD163 is unknown, but during inflammation and macrophage activation, sCD163 levels increase acutely due to metalloproteinase-mediated cleavage near the cell membrane. It is now evident that sCD163 is very useful as a biomarker of macrophage activation in various inflammatory diseases......, such as macrophage activation syndrome, sepsis, and liver disease. Moreover, sCD163 is a general risk marker of comorbidity and mortality in several chronic inflammatory disease states. Recently, sCD163 has been shown to be strongly associated with later development of type 2 diabetes in both lean and obese subjects...

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

    Science.gov (United States)

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

    2011-09-01

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

  2. Genome-Wide Analysis of the Sus Gene Family in Cotton

    Institute of Scientific and Technical Information of China (English)

    Changsong Zou; Cairui Lu; Haihong Shang; Xinrui Jing; Hailiang Cheng; Youping Zhang; Guoli Song

    2013-01-01

    Sucrose synthase (Sus) is a key enzyme in plant sucrose metabolism.In cotton,Sus (EC 2.4.1.13) is the main enzyme that degrades sucrose imported into cotton fibers from the phloem of the seed coat.This study demonstrated that the genomes of Gossypium arboreum L.,G.raimondii Ulbr.,and G.hirsutum L.,contained 8,8,and 15 Sus genes,respectively.Their structural organizations,phylogenetic relationships,and expression profiles were characterized.Comparisons of genomic and coding sequences identified multiple introns,the number and positions of which were highly conserved between diploid and allotetraploid cotton species.Most of the phylogenetic clades contained sequences from all three species,suggesting that the Sus genes of tetraploid G.hirsutum derived from those of its diploid ancestors.One Sus group (Sus I) underwent expansion during cotton evolution.Expression analyses indicated that most Sus genes were differentially expressed in various tissues and had development-dependent expression profiles in cotton fiber cells.Members of the same orthologous group had very similar expression patterns in all three species.These results provide new insights into the evolution of the cotton Sus gene family,and insight into its members' physiological functions during fiber growth and development.

  3. Population Genomic Analysis Reveals Differential Evolutionary Histories and Patterns of Diversity across Subgenomes and Subpopulations of Brassica napus L.

    Science.gov (United States)

    Gazave, Elodie; Tassone, Erica E; Ilut, Daniel C; Wingerson, Megan; Datema, Erwin; Witsenboer, Hanneke M A; Davis, James B; Grant, David; Dyer, John M; Jenks, Matthew A; Brown, Jack; Gore, Michael A

    2016-01-01

    The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed) and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia, and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP), winter Europe (WE), and winter Asia (WA). Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.

  4. Chromosome studies of European cyprinid fishes: cross-species painting reveals natural allotetraploid origin of a Carassius female with 206 chromosomes.

    Science.gov (United States)

    Knytl, M; Kalous, L; Symonová, R; Rylková, K; Ráb, P

    2013-01-01

    A single female with 206 chromosomes and another 26 females with 156 chromosomes identified as Prussian carp, Carassius gibelio, and 5 individuals with 100 chromosomes identified as crucian carp, C. carassius, were sampled during field survey in one locality in the upper Elbe River. To identify the origin of females with high chromosome numbers, comparative karyotype analysis, GISH, with whole C. carassius DNA as probe and phylogenetic positions of sampled individuals revealed by cytochrome b mitochondrial marker were performed. GISH showed consistently bright labeling of 50 chromosomal elements out of 206, corresponding to the haploid chromosome number of C. carassius. The position of these females with high chromosome numbers in a reconstructed phylogenetic tree was within the clade of C. gibelio, documenting its affiliation to C. gibelio mitochondrial, i.e. maternal lineage. Our findings indicated that the mother of the female with high chromosome numbers was a gynogenetically reproducing 156-chromosome C. gibelio female and the father a bisexually reproducing C. carassius male. We, therefore, hypothesized that the C. gibelio × C. carassius allopolyploid female with 206 chromosomes arose by a mechanism of sperm genome addition to an unreduced egg of the mother.

  5. 利用叶绿体基因探讨稻属BBCC基因组物种的系统起源%Phylogenetic Origin of BBCC Genome Allotetraploids in Oryza Revealed by Chloroplast Gene Sequences

    Institute of Scientific and Technical Information of China (English)

    杜家潇; 秦宗燕; 徐思; 景翔; 包颖

    2016-01-01

    基于9个叶绿体基因片段(atpA、atpB、matK、petA、psaA、psbA、psbB、psbC和rbcL),深入探讨了稻属(Oryza)3个BBCC基因组异源四倍体和5个与之相关的BB或CC基因组二倍体物种间的谱系关系.进一步的系统发育分析表明:3个具有相同BBCC基因组的四倍体物种并非同一次物种形成事件的产物,而是在不同的分布区经历了至少3次分别的物种起源.其中,四倍体Oryza punctata的母本可能来自同样分布在非洲并具有CC基因组的二倍体物种O.eichingeri;而四倍体O.malampuzhaensis和O.minuta的母本则可能来自亚洲已经灭绝的具有BB基因组的不同二倍体.研究结果不但为追溯稻属异源四倍体的复杂网状进化提供了重要的分子证据,而且拓展了我们对有花植物复杂物种形成的深入理解.

  6. Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers.

    Science.gov (United States)

    Molnár, István; Šimková, Hana; Leverington-Waite, Michelle; Goram, Richard; Cseh, András; Vrána, Jan; Farkas, András; Doležel, Jaroslav; Molnár-Láng, Márta; Griffiths, Simon

    2013-01-01

    Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS) markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.

  7. Syntenic relationships between the U and M genomes of Aegilops, wheat and the model species Brachypodium and rice as revealed by COS markers.

    Directory of Open Access Journals (Sweden)

    István Molnár

    Full Text Available Diploid Aegilops umbellulata and Ae. comosa and their natural allotetraploid hybrids Ae. biuncialis and Ae. geniculata are important wild gene sources for wheat. With the aim of assisting in alien gene transfer, this study provides gene-based conserved orthologous set (COS markers for the U and M genome chromosomes. Out of the 140 markers tested on a series of wheat-Aegilops chromosome introgression lines and flow-sorted subgenomic chromosome fractions, 100 were assigned to Aegilops chromosomes and six and seven duplications were identified in the U and M genomes, respectively. The marker-specific EST sequences were BLAST-ed to Brachypodium and rice genomic sequences to investigate macrosyntenic relationships between the U and M genomes of Aegilops, wheat and the model species. Five syntenic regions of Brachypodium identified genome rearrangements differentiating the U genome from the M genome and from the D genome of wheat. All of them seem to have evolved at the diploid level and to have been modified differentially in the polyploid species Ae. biuncialis and Ae. geniculata. A certain level of wheat-Aegilops homology was detected for group 1, 2, 3 and 5 chromosomes, while a clearly rearranged structure was showed for the group 4, 6 and 7 Aegilops chromosomes relative to wheat. The conserved orthologous set markers assigned to Aegilops chromosomes promise to accelerate gene introgression by facilitating the identification of alien chromatin. The syntenic relationships between the Aegilops species, wheat and model species will facilitate the targeted development of new markers specific for U and M genomic regions and will contribute to the understanding of molecular processes related to allopolyploidization.

  8. Comparative Studies of Vertebrate Platelet Glycoprotein 4 (CD36

    Directory of Open Access Journals (Sweden)

    Roger S. Holmes

    2012-09-01

    Full Text Available Platelet glycoprotein 4 (CD36 (or fatty acyl translocase [FAT], or scavenger receptor class B, member 3 [SCARB3] is an essential cell surface and skeletal muscle outer mitochondrial membrane glycoprotein involved in multiple functions in the body. CD36 serves as a ligand receptor of thrombospondin, long chain fatty acids, oxidized low density lipoproteins (LDLs and malaria-infected erythrocytes. CD36 also influences various diseases, including angiogenesis, thrombosis, atherosclerosis, malaria, diabetes, steatosis, dementia and obesity. Genetic deficiency of this protein results in significant changes in fatty acid and oxidized lipid uptake. Comparative CD36 amino acid sequences and structures and CD36 gene locations were examined using data from several vertebrate genome projects. Vertebrate CD36 sequences shared 53–100% identity as compared with 29–32% sequence identities with other CD36-like superfamily members, SCARB1 and SCARB2. At least eight vertebrate CD36 N-glycosylation sites were conserved which are required for membrane integration. Sequence alignments, key amino acid residues and predicted secondary structures were also studied. Three CD36 domains were identified including cytoplasmic, transmembrane and exoplasmic sequences. Conserved sequences included N- and C-terminal transmembrane glycines; and exoplasmic cysteine disulphide residues; TSP-1 and PE binding sites, Thr92 and His242, respectively; 17 conserved proline and 14 glycine residues, which may participate in forming CD36 ‘short loops’; and basic amino acid residues, and may contribute to fatty acid and thrombospondin binding. Vertebrate CD36 genes usually contained 12 coding exons. The human CD36 gene contained transcription factor binding sites (including PPARG and PPARA contributing to a high gene expression level (6.6 times average. Phylogenetic analyses examined the relationships and potential evolutionary origins of the vertebrate CD36 gene with vertebrate

  9. Comparative genome analysis between Agrostis stolonifera and members of the Pooideae subfamily, including Brachypodium distachyon.

    Directory of Open Access Journals (Sweden)

    Loreto Araneda

    Full Text Available Creeping bentgrass (Agrostis stolonifera, allotetraploid 2n = 4x = 28 is one of the major cool-season turfgrasses. It is widely used on golf courses due to its tolerance to low mowing and aggressive growth habit. In this study, we investigated genome relationships of creeping bentgrass relative to the Triticeae (a consensus map of Triticum aestivum, T. tauschii, Hordeum vulgare, and H. spontaneum, oat, rice, and ryegrass maps using a common set of 229 EST-RFLP markers. The genome comparisons based on the RFLP markers revealed large-scale chromosomal rearrangements on different numbers of linkage groups (LGs of creeping bentgrass relative to the Triticeae (3 LGs, oat (4 LGs, and rice (8 LGs. However, we detected no chromosomal rearrangement between creeping bentgrass and ryegrass, suggesting that these recently domesticated species might be closely related, despite their memberships to different Pooideae tribes. In addition, the genome of creeping bentgrass was compared with the complete genome sequence of Brachypodium distachyon in Pooideae subfamily using both sequences of the above-mentioned mapped EST-RFLP markers and sequences of 8,470 publicly available A. stolonifera ESTs (AgEST. We discovered large-scale chromosomal rearrangements on six LGs of creeping bentgrass relative to B. distachyon. Also, a total of 24 syntenic blocks based on 678 orthologus loci were identified between these two grass species. The EST orthologs can be utilized in further comparative mapping of Pooideae species. These results will be useful for genetic improvement of Agrostis species and will provide a better understanding of evolution within Pooideae species.

  10. Samfundslex-cd

    DEFF Research Database (Denmark)

    Qvist, Palle; Nørbæk Hansen, Peter

    2009-01-01

    CD med mere end 2500 samfundsfaglige opslagsord med fritekstsøgning og mulighed for at kopiere tekstafsnit og figurer over i egne dokumenter ved opgaveskrivning......CD med mere end 2500 samfundsfaglige opslagsord med fritekstsøgning og mulighed for at kopiere tekstafsnit og figurer over i egne dokumenter ved opgaveskrivning...

  11. Thymic Nurse Cells Support CD4-CD8+ Thymocytes to Differentiate into CD4+CD8+ Cells

    Institute of Scientific and Technical Information of China (English)

    Aidong Li; Xueli Liu; Baochun Duan; Jie Ma

    2005-01-01

    Thymic nurse cells (TNCs) represent a unique microenvironment in the thymus for T cell maturation. In order to investigate the role of thymic nurse cells during T cell differentiation, a TNC clone, RWTE-1, which formed a typical complex with fetal thymocytes in vitro was established from normal Wistar rat. Hanging drop culture method was applied to reveal the interaction between TNCs and thymocytes. Our result revealed that eighty percent of immature CD4-CD8+ cells differentiated into CD4+CD8+ cells after a 12-hour hanging drop culture with RWTE-1. However, in a 12-hour culture of immature CD4-CD8+ cells with or without RWTE-1 supernatant, only 30% of the cells differentiated into CD4+CD8+ cells spontaneously. This observation led to the conclusion that RWTE-1 cell has the capacity to facilitate immature CD4-CD8+ thymocytes to differentiate into CD4+CD8+ T cells by direct interaction.

  12. Influence of membrane CD25 stability on T lymphocyte activity: implications for immunoregulation.

    Directory of Open Access Journals (Sweden)

    Todd M Brusko

    Full Text Available BACKGROUND: CD25, a component of the IL-2 receptor, is important in T cell proliferation, activation induced cell death, as well as the actions of both regulatory (Treg and effector (Teff T cells. Recent genome wide association studies have implicated the CD25 locus as an important region for genetic susceptibility to a number of autoimmune disorders, with serum levels of soluble CD25 receptor (sCD25 serving as a potential phenotypic marker for this association. However, the functional impact of CD25 cleavage, as well as the influence of sCD25 on immunoregulatory activities, remain largely unknown and form the basis of this effort. METHODOLOGY/PRINCIPAL FINDINGS: The generation of sCD25 by Treg (CD4(+CD25(+ and Teff (CD4(+CD25(- cells was examined during in vitro suppression assays, efforts that demonstrated constitutive and stable surface CD25 expression on Treg throughout the period of in vitro assessment. In contrast, Teff cells increased CD25 expression during the process of in vitro suppression, with supernatant sCD25 levels correlating to the amount of cellular proliferation. Interestingly, under serum-free conditions, Tregs partially lost their characteristic anergic and suppressive properties. sCD25 supplementation at physiological concentrations to serum free in vitro suppression assays reduced Teff proliferation without specifically influencing suppression. Indeed, sCD25 production within these cultures correlated with cell death. CONCLUSIONS/SIGNIFICANCE: These results support the notion that sCD25 functions as both a surrogate marker of T cell activation as well as an indicator of subsequent cellular death. In addition, the role of CD25 in immunomodulation is likely dependent on the local inflammatory milieu, with molecules capable of modulating surface CD25 expression playing a key role in defining immune responsiveness.

  13. The gene expression profile of CD11c+ CD8α- dendritic cells in the pre-diabetic pancreas of the NOD mouse.

    Directory of Open Access Journals (Sweden)

    Wouter Beumer

    Full Text Available Two major dendritic cell (DC subsets have been described in the pancreas of mice: The CD11c+ CD8α- DCs (strong CD4+ T cell proliferation inducers and the CD8α+ CD103+ DCs (T cell apoptosis inducers. Here we analyzed the larger subset of CD11c+ CD8α- DCs isolated from the pancreas of pre-diabetic NOD mice for genome-wide gene expression (validated by Q-PCR to elucidate abnormalities in underlying gene expression networks. CD11c+ CD8α- DCs were isolated from 5 week old NOD and control C57BL/6 pancreas. The steady state pancreatic NOD CD11c+ CD8α- DCs showed a reduced expression of several gene networks important for the prime functions of these cells, i.e. for cell renewal, immune tolerance induction, migration and for the provision of growth factors including those for beta cell regeneration. A functional in vivo BrdU incorporation test showed the reduced proliferation of steady state pancreatic DC. The reduced expression of tolerance induction genes (CD200R, CCR5 and CD24 was supported on the protein level by flow cytometry. Also previously published functional tests on maturation, immune stimulation and migration confirm the molecular deficits of NOD steady state DC. Despite these deficiencies NOD pancreas CD11c+ CD8α- DCs showed a hyperreactivity to LPS, which resulted in an enhanced pro-inflammatory state characterized by a gene profile of an enhanced expression of a number of classical inflammatory cytokines. The enhanced up-regulation of inflammatory genes was supported by the in vitro cytokine production profile of the DCs. In conclusion, our data show that NOD pancreatic CD11c+ CD8α- DCs show various deficiencies in steady state, while hyperreactive when encountering a danger signal such as LPS.

  14. ALE-CdS/CdTe-PV-cells

    Energy Technology Data Exchange (ETDEWEB)

    Skarp, J.; Anttila, E.; Rautiainen, A.; Suntola, T. (Microchemistry Ltd., Espoo (Finland))

    1992-01-01

    Atomic Layer Epitaxy, ALE, has been applied to grow CdS/CdTe-thin film solar cells. ALE offers the possibility of growing both CdS and CdTe in a single process and tailoring the interface of CdS and CdTe. The thickness of CdS was varied and the optimum was found to be in the range of 50-100 nm with good heterojunction performance and CdTe-crystallinity leading to excellent photovoltaic properties. The structures with thinner CdS layers suffered low open circuit voltage but on the other hand with thicker CdS the short circuit current was limited by the absorption of CdS. (author)

  15. Translational Genomics for the Improvement of Switchgrass

    Energy Technology Data Exchange (ETDEWEB)

    Carpita, Nicholas; McCann, Maureen

    2014-05-07

    Our objectives were to apply bioinformatics and high throughput sequencing technologies to identify and classify the genes involved in cell wall formation in maize and switchgrass. Targets for genetic modification were to be identified and cell wall materials isolated and assayed for enhanced performance in bioprocessing. We annotated and assembled over 750 maize genes into gene families predicted to function in cell wall biogenesis. Comparative genomics of maize, rice, and Arabidopsis sequences revealed differences in gene family structure. In addition, differences in expression between gene family members of Arabidopsis, maize and rice underscored the need for a grass-specific genetic model for functional analyses. A forward screen of mature leaves of field-grown maize lines by near-infrared spectroscopy yielded several dozen lines with heritable spectroscopic phenotypes, several of which near-infrared (nir) mutants had altered carbohydrate-lignin compositions. Our contributions to the maize genome sequencing effort built on knowledge of copy number variation showing that uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. For example, although about 25% of all duplicated genes remain genome-wide, all of the cellulose synthase (CesA) homologs were retained. We showed that guaiacyl and syringyl lignin in lignocellulosic cell-wall materials from stems demonstrate a two-fold natural variation in content across a population of maize Intermated B73 x Mo7 (IBM) recombinant inbred lines, a maize Association Panel of 282 inbreds and landraces, and three populations of the maize Nested Association Mapping (NAM) recombinant inbred lines grown in three years. We then defined quantitative trait loci (QTL) for stem lignin content measured using pyrolysis molecular-beam mass spectrometry, and glucose and xylose yield measured using an enzymatic hydrolysis assay. Among five multi-year QTL for lignin

  16. Haptoglobin and CD163

    DEFF Research Database (Denmark)

    Madsen, M; Graversen, Jonas Heilskov; Moestrup, S K

    2001-01-01

    The plasma protein haptoglobin and the endocytic hemoglobin receptor HbSR/CD163 are key molecules in the process of removing hemoglobin released from ruptured erythrocytes. Hemoglobin in plasma is instantly bound with high affinity to haptoglobin--an interaction leading to the recognition...... of the complex by HbSR/CD163 and endocytosis in macrophages. The haptoglobin-dependent HbSR/CD163 scavenging system for hemoglobin clearance prevents toxic effects of hemoglobin in plasma and kidney and explains the decrease in the haptoglobin plasma concentration in patients with accelerated hemolysis. The Hb...

  17. Listeria Genomics

    Science.gov (United States)

    Cabanes, Didier; Sousa, Sandra; Cossart, Pascale

    The opportunistic intracellular foodborne pathogen Listeria monocytogenes has become a paradigm for the study of host-pathogen interactions and bacterial adaptation to mammalian hosts. Analysis of L. monocytogenes infection has provided considerable insight into how bacteria invade cells, move intracellularly, and disseminate in tissues, as well as tools to address fundamental processes in cell biology. Moreover, the vast amount of knowledge that has been gathered through in-depth comparative genomic analyses and in vivo studies makes L. monocytogenes one of the most well-studied bacterial pathogens. This chapter provides an overview of progress in the exploration of genomic, transcriptomic, and proteomic data in Listeria spp. to understand genome evolution and diversity, as well as physiological aspects of metabolism used by bacteria when growing in diverse environments, in particular in infected hosts.

  18. Marine genomics

    DEFF Research Database (Denmark)

    Oliveira Ribeiro, Ângela Maria; Foote, Andrew D.; Kupczok, Anne

    2017-01-01

    Marine ecosystems occupy 71% of the surface of our planet, yet we know little about their diversity. Although the inventory of species is continually increasing, as registered by the Census of Marine Life program, only about 10% of the estimated two million marine species are known. This lag......-throughput sequencing approaches have been helping to improve our knowledge of marine biodiversity, from the rich microbial biota that forms the base of the tree of life to a wealth of plant and animal species. In this review, we present an overview of the applications of genomics to the study of marine life, from...... evolutionary biology of non-model organisms to species of commercial relevance for fishing, aquaculture and biomedicine. Instead of providing an exhaustive list of available genomic data, we rather set to present contextualized examples that best represent the current status of the field of marine genomics....

  19. Naiskoori uus CD

    Index Scriptorium Estoniae

    2007-01-01

    Tallinna Tehnikaülikooli Akadeemilise Naiskoori uue CD "...nagu puhas mõte" esitluskontserdist 21. veebr. Tallinna Matkamajas. TTÜ Akadeemilise Naiskoori 55. aastapäeva kontserdist 23. mail TTÜ aulas

  20. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen

    2015-01-01

    by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans......, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  1. Genome Sequencing

    DEFF Research Database (Denmark)

    Sato, Shusei; Andersen, Stig Uggerhøj

    2014-01-01

    The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based on transcr......The current Lotus japonicus reference genome sequence is based on a hybrid assembly of Sanger TAC/BAC, Sanger shotgun and Illumina shotgun sequencing data generated from the Miyakojima-MG20 accession. It covers nearly all expressed L. japonicus genes and has been annotated mainly based...

  2. Genome-Wide Transcriptome Analysis of Cadmium Stress in Rice

    Directory of Open Access Journals (Sweden)

    Youko Oono

    2016-01-01

    Full Text Available Rice growth is severely affected by toxic concentrations of the nonessential heavy metal cadmium (Cd. To elucidate the molecular basis of the response to Cd stress, we performed mRNA sequencing of rice following our previous study on exposure to high concentrations of Cd (Oono et al., 2014. In this study, rice plants were hydroponically treated with low concentrations of Cd and approximately 211 million sequence reads were mapped onto the IRGSP-1.0 reference rice genome sequence. Many genes, including some identified under high Cd concentration exposure in our previous study, were found to be responsive to low Cd exposure, with an average of about 11,000 transcripts from each condition. However, genes expressed constitutively across the developmental course responded only slightly to low Cd concentrations, in contrast to their clear response to high Cd concentration, which causes fatal damage to rice seedlings according to phenotypic changes. The expression of metal ion transporter genes tended to correlate with Cd concentration, suggesting the potential of the RNA-Seq strategy to reveal novel Cd-responsive transporters by analyzing gene expression under different Cd concentrations. This study could help to develop novel strategies for improving tolerance to Cd exposure in rice and other cereal crops.

  3. Cephalopod genomics

    DEFF Research Database (Denmark)

    Albertin, Caroline B.; Bonnaud, Laure; Brown, C. Titus

    2012-01-01

    The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, ``Paths to Cephalopod Genomics-Strategies, Choices, Organization,'' held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austri...

  4. Ancient genomics

    DEFF Research Database (Denmark)

    Der Sarkissian, Clio; Allentoft, Morten Erik; Avila Arcos, Maria del Carmen;

    2015-01-01

    , archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when...

  5. CD30 in Systemic Mastocytosis

    NARCIS (Netherlands)

    van Anrooij, Bjorn; Kluin, Philip M.; Oude Elberink, Joanne N.G.; Kluin-Nelemans, Johanna C.

    2014-01-01

    CD30 is a transmembrane receptor, normally not expressed by mast cells, which regulates proliferation/apoptosis and antibody responses. Aberrant expression of CD30 by mastocytosis mast cells and interaction with its ligand CD30L (CD153) appears to play an important role in the pathogenesis and clini

  6. INVESTIGATION OF CdTe/CdS HETEROJUNCTION CHARACTERISTICS%CdTe/CdS异质结特性

    Institute of Scientific and Technical Information of China (English)

    郭江; 王万录; 刘高斌; 冯良桓

    2003-01-01

    从理论上对CdTe/CdS太阳电池CdS/CdTe异质结的特性进行了研究和讨论,结果表明可以简单利用改变CdTe、CdS两种半导体材料的掺杂浓度来改变CdS/CdTe异质结的能带结构.针对不同的能带结构采用了不同的物理模型,得到的CdS/CdTe异质结伏安特性曲线有一折点,且折点位置随异质结能带结构的变化而变化.

  7. [CD4+, CD8+ AND CD19+ cells in individuals with dyslipidemia].

    Science.gov (United States)

    Pereira de Moura, Jose; Santos Rosa, Manuel; Alves, Vera; Mota Pinto, Anabela; Rodrigues, Victor; Silva, José Manuel; Alves de Moura, J J

    2013-01-01

    Introdução: Os mecanismos imunológicos e inflamatórios têm um papel crucial no desenvolvimento da aterosclerose e na sua tradução clínica. São inúmeros os estudos que procuraram relacionar os mais diversos marcadores inflamatórios – leucócitos, proteína C reactiva, interleucinas, quimiocinas, moléculas de adesão, metaloproteinases, etc – com os factores de risco clássicos da aterosclerose, a formação da placa e os fenómenos clínicos. Não são tantos, que tenhamos conhecimento, os trabalhos que analisaram o comportamento das diversas células mononucleares na fisiopatologia da aterosclerose. Sendo os monócitos/macrófagos e os linfócitos células fundamentais no desencadear e posterior evolução desta doença vascular, procurámos determinar as percentagens das diversas populações celulares periféricas em indivíduos dislipidémicos e em normolipidémicos.Material e Métodos: Por citometria de fluxo, determinámos em indivíduos com dislipidemia e num grupo controlo, as concentrações no sangue periférico dos CD3+, CD4+, CD8+, CD19+, CD56+, CD56CD8+, DN, CD25+, CD26+, CD25CD3+, CD26CD3+, CD25CD26CD3+, CCR5+, CCR5CD3+, CCR5CD4+, HLADR+, HLADRCD4+, HLADRCD8h+, HLADRCD8low+, HLADRCD8+, CD95+, CD95CD95L+, CD3CD95+, CD3CD95L+, CD62L+, CD3CD62L+, CD69+, CD69CD3+ e CD69CD4+. Resultados: Embora na sua grande maioria não tenham sido encontradas diferenças significativas entre os dois grupos de participantes, verificaram-se em algumas populações celulares, resultados que nos mereceram alguns comentários. Neste artigo debruçámo-nos apenas sobre as populações positivas para os CD4, CD8 e CD19.Discussão: A menor concentração das células CD4+ na nossa população de dislipidémicos foi aparentemente inesperada devido ao relacionamento existente entre este tipo celular, os factores de risco e a aterosclerose. Não foram determinados os subtipos Th1 e Th2, nem a população de células reguladoras CD4+CD25+, que poderiam explicar a

  8. QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium.

    Science.gov (United States)

    Ma, Xuexia; Ding, Yezhang; Zhou, Baoliang; Guo, Wangzhen; Lv, Yanhui; Zhu, Xiefei; Zhang, Tianzhen

    2008-12-01

    Asiatic cotton (Gossypium arboreum L.) is an Old World cultivated cotton species. The sinense race was planted extensively in China. Due to the advances in spinning technology during the last century, the species was replaced by the New World allotetraploid cotton G. hirsutum L. Gossypium arboreum is still grown in India and Pakistan and also used as an elite in current cotton breeding programs. In addition, G. arboreum serves as a model for genomic research in Gossypium. In the present study, we generated an A-genome diploid cotton intraspecific genetic map including 264 SSR loci with three morphological markers mapped to 13 linkage groups. The map spans 2,508.71 cM with an average distance of 9.4 cM between adjacent loci. A population containing 176 F(2:3) families was used to perform quantitative trait loci (QTL) mapping for 17 phenotypes using Multiple QTL Model (MQM) of MapQTL ver 5.0. Overall, 108 QTLs were detected on 13 chromosomes. Thirty-one QTLs for yield and its components were detected in the F2 population. Forty-one QTLs for yield and its components were detected in the F(2:3) families with a total of 43 QTLs for fiber qualities. Two QTLs for seed cotton weight/plant and lint index and three QTLs for seed index were consistently detected both in F2 and F(2:3). Most QTLs for fiber qualities and yields were located at the same interval or neighboring intervals. These results indicated that the negative correlation between fiber qualities and yield traits may result from either pleiotropic effect of one gene or linkage effects of multiple closely linked genes.

  9. Effects of Cd Interlayer on CdS/CdTe Thin Film Photovoltaics

    Science.gov (United States)

    Rivella, David; Cerqueira, Luis; Sahiner, M. Alper

    CdS/CdTe thin films are well known for their photovoltaic effects. However, it is also known that there are various factors that limit the output of the photovoltaic cells. In these particular thin films, a limiting factor is the interaction of CdS and the CdTe layers. By adding a Cd layer between CdS and CdTe, a buffer zone was created. Therefore, the interaction between the aforementioned layers was changed. In this study, the buffer zone was added to the photovoltaic cells, while the ratio of Cd to Te in the CdTe layer was varied, in order to observe the effects of the buffer in regards to the diffusion of Te in traditional CdTe/CdS photovoltaics. The samples were created on ITO coated glass using pulsed laser deposition. This created uniform samples with an approximate thickness of 0.75 microns. In order to test the effect of the Cd buffer layer, the CdTe layers were deposited with varying ratios of Cd to Te. XRD analysis confirmed that the deposited Cd and Te formed crystalline CdTe. The active carrier concentrations were then determined using Hall Effect measurements. The photovoltaic properties were measured using Keithley source meter set-up. The effect of structural modifications on the active carrier concentrations and photovoltaic properties will be discussed.

  10. 光穗鹅观草的染色体组组成%Genomic constitution of Roegneria glaberrima

    Institute of Scientific and Technical Information of China (English)

    周永红; 杨瑞武; 丁春邦; 张利

    2004-01-01

    Intergeneric and interspecific hybridization of Roegneria glaberrima (tetraploid: 2n=4x=28) with three "analyzer" species, i.e., Pseudoroegneria spicata (diploid: 2n=2x=14, St), Roegneria dolichathera (tetraploid: 2n=4x=28, StY) and Roegneria kamoji (hexaploid: 2n=6x=42, StYH), were performed successfully. Chromosome pairing at metaphaseI in meiosis of pollen mother cells was studied in the parental species and hybrids to determine the genomic constitution of R. glaberrima . It is concluded from this study that R. glaberrima i) behaves in a strict allotetraploid nature, comprised of two different genomes; ii) contains the St and Y genomes; iii) is closely related to R. dolichathera ; and i(v¨)is a valid species of Roegneria , which comprises taxa with StY and StYH genomes.%为了研究小麦族鹅观草属光穗鹅观草 (2n=4x=28)的染色体组组成,本研究成功地获得了它与斯皮卡他草 (2n=2x=14, St)、长芒鹅观草(2n=4x=28, StY)和鹅观草(2n=6x=42, StYH)的属、种间杂种,对亲本和杂种F1花粉母细胞减数分裂中期I染色体配对行为进行了分析.结果表明:光穗鹅观草是严格的异源四倍体,拥有St和Y两组完全不同的染色体组;与长芒鹅观草的染色体组同源,有较近的亲缘关系;是鹅观草属有效的物种.

  11. Cloning and expression analysis of CD3γ/δ, CD3εand CD3ζchains in Chinese soft-shelled turtle, Pelodiscus sinensis%中华鳖CD3γ/δ、CD3ε和CD3ζ分子的克隆与表达分析

    Institute of Scientific and Technical Information of China (English)

    付建平; 郭政; 高谦; 罗璋; 聂品

    2014-01-01

    The Chinese soft-shelled turtle, Pelodiscus sinensis has a wide geographical distribution ranging from south-eastern Siberia and Korea through most parts of China to Vietnam. Besides its nutritive and medical value, the turtle also became a model animal for investigating the development and evolution of their unique body and evolution of other biological as well as immune functions. CD3 molecules which are composed of four chains [γ,δ,ε,ζ(η)] act as markers of T lymphocytes and play important roles in T cell signaling, TCR-CD3 complex assembly and T cell mature. To understand its molecular structures, function and evolution in reptile, we cloned the cDNA sequences of CD3γ/δ, CD3εand CD3ζin the Chinese soft-shelled turtle using the SMART RACE technology and analyzed its expression pat-tern in normal and bacterial infected individuals using real time quantitative PCR (rt-qPCR). The deduced CD3γ/δ, CD3εand CD3ζencoded 170 aa, 183 aa and 168 aa, respectively. The CD3γ/δand CD3εare structurally related with an extracellular immunoglobulin-like domain, a transmembrane region and an ITAM motif containing cytoplasmic tail. The Di-leucine based internalization motif (D138RQNLI) and a potential N-glycosylation site (N81TS) were also found in CD3γ/δ amino acid sequence, and a proline-rich motif (R155PPPVP) and ER rention motif (Y175AGLDSR) were found in CD3εamino acid sequence with the absence of the potential N-glycosylation site. The deduced CD3ζamino acid sequence has a different structure with a 10 aa extracellular part, a transmembrane region and three ITAM motifs containing cytoplasmic tail. The phylogenetic tree showed that each chain was clustered together and Chinese soft-shelled turtle had a closer relationship with birds and amphibians. Bioinformatics analysis in genomic sequences showed that CD3γ/δgene, containing 6 exons and 5 introns, and CD3εgene, containing 7 exons and 6 introns located and transcribed oppositely in the Chromosome

  12. Downregulation of CD44 reduces doxorubicin resistance of CD44+CD24- breast cancer cells

    Directory of Open Access Journals (Sweden)

    Phuc PV

    2011-06-01

    Full Text Available Pham Van Phuc, Phan Lu Chinh Nhan, Truong Hai Nhung, Nguyen Thanh Tam, Nguyen Minh Hoang, Vuong Gia Tue, Duong Thanh Thuy, Phan Kim NgocLaboratory of Stem Cell Research and Application, University of Science, Vietnam National University, Ho Chi Minh, VietnamBackground: Cells within breast cancer stem cell populations have been confirmed to have a CD44+CD24- phenotype. Strong expression of CD44 plays a critical role in numerous types of human cancers. CD44 is involved in cell differentiation, adhesion, and metastasis of cancer cells.Methods: In this study, we reduced CD44 expression in CD44+CD24- breast cancer stem cells and investigated their sensitivity to an antitumor drug. The CD44+CD24- breast cancer stem cells were isolated from breast tumors; CD44 expression was downregulated with siRNAs followed by treatment with different concentrations of the antitumor drug.Results: The proliferation of CD44 downregulated CD44+CD24- breast cancer stem cells was decreased after drug treatment. We noticed treated cells were more sensitive to doxorubicin, even at low doses, compared with the control groups.Conclusions: It would appear that expression of CD44 is integral among the CD44+CD24- cell population. Reducing the expression level of CD44, combined with doxorubicin treatment, yields promising results for eradicating breast cancer stem cells in vitro. This study opens a new direction in treating breast cancer through gene therapy in conjunction with chemotherapy.Keywords: antitumor drugs, breast cancer stem cells, CD44, CD44+CD24- cells, doxorubicin

  13. CD4~+CD56~+ hematodermic neoplasm in a child

    Institute of Scientific and Technical Information of China (English)

    GUO Xia; LI Qiang; ZHOU Chen-yan

    2010-01-01

    @@ CD4~+CD56~+ hematodermic neoplasm (HN) is a rare, highly aggressive systemic neoplasm, which had been described under various names including lymphoblastic lymphoma of natural killer (NK) phenotype, blastic NK cell lymphoma (BNK), leukemic lymphoma of immature NK lineage and CD4~+CD56~+ HN. This malignancy is mainly involved in elderly people and usually a rapidly fatal disease, since consistently effective treatments have not yet been developed. It is relatively rare in children.~(1-6) Herein we report a boy with CD4~+CD56~+ HN.

  14. Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (creole bean, and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis.

    Directory of Open Access Journals (Sweden)

    Sompong Chankaew

    Full Text Available Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.

  15. Detection of genome donor species of neglected tetraploid crop Vigna reflexo-pilosa (créole bean), and genetic structure of diploid species based on newly developed EST-SSR markers from azuki bean (Vigna angularis).

    Science.gov (United States)

    Chankaew, Sompong; Isemura, Takehisa; Isobe, Sachiko; Kaga, Akito; Tomooka, Norihiko; Somta, Prakit; Hirakawa, Hideki; Shirasawa, Kenta; Vaughan, Duncan A; Srinives, Peerasak

    2014-01-01

    Vigna reflexo-pilosa, which includes a neglected crop, is the only one tetraploid species in genus Vigna. The ancestral species that make up this allotetraploid species have not conclusively been identified, although previous studies suggested that a donor genome of V. reflexo-pilosa is V. trinervia. In this study, 1,429 azuki bean EST-SSR markers were developed of which 38 EST-SSR primer pairs that amplified one product in diploid species and two discrete products in tetraploid species were selected to analyze 268 accessions from eight taxa of seven Asian Vigna species including V. reflexo-pilosa var. glabra, V. reflexo-pilosa var. reflexo-pilosa, V. exilis, V. hirtella, V. minima, V. radiata var. sublobata, V. tenuicaulis and V. trinervia to identify genome donor of V. reflexo-pilosa. Since both diploid and tetraploid species were analyzed and each SSR primer pair detected two loci in the tetraploid species, we separated genomes of the tetraploid species into two different diploid types, viz. A and B. In total, 445 alleles were detected by 38 EST-SSR markers. The highest gene diversity was observed in V. hirtella. By assigning the discrete PCR products of V. reflexo-pilosa into two distinguished genomes, we were able to identify the two genome donor parents of créole bean. Phylogenetic and principal coordinate analyses suggested that V. hirtella is a species complex and may be composed of at least three distinct taxa. Both analyses also clearly demonstrated that V. trinervia and one taxon of V. hirtella are the genome donors of V. reflexo-pilosa. Gene diversity indicates that the evolution rate of EST-SSRs on genome B of créole bean might be faster than that on genome A. Species relationship among the Vigna species in relation to genetic data, morphology and geographical distribution are presented.

  16. The function genomics study

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Genomics is a biology term appeared ten years ago, used to describe the researches of genomic mapping, sequencing, and structure analysis, etc. Genomics, the first journal for publishing papers on genomics research was born in 1986. In the past decade, the concept of genomics has been widely accepted by scientists who are engaging in biology research. Meanwhile, the research scope of genomics has been extended continuously, from simple gene mapping and sequencing to function genomics study. To reflect the change, genomics is divided into two parts now, the structure genomics and the function genomics.

  17. Visualization for genomics: the Microbial Genome Viewer.

    NARCIS (Netherlands)

    Kerkhoven, R.; Enckevort, F.H.J. van; Boekhorst, J.; Molenaar, D.; Siezen, R.J.

    2004-01-01

    SUMMARY: A Web-based visualization tool, the Microbial Genome Viewer, is presented that allows the user to combine complex genomic data in a highly interactive way. This Web tool enables the interactive generation of chromosome wheels and linear genome maps from genome annotation data stored in a My

  18. Regulation and gene expression profiling of NKG2D positive human cytomegalovirus-primed CD4+ T-cells

    DEFF Research Database (Denmark)

    Jensen, Helle; Folkersen, Lasse; Skov, Søren

    2012-01-01

    we used genome-wide analysis of individual genes and gene set enrichment analysis (GSEA) to investigate the gene expression profile of NKG2D(+) CD4(+) T-cells, generated from HCMV-primed CD4(+) T-cells. We show that the HCMV-primed NKG2D(+) CD4(+) T-cells possess a higher differentiated phenotype...... CD4(+) T-cells. These findings provide novel information about the gene expression profile of HCMV-primed NKG2D(+) CD4(+) T-cells, as well as the mechanisms regulating NKG2D cell surface expression....

  19. Various domains of the B-cell regulatory molecule CD72 has diverged at different rates in mammals

    DEFF Research Database (Denmark)

    Petersen, Cathrine Bie; Hillig, Ann-Britt Nygaard; Fredholm, Merete;

    2007-01-01

    We report the cloning of the porcine B-cell co-receptor CD72, as well as genomic mapping and examination of transcription. The B-cell receptor (BCR) complex mediates signalling upon antigen recognition by the membrane bound BCR. Several co-receptors modulate this signal positively or negatively. CD......72 has been shown to be a negatively regulating BCR co-receptor. We isolated and sequenced three porcine CD72 transcript variants. Using a pig radiation hybrid panel we found the porcien CD72 gene to be located on chromosome 1q21-28 in a region syntenic to human chromosome 9. The porcine CD72 gene...

  20. CdS/CdSSe quantum dots in glass matrix

    Indian Academy of Sciences (India)

    R S Sonawane; S D Naik; S K Apte; M V Kulkarni; B B Kale

    2008-06-01

    The compositions containing 55 and 60% of silica have been formulated for preparation of glass filters having sharp cut-off at 475 and 575 nm. To achieve cut-off at these wavelengths, the glasses have been doped with CdS/CdSSe and melted at 1200–1300°C. The glass samples were transparent and pale yellow in colour due to presence of CdS/CdSSe tiny nano crystal (Q-dots). in situ growth of CdS/CdSSe nano crystals imparts the yellow/orange/red colour to these glasses. Optical study shows that as prepared glasses have optical cut-off in the range 350–370 nm. The linear crystal growth of CdS/CdSSe in glasses exhibits red shift in optical cut-off. The optical filter having cut-off at 475 nm can be prepared by doping CdS and cut-off filter of wavelength 575 nm by CdSSe. The TEM results show that the CdS/CdSSe nano crystals (Q-dots) ranging from 2–5 nm are uniformly distributed into the glass matrix.

  1. Novel insights into the regulatory architecture of CD4+ T cells in rheumatoid arthritis.

    Directory of Open Access Journals (Sweden)

    Adrià Aterido

    Full Text Available Rheumatoid arthritis (RA is the most frequent autoimmune chronic inflammatory disease of the joints and it is characterized by the inflammation of the synovial membrane and the subsequent destruction of the joints. In RA, CD4+ T cells are the main drivers of disease initiation and the perpetuation of the damaging inflammatory process. To date, however, the genetic regulatory mechanisms of CD4+ T cells associated with RA etiology are poorly understood. The genome-wide analysis of expression quantitative trait loci (eQTL in disease-relevant cell types is a recent genomic integration approach that is providing significant insights into the genetic regulatory mechanisms of many human pathologies. The objective of the present study was to analyze, for the first time, the genome-wide genetic regulatory mechanisms associated with the gene expression of CD4+ T cells in RA. Whole genome gene expression profiling of CD4+ T cells and the genome-wide genotyping (598,258 SNPs of 29 RA patients with an active disease were performed. In order to avoid the excessive burden of multiple testing associated with genome-wide trans-eQTL analysis, we developed and implemented a novel systems genetics approach. Finally, we compared the genomic regulation pattern of CD4+ T cells in RA with the genomic regulation observed in reference lymphoblastoid cell lines (LCLs. We identified a genome-wide significant cis-eQTL associated with the expression of FAM66C gene (P = 6.51e-9. Using our new systems genetics approach we identified six statistically significant trans-eQTLs associated with the expression of KIAA0101 (P<7.4e-8 and BIRC5 (P = 5.35e-8 genes. Finally, comparing the genomic regulation profiles between RA CD4+ T cells and control LCLs we found 20 genes showing differential regulatory patterns between both cell types. The present genome-wide eQTL analysis has identified new genetic regulatory elements that are key to the activity of CD4+ T cells in RA.

  2. Development and evaluation of a genome-wide 6K SNP array for diploid sweet cherry and tetraploid sour cherry.

    Directory of Open Access Journals (Sweden)

    Cameron Peace

    Full Text Available High-throughput genome scans are important tools for genetic studies and breeding applications. Here, a 6K SNP array for use with the Illumina Infinium® system was developed for diploid sweet cherry (Prunus avium and allotetraploid sour cherry (P. cerasus. This effort was led by RosBREED, a community initiative to enable marker-assisted breeding for rosaceous crops. Next-generation sequencing in diverse breeding germplasm provided 25 billion basepairs (Gb of cherry DNA sequence from which were identified genome-wide SNPs for sweet cherry and for the two sour cherry subgenomes derived from sweet cherry (avium subgenome and P. fruticosa (fruticosa subgenome. Anchoring to the peach genome sequence, recently released by the International Peach Genome Initiative, predicted relative physical locations of the 1.9 million putative SNPs detected, preliminarily filtered to 368,943 SNPs. Further filtering was guided by results of a 144-SNP subset examined with the Illumina GoldenGate® assay on 160 accessions. A 6K Infinium® II array was designed with SNPs evenly spaced genetically across the sweet and sour cherry genomes. SNPs were developed for each sour cherry subgenome by using minor allele frequency in the sour cherry detection panel to enrich for subgenome-specific SNPs followed by targeting to either subgenome according to alleles observed in sweet cherry. The array was evaluated using panels of sweet (n = 269 and sour (n = 330 cherry breeding germplasm. Approximately one third of array SNPs were informative for each crop. A total of 1825 polymorphic SNPs were verified in sweet cherry, 13% of these originally developed for sour cherry. Allele dosage was resolved for 2058 polymorphic SNPs in sour cherry, one third of these being originally developed for sweet cherry. This publicly available genomics resource represents a significant advance in cherry genome-scanning capability that will accelerate marker-locus-trait association discovery

  3. Characterization of intermixing at the CdS/CdTe interface in CSS deposited CdTe

    Science.gov (United States)

    Dhere, R. G.; Asher, S. E.; Jones, K. M.; Al-Jassim, M. M.; Moutinho, H. R.; Rose, D. H.; Dippo, P.; Sheldon, P.

    1996-01-01

    CdS/CdTe structures deposited on different substrates are analyzed using transmission electron microscopy (TEM), secondary ion mass spectrometry (SIMS), optical transmission, atomic force microscopy (AFM), X-ray diffraction (XRD) and photoluminescence (PL). The microstructure of CdTe was found to be independent of CdS crystallinity, and the structural defects at CdS/CdTe interface are generated principally by the lattice mismatch between CdS and CdTe. The interdiffusion at the CdS/CdTe interface was found to be a function of substrate temperature and CdCl2 heat treatment.

  4. Electrical properties of CdS/CdTe heterojunctions

    Science.gov (United States)

    Chu, T. L.; Chu, Shirley S.; Ang, S. T.

    1988-08-01

    The electrical properties of n-CdS/p-CdTe heterojunctions depend strongly on the cleanliness of the interface region. In this work, CdTe films were deposited on CdS/glass substrates by close-spaced sublimation (CSS) under various conditions. The dark current-voltage characteristics of the resulting heterojunctions were measured over a wide temperature range, and the capacitance-voltage characteristics were measured in the dark and under illumination. When the CdS surface is in situ cleaned prior to the deposition of the CdTe film, the current transport across the junction is controlled by a thermally activated process. Tunneling makes an important contribution to the interface recombination at temperatures below room temperature when the in situ cleaning of CdS is not used. The dark capacitance of CdS/CdTe heterojunctions prepared with in situ etching is essentially independent of the reverse bias due to intrinsic interface states. Under white light illumination, the 1/C 2 vs V relation is nearly linear. The CdS/CdTe heterojunctions without in situ cleaning showed different 1/C 2 vs V relations due to higher density of interface states. The in situ cleaning also has pronounced effects on the frequency dependence of dark and illuminated capacitances. Using the in situ cleaning technique, solar cells of about 1 cm2 area have achieved an AM 1.5 (global) efficiency of about 10.5%.

  5. Genome-wide identification of microsatellites in white clover (Trifolium repens L. using FIASCO and phpSSRMiner

    Directory of Open Access Journals (Sweden)

    Bouton Joseph H

    2008-07-01

    Full Text Available Abstract Background Allotetraploid white clover (Trifolium repens L. is an important forage legume widely cultivated in most temperate regions. Only a small number of microsatellite markers are publicly available and can be utilized in white clover breeding programs. The objectives of this study were to develop an integrated approach for microsatellite development and to evaluate the approach for the development of new SSR markers for white clover. Results Genomic libraries containing simple sequence repeat (SSR sequences were constructed using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO procedure and phpSSRMiner was used to develop the microsatellite markers. SSR motifs were isolated using two biotin-labeled probes, (CA17 and (ATG12. The sequences of 6,816 clones were assembled into 1,698 contigs, 32% of which represented novel sequences based on BLASTN searches. Approximately 32%, 28%, and 16% of these SSRs contained hexa-, tri-, and di-nucleotide repeats, respectively. The most frequent motifs were the CA and ATG complementary repeats and the associated compound sequences. Primer pairs were designed for 859 SSR loci based on sequences from these genomic libraries and from GenBank white clover nucleotide sequences. A total of 191 SSR primers developed from the two libraries were tested for polymorphism in individual clones from the parental genotypes GA43 ('Durana', 'SRVR' and six F1 progeny from a mapping population. Ninety two percent produced amplicons and 66% of these were polymorphic. Conclusion The combined approach of identifying SSR-enriched fragments by FIASCO coupled with the primer design and in silico amplification using phpSSRMiner represents an efficient and low cost pipeline for the large-scale development of microsatellite markers in plants. The approach described here could be readily adapted and utilized in other non-related species with none or limited genomic resources.

  6. In ovo injection of anti-chicken CD25 monoclonal antibodies depletes CD4+CD25+ T cells in chickens.

    Science.gov (United States)

    Shanmugasundaram, Revathi; Selvaraj, Ramesh K

    2013-01-01

    The CD4(+)CD25(+) cells have T regulatory cell properties in chickens. This study investigated the effect of in ovo injection of anti-chicken CD25 monoclonal antibodies (0.5 mg/egg) on CD4(+)CD25(+) cell depletion and on amounts of interleukin-2 mRNA and interferon-γ mRNA in CD4(+)CD25(-) cells posthatch. Anti-chicken CD25 or PBS (control) was injected into 16-d-old embryos. Chicks hatched from eggs injected with anti-chicken CD25 antibodies had a lower CD4(+)CD25(+) cell percentage in the blood until 25 d posthatch. The anti-chicken CD25 antibody injection nearly depleted CD4(+)CD25(+) cells in the blood until 16 d posthatch. At 30 d posthatch, the CD4(+)CD25(+) cell percentage in the anti-CD25-antibody-injected group was comparable with the percentage in the control group. At 16 d posthatch, the anti-chicken CD25 antibody injection decreased CD4(+)CD25(+) cell percentages in the thymus, spleen, and cecal tonsils. Chickens hatched from anti-CD25-antibody-injected eggs had approximately 25% of CD4(+)CD25(+) cells in the cecal tonsils and thymus compared with those in the cecal tonsils and thymus of the control group. The CD4(+)CD25(-) cells from the spleen and cecal tonsils of chicks hatched from anti-chicken-CD25-injected eggs had higher amounts of interferon-γ and interleukin-2 mRNA than CD4(+)CD25(-) cells from the control group. It could be concluded that injecting anti-chicken CD25 antibodies in ovo at 16 d of incubation nearly depleted the CD4(+)CD25(+) cells until 25 d posthatch.

  7. Forced extinction of CD24 stem-like breast cancer marker alone promotes radiation resistance through the control of oxidative stress.

    Science.gov (United States)

    Bensimon, Julie; Biard, Denis; Paget, Vincent; Goislard, Maud; Morel-Altmeyer, Sandrine; Konge, Julie; Chevillard, Sylvie; Lebeau, Jérôme

    2016-03-01

    Along with CD44, CD24 is a key marker of breast cancer stem cells (CSCs), frequently defined by CD24(-)/CD44(+) labeling. Among all phenotypes classically attributed to breast CD24(-)/CD44(+) cancer cells, radiation resistance has been extensively described and seen as being implicated in radiotherapy failure. Our previous data indicated that CD24(-) cells constitute a radiation-resistant subpopulation transitory selected by high doses of ionizing radiation. However, little is known about the biological role of CD24 in breast cancers, and no function has been assigned to CD24 in radiation response. Here, CD24 expression was induced in CD24(-) cells or knocked-down in CD24(+) cells. We show that forced extinction of CD24 expression is associated with decreased proliferation rate, lower levels of reactive oxygen species (ROS) and decreased genomic instability. On the opposite when CD24 is artificially expressed in CD24(-) cells, proliferation rates in vitro and in vivo, ROS levels and genomic instability are enhanced. Moreover, we observe that loss of CD24 expression leads to radiation resistance, by preventing radiation-induced cell death and promoting generation of progeny in relation to lower G2/M blockade and a smaller proportion of polyploid cells. Finally, control of ROS levels appears to be the key event in the CD24-mediated radiation response. For the first time, CD24 is proposed as a direct actor in radiation response of breast cancer cells, independently of CD44 expression. These findings could have interesting applications in evaluating the intrinsic radiation response of primary tumors.

  8. Plant Genome Duplication Database.

    Science.gov (United States)

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

    2017-01-01

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

  9. Rodent malaria parasites : genome organization & comparative genomics

    NARCIS (Netherlands)

    Kooij, Taco W.A.

    2006-01-01

    The aim of the studies described in this thesis was to investigate the genome organization of rodent malaria parasites (RMPs) and compare the organization and gene content of the genomes of RMPs and the human malaria parasite P. falciparum. The release of the complete genome sequence of P. falciparu

  10. Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

    Directory of Open Access Journals (Sweden)

    Guo Yufang

    2012-11-01

    Full Text Available Abstract Background Cultivated peanut or groundnut (Arachis hypogaea L. is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40. Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20, which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. Results A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons derived from 70,771 long-read (Sanger and 270,957 short-read (454 sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639 and GKBSPSc 30081 (PI 468327 in the B-genome species A. batizocoi. A high degree of macrosynteny was observed

  11. 新生儿感染时CD64、CD3、CD4、CD8的表达研究%Neonatal infection CD64, CD3, CD4, CD8 expression studies

    Institute of Scientific and Technical Information of China (English)

    王丽丽; 刘光辉; 郑洪

    2014-01-01

    目的:探讨新生儿感染时外周血CD64及CD3、CD4、CD8的表达,为新生儿细菌感染的早期诊断和细菌感染时细胞免疫功能的评价提供循证支持。方法应用流式细胞仪定量检测120例感染和非感染新生儿外周血CD64分子及CD3、CD4、CD8的表达变化,并将败血症组患儿的CD64与C反应蛋白(CRP)、白细胞计数及血培养进行比较。结果败血症组CD64为(6.7±2.8),高于局部感染组(4.1±1.4)与非感染组(2.9±0.5),差异有统计学意义(P0.05),各组间CD8差异无统计学意义(P>0.05)。结论 CD64可作为新生儿细菌感染的早期诊断指标,严重细菌感染患儿存在细胞免疫功能紊乱,T淋巴细胞亚群检测对新生儿细胞免疫功能的评价有重要意义。%Objective To investigate neonatal infection in peripheral blood CD64 and CD3, CD4, CD8 expression for the early diagnosis of neonatal bacterial infection and bacterial infection celular immune function evaluation of evidence-based support. Methods 120 cases of flow cytometry detection of neonatal infection and non-infected peripheral blood CD64 molecule and CD3, CD4, CD8 expression changes, and sepsis in children with CD64 and C-reactive protein (CRP), white blood cellcount and blood training for comparison. Result CD64 as a result of sepsis group (6.7±2.8), higher than the local infection group (4.1±1.4) and non-infected group (2.9±0.5), the difference was statisticaly significant (P0.05), CD8 difference between the groups was not statisticaly significant (P>0.05). Conclusion CD64 can be used as an early diagnosis of neonatal bacterial infection indicators of serious bacterial infections in children with immune dysfunction, T lymphocyte subsets in the newborn immune function evaluation is important.

  12. Genome editing for human gene therapy.

    Science.gov (United States)

    Meissner, Torsten B; Mandal, Pankaj K; Ferreira, Leonardo M R; Rossi, Derrick J; Cowan, Chad A

    2014-01-01

    The rapid advancement of genome-editing techniques holds much promise for the field of human gene therapy. From bacteria to model organisms and human cells, genome editing tools such as zinc-finger nucleases (ZNFs), TALENs, and CRISPR/Cas9 have been successfully used to manipulate the respective genomes with unprecedented precision. With regard to human gene therapy, it is of great interest to test the feasibility of genome editing in primary human hematopoietic cells that could potentially be used to treat a variety of human genetic disorders such as hemoglobinopathies, primary immunodeficiencies, and cancer. In this chapter, we explore the use of the CRISPR/Cas9 system for the efficient ablation of genes in two clinically relevant primary human cell types, CD4+ T cells and CD34+ hematopoietic stem and progenitor cells. By using two guide RNAs directed at a single locus, we achieve highly efficient and predictable deletions that ablate gene function. The use of a Cas9-2A-GFP fusion protein allows FACS-based enrichment of the transfected cells. The ease of designing, constructing, and testing guide RNAs makes this dual guide strategy an attractive approach for the efficient deletion of clinically relevant genes in primary human hematopoietic stem and effector cells and enables the use of CRISPR/Cas9 for gene therapy.

  13. CD74 in kidney disease

    Directory of Open Access Journals (Sweden)

    Lara eValiño-Rivas

    2015-09-01

    Full Text Available CD74 (invariant MHC class II regulates protein trafficking and is a receptor for macrophage migration inhibitory factor (MIF and D-dopachrome tautomerase (D-DT/MIF-2. CD74 expression is increased in tubular cells and/or glomerular podocytes and parietal cells in human metabolic nephropathies, polycystic kidney disease, graft rejection and kidney cancer and in experimental diabetic nephropathy and glomerulonephritis. Stressors like abnormal metabolite (glucose, lyso-Gb3 levels and inflammatory cytokines increase kidney cell CD74. MIF activates CD74 to increase inflammatory cytokines in podocytes and tubular cells and proliferation in glomerular parietal epithelial cells and cyst cells. MIF overexpression promotes while MIF targeting protects from experimental glomerular injury and kidney cysts, and interference with MIF/CD74 signaling or CD74 deficiency protected from crescentic glomerulonephritis. However, CD74 may protect from interstitial kidney fibrosis. Furthermore, CD74 expression by stressed kidney cells raises questions about the kidney safety of cancer therapy strategies delivering lethal immunoconjugates to CD74-expressing cells. Thus, understanding CD74 biology in kidney cells is relevant for kidney therapeutics.

  14. Diverged Copies of the Seed Regulatory Opaque-2 Gene by a Segmental Duplication in the Progenitor Genome of Rice,Sorghum,and Maize

    Institute of Scientific and Technical Information of China (English)

    Jian-Hong Xu; Joachim Messing

    2008-01-01

    Comparative analyses of the sequence of entire genomes have shown that gene duplications,chromosomal segmental duplications.or even whole genome duplications(WGD)have played prominent roles in the evolution of many eukaryotic species.Here,we used the ancient duplication of a well known transcription factor in maize,encoded by the Opaque-2(02)IOCUS,to examine the generaI features of divergences of chromosomaI segmentaI duplications in a lineagespecific manner.We took advantage of contiguous chromosomal sequence information in rice(Oryza sativa,Nipponbare).sorghum(Sorghum bicoloc Btx623),and maize(Zea mays,B73)that were aligned by conserved gene order(synteny).This analysis showed that the maize O2 locus is contained within a 1.25 million base-pair(Mb)segment on chromosome 7.which was duplicated≈56 million years ago(mya)before the split of rice and maize 50 mya.The duplicated region on chromosome 1 is only half the size and contains the maize OHP gene.which does not restore the o2 mutation although it encodes a protein with the same DNA and protein binding properties in endosperm.The segmental duplication iS not only found in rice,but also in sorghum,which split from maize 11.9 mya.A detailed analysis of the duplicated regions provided examples for complex rearrangements including deletions.duplications,conversions,inversions,and translocations.Furthermore,the rice and sorghum genomes appeared to be more stable than the maize genome,probably because maize underwent allotetraploidization and then diploidization.

  15. Funding Opportunity: Genomic Data Centers

    Science.gov (United States)

    Funding Opportunity CCG, Funding Opportunity Center for Cancer Genomics, CCG, Center for Cancer Genomics, CCG RFA, Center for cancer genomics rfa, genomic data analysis network, genomic data analysis network centers,

  16. Ontology for Genome Comparison and Genomic Rearrangements

    Directory of Open Access Journals (Sweden)

    Anil Wipat

    2006-04-01

    Full Text Available We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation.

  17. Genome Mapping in Plant Comparative Genomics.

    Science.gov (United States)

    Chaney, Lindsay; Sharp, Aaron R; Evans, Carrie R; Udall, Joshua A

    2016-09-01

    Genome mapping produces fingerprints of DNA sequences to construct a physical map of the whole genome. It provides contiguous, long-range information that complements and, in some cases, replaces sequencing data. Recent advances in genome-mapping technology will better allow researchers to detect large (>1kbp) structural variations between plant genomes. Some molecular and informatics complications need to be overcome for this novel technology to achieve its full utility. This technology will be useful for understanding phenotype responses due to DNA rearrangements and will yield insights into genome evolution, particularly in polyploids. In this review, we outline recent advances in genome-mapping technology, including the processes required for data collection and analysis, and applications in plant comparative genomics.

  18. Enabling functional genomics with genome engineering.

    Science.gov (United States)

    Hilton, Isaac B; Gersbach, Charles A

    2015-10-01

    Advances in genome engineering technologies have made the precise control over genome sequence and regulation possible across a variety of disciplines. These tools can expand our understanding of fundamental biological processes and create new opportunities for therapeutic designs. The rapid evolution of these methods has also catalyzed a new era of genomics that includes multiple approaches to functionally characterize and manipulate the regulation of genomic information. Here, we review the recent advances of the most widely adopted genome engineering platforms and their application to functional genomics. This includes engineered zinc finger proteins, TALEs/TALENs, and the CRISPR/Cas9 system as nucleases for genome editing, transcription factors for epigenome editing, and other emerging applications. We also present current and potential future applications of these tools, as well as their current limitations and areas for future advances.

  19. Adoptive immunotherapy via CD4+ versus CD8+ T cells

    Directory of Open Access Journals (Sweden)

    Vy Phan-Lai

    2016-04-01

    Full Text Available The goal of cancer immunotherapy is to induce specific and durable antitumor immunity. Adoptive T cell therapy (ACT has garnered wide interest, particularly in regard to strategies to improve T cell efficacy in trials. There are many types of T cells (and subsets which can be selected for use in ACT. CD4+ T cells are critical for the regulation, activation and aid of host defense mechanisms and, importantly, for enhancing the function of tumor-specific CD8+ T cells. To date, much research in cancer immunotherapy has focused on CD8+ T cells, in melanoma and other cancers. Both CD4+ T cells and CD8+ T cells have been evaluated as ACT in mice and humans, and both are effective at eliciting antitumor responses. IL-17 producing CD4+ T cells are a new subset of CD4+ T cells to be evaluated in ACT models. This review discusses the benefits of adoptive immunotherapy mediated by CD8+ and CD4+ cells. It also discusses the various type of T cells, source of T cells, and ex vivo cytokine growth factors for augmenting clinical efficacy of ACT. [Biomed Res Ther 2016; 3(4.000: 588-595

  20. Exploring Other Genomes: Bacteria.

    Science.gov (United States)

    Flannery, Maura C.

    2001-01-01

    Points out the importance of genomes other than the human genome project and provides information on the identified bacterial genomes Pseudomonas aeuroginosa, Leprosy, Cholera, Meningitis, Tuberculosis, Bubonic Plague, and plant pathogens. Considers the computer's use in genome studies. (Contains 14 references.) (YDS)

  1. Tolerance of Ricinus communis L. to Cd and screening of high Cd accumulation varieties for remediation of Cd contaminated soils.

    Science.gov (United States)

    Wu, Shanshan; Shen, Chuang; Yang, Zhongyi; Lin, Biyun; Yuan, Jiangang

    2016-11-01

    Response of castor (Ricinus communis L.) to cadmium (Cd) was assessed by a seed-suspending seedbed approach. Length of total radicle was the most sensitive indicator of Cd tolerance among the tested germination and growth characters. The ED50 value for Cd was 11.87 mg L(-1), indicating high Cd tolerance in castor. A pot experiment was conducted by growing 46 varieties of castor under CK (without Cd) and Cd1 (10 mg kg(-1) of Cd) and Cd2 (50 mg kg(-1) of Cd) treatments to investigate genotype variations in growth response and Cd accumulation of castor under different Cd exposures. Castor possessed high Cd accumulation ability; average shoot and root Cd concentrations of the 46 tested varieties were 21.83 and 185.43 mg kg(-1), and 174.99 and 1181.96 mg kg(-1) under Cd1 and Cd2, respectively. Great variation in Cd accumulation was observed among varieties, and Cd concentration of castor was genotype dependent. The correlation between biomass and Cd accumulation was significantly positive, while no significant correlation was observed between Cd concentration and Cd accumulation, which indicated that biomass performance is the dominant factor in determining Cd accumulation ability.

  2. Neoplasia hematodérmica CD4+ CD56+ en la infancia Hematodermic CD4+ CD56+ neoplasm in childhood

    Directory of Open Access Journals (Sweden)

    Erica A. Rojas Bilbao

    2008-04-01

    Full Text Available La neoplasia hematodérmica CD4+ CD56+ con fenotipo de célula dendrítica plasmocitoide es una rara y agresiva neoplasia recientemente reconocida por la WHO-EORTC classification. Afecta adultos de edad media y ancianos, siendo muy pocos los casos descriptos en niños. Presentamos el caso de una niña de 12 años con grave retraso mental, estigmas genéticos y múltiples lesiones cutáneas localizadas en miembros inferiores y superiores. Histológicamente se observó un infiltrado dérmico difuso de células pequeñas y medianas con expresión de CD4, CD56, CD43 y S100 así como de marcadores dendríticos plasmocitoides: CD 123 y BDCA-2 confirmados por citometría de flujo, sin compromiso de sangre periférica ni médula ósea. Cumpliendo dos semanas de tratamiento para leucemia linfoblástica aguda evolucionó con remisión clínica de las lesiones cutaneas.Hematodermic CD4+ CD56+ neoplasm with plasmacytoid dendritic cell phenotype is a rare and aggressive neoplasm recently recognized by the WHO-EORTC classification. It generally appears in elderly adults, exceptionally in childhood. We present a 12-year-old girl with severe mental retardation, genetic clinical features and multiple nodular cutaneous lesions on legs and arms. Histologically the nodules showed diffuse dermal infiltrate of medium and small cells and expression of CD4, CD56, CD43, S100 and plasmacytoid dendritic markers: CD123, BDCA-2 under flow cytometry study. Peripheral blood and bone marrow were not involved. Clinical remission of cutaneous lesions was observed after two weeks of acute lymphoblastic leukemia therapy.

  3. GENOMIC MEDICINE

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-03-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence. The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others.There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine. For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc..Legal aspects are also present in this new conception of medicine. For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others.We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the disease

  4. Genomic Medicine

    Directory of Open Access Journals (Sweden)

    Ignacio Briceño Balcázar

    2011-04-01

    Full Text Available Until the twilight of the 20th century, genetics was a branch of medicine applied to diseases of rare occurrence.  The advent of the human genome sequence and the possibility of studying it at affordable costs for patients and healthcare institutions, has permitted its application in high-priority diseases like cancer, cardiovascular disease, diabetes, and Alzheimer’s, among others. There is great potential in predictive and preventive medicine, through studying polymorphic genetic variants associated to risks for different diseases. Currently, clinical laboratories offer studies of over 30,000 variants associated with susceptibilities, to which individuals can access without much difficulty because a medical prescription is not required. These exams permit conducting a specific plan of preventive medicine.  For example, upon the possibility of finding a deleterious mutation in the BRCA1 and BRCA2 genes, the patient can prevent the breast cancer by mastectomy or chemoprophylaxis and in the presence of polymorphisms associated to cardiovascular risk preventive action may be undertaken through changes in life style (diet, exercise, etc.. Legal aspects are also present in this new conception of medicine.  For example, currently there is legislation for medications to indicate on their labels the different responses such medication can offer regarding the genetic variants of the patients, given that similar doses may provoke adverse reactions in an individual, while for another such dosage may be insufficient. This scenario would allow verifying the polymorphisms of drug response prior to administering medications like anticoagulants, hyperlipidemia treatments, or chemotherapy, among others. We must specially mention recessive diseases, produced by the presence of two alleles of a mutated gene, which are inherited from the mother, as well as the father. By studying the mutations, we may learn if a couple is at risk of bearing children with the

  5. Between Two Fern Genomes

    OpenAIRE

    Sessa, Emily B.; Banks, Jo; Michael S Barker; Der, Joshua P; Duffy, Aaron M; Graham, Sean W.; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D; Kathleen M. Pryer; Rothfels, Carl J.; Roux, Stanley J.; Salmi, Mari L; Sigel, Erin M.

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense divers...

  6. Genomes and evolutionary genomics of animals

    Institute of Scientific and Technical Information of China (English)

    Luting SONG; Wen WANG

    2013-01-01

    Alongside recent advances and booming applications of DNA sequencing technologies,a great number of complete genome sequences for animal species are available to researchers.Hundreds of animals have been involved in whole genome sequencing,and at least 87 non-human animal species' complete or draft genome sequences have been published since 1998.Based on these technological advances and the subsequent accumulation of large quantity of genomic data,evolutionary genomics has become one of the most rapidly advancing disciplines in biology.Scientists now can perform a number of comparative and evolutionary genomic studies for animals,to identify conserved genes or other functional elements among species,genomic elements that confer animals their own specific characteristics and new phenotypes for adaptation.This review deals with the current genomic and evolutionary research on non-human animals,and displays a comprehensive landscape of genomes and the evolutionary genomics of non-human animals.It is very helpful to a better understanding of the biology and evolution of the myriad forms within the animal kingdom [Current Zoology 59 (1):87-98,2013].

  7. Genome Maps, a new generation genome browser.

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-07-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org.

  8. Genome Maps, a new generation genome browser

    Science.gov (United States)

    Medina, Ignacio; Salavert, Francisco; Sanchez, Rubén; de Maria, Alejandro; Alonso, Roberto; Escobar, Pablo; Bleda, Marta; Dopazo, Joaquín

    2013-01-01

    Genome browsers have gained importance as more genomes and related genomic information become available. However, the increase of information brought about by new generation sequencing technologies is, at the same time, causing a subtle but continuous decrease in the efficiency of conventional genome browsers. Here, we present Genome Maps, a genome browser that implements an innovative model of data transfer and management. The program uses highly efficient technologies from the new HTML5 standard, such as scalable vector graphics, that optimize workloads at both server and client sides and ensure future scalability. Thus, data management and representation are entirely carried out by the browser, without the need of any Java Applet, Flash or other plug-in technology installation. Relevant biological data on genes, transcripts, exons, regulatory features, single-nucleotide polymorphisms, karyotype and so forth, are imported from web services and are available as tracks. In addition, several DAS servers are already included in Genome Maps. As a novelty, this web-based genome browser allows the local upload of huge genomic data files (e.g. VCF or BAM) that can be dynamically visualized in real time at the client side, thus facilitating the management of medical data affected by privacy restrictions. Finally, Genome Maps can easily be integrated in any web application by including only a few lines of code. Genome Maps is an open source collaborative initiative available in the GitHub repository (https://github.com/compbio-bigdata-viz/genome-maps). Genome Maps is available at: http://www.genomemaps.org. PMID:23748955

  9. Time-Resolved Photoluminescence Spectroscopy Evaluation of CdTe and CdTe/CdS Quantum Dots

    OpenAIRE

    Yuan, Zhimin; Yang, Ping; Cao, Yongqiang

    2012-01-01

    CdTe and CdTe/CdS quantum dots (QDs) were prepared in aqueous solutions using thioglycolic acid as a stabilizing agent. The photoluminescence (PL) wavelength of the QDs depended strongly on the size of CdTe cores and the thickness of CdS shells. Being kept at room temperature for 130 days, the PL wavelength of CdTe and CdTe/CdS QDs was red-shifted. However the red-shifted degree of CdTe QDs is larger than that of CdTe/CdS QDs. The size of CdTe QDs and the thickness of CdS play important roles...

  10. Fluorescence relaxation dynamics of CdSe and CdSe/CdS core/shell quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Kaur, Gurvir; Kaur, Harmandeep [Centre of Advanced Study in Physics, Department of Physics, Panjab University, Chandigarh-160014 (India); Tripathi, S. K., E-mail: surya@pu.ac.in [Centre of Advanced Study in Physics, Panjab University, Chandigarh- 160014 (India)

    2014-04-24

    Time-resolved fluorescence spectra for colloidal CdSe and CdSe/CdS core/shell quantum dots have been investigated to know their electron relaxation dynamics at the maximum steady state fluorescence intensity. CdSe core and CdSe/CdS type I core-shell materials with different shell (CdS) thicknesses have been synthesized using mercaptoacetic acid as a capping agent. Steady state absorption and emission studies confirmed successful synthesis of CdSe and CdSe/CdS core-shell quantum dots. The fluorescence shows a tri-exponential decay with lifetimes 57.39, 7.82 and 0.96 ns for CdSe quantum dots. The lifetime of each recombination decreased with growth of CdS shell over the CdSe core, with maximum contribution to fluorescence by the fastest transition.

  11. Sequestration of host-CD59 as potential immune evasion strategy of Trichomonas vaginalis.

    Science.gov (United States)

    Ibáñez-Escribano, Alexandra; Nogal-Ruiz, Juan José; Pérez-Serrano, Jorge; Gómez-Barrio, Alicia; Escario, J Antonio; Alderete, J F

    2015-09-01

    Trichomonas vaginalis is known to evade complement-mediated lysis. Because the genome of T. vaginalis does not possess DNA sequence with homology to human protectin (CD59), a complement lysis restricting factor, we tested the hypothesis that host CD59 acquisition by T. vaginalis organisms mediates resistance to complement killing. This hypothesis was based on the fact that trichomonads are known to associate with host proteins. No CD59 was detected on the surface of T. vaginalis grown in serum-based medium using as probe anti-CD59 monoclonal antibody (MAb). We, therefore, infected mice intraperitoneally with live T. vaginalis, and trichomonads harvested from ascites were tested for binding of CD59. Immunofluorescence showed that parasites had surface CD59. Furthermore, as mouse erythrocytes (RBCs) possess membrane-associated CD59, and trichomonads use RBCs as a nutrient source, organisms were co-cultured with murine RBCs for one week. Parasites were shown to have detectable surface CD59. Importantly, live T. vaginalis with bound CD59 were compared with batch-grown parasites without surface-associated CD59 for sensitivity to complement in human serum. Trichomonads without surface-bound CD59 had a higher level of killing by complement than did parasites with surface CD59. These data show that host CD59 acquired onto the surface by live T. vaginalis may be an alternative mechanism for complement evasion. We describe a novel strategy by T. vaginalis consistent with host protein procurement by this parasite to evade the lytic action of complement.

  12. Description of an elasmobranch TCR coreceptor: CD8α from Rhinobatos productus

    Science.gov (United States)

    Hansen, J.D.; Farrugia, T.J.; Woodson, J.; Laing, K.J.

    2011-01-01

    Cell-mediated immunity plays an essential role for the control and eradication of intracellular pathogens. To learn more about the evolutionary origins of the first signal (Signal 1) for T-cell activation, we cloned CD8α from an elasmobranch, Rhinobatos productus. Similar to full-length CD8α cDNAs from other vertebrates, Rhpr-CD8α (1800 bp) encodes a 219 amino acid open reading frame composed of a signal peptide, an extracellular IgSF V domain and a stalk/hinge region followed by a well-conserved transmembrane domain and cytoplasmic tail. Overall, the mature Rhpr-CD8α protein (201 aa) displays ~30% amino acid identity with mammalian CD8α including absolute conservation of cysteine residues involved in the IgSf V domain fold and dimerization of CD8αα and CD8αβ. One prominent feature is the absence of the LCK association motif (CXC) that is needed for achieving signal 1 in tetrapods. Both elasmobranch and teleost CD8α protein sequences possess a similar but distinctly different motif (CXH) in the cytoplasmic tail. The overall genomic structure of CD8α has been conserved during the course of vertebrate evolution both for the number of exons and phase of splicing. Finally, quantitative RTPCR demonstrated that elasmobranch CD8α is expressed in lymphoid-rich tissues similar to CD8 in other vertebrates. The results from this study indicate the existence of CD8 prior to the emergence of the gnathostomes (>450 MYA) while providing evidence that the canonical LCK association motif in mammals is likely a derived characteristic of tetrapod CD8α, suggesting potential differences for T-cell education and activation in the various gnathostomes.

  13. Critical role for CD8 T cells in allograft acceptance induced by DST and CD40/CD154 costimulatory blockade.

    Science.gov (United States)

    Gao, Donghong; Lunsford, Keri E; Eiring, Anna M; Bumgardner, Ginny L

    2004-07-01

    Donor-specific transfusion (DST) and CD40/CD154 costimulation blockade is a powerful immunosuppressive strategy which prolongs survival of many allografts. The efficacy of DST and anti-CD154 mAb for prolongation of hepatocellular allograft survival was only realized in C57BL/6 mice that have both CD4- and CD8-dependent pathways available (median survival time, MST, 82 days). Hepatocyte rejection in CD8 KO mice which is CD4-dependent was not suppressed by DST and anti-CD154 mAb treatment (MST, 7 days); unexpectedly DST abrogated the beneficial effects of anti-CD154 mAb for suppression of hepatocyte rejection (MST, 42 days) and on donor-reactive alloantibody production. Hepatocyte rejection in CD4 KO mice which is CD8-dependent was suppressed by treatment with DST and anti-CD154 mAb therapy (MST, 35 days) but did not differ significantly from immunotherapy with anti-CD154 mAb alone (MST, 32 days). Induction of hepatocellular allograft acceptance by DST and anti-CD154 mAb immunotherapy was dependent on host CD8(+) T cells, as demonstrated by CD8 depletion studies in C57BL/6 mice (MST, 14 days) and CD8 reconstitution of CD8 KO mice (MST, 56 days). These studies demonstrate that both CD4(+) and CD8(+) T-cell subsets contribute to induction of hepatocellular allograft acceptance by this immunotherapeutic strategy.

  14. IBIC analysis of CdTe/CdS solar cells

    CERN Document Server

    Colombo, E; Calusi, S; Giuntini, L; Giudice, A Lo; Manfredotti, C; Massi, M; Olivero, P; Romeo, A; Romeo, N; Vittone, E

    2016-01-01

    This paper reports on the investigation of the electronic properties of a thin film CdS/CdTe solar cell with the Ion Beam Induced Charge (IBIC) technique. The device under test is a thin film (total thickness around 10 um) multilayer heterojunction solar cell, displaying an efficiency of 14% under AM1.5 illumination conditions. The IBIC measurements were carried out using focused 3.150 MeV He ions raster scanned onto the surface of the back electrode. The charge collection efficiency (CCE) maps show inhomogeneous response of the cell to be attributed to the polycrystalline nature of the CdTe bulk material. Finally, the evolution of the IBIC signal vs. the ion fluence was studied in order to evaluate the radiation hardness of the CdS/CdTe solar cells in view of their use in solar modules for space applications.

  15. Genomic Encyclopedia of Fungi

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-08-10

    Genomes of fungi relevant to energy and environment are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 150 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such parts suggested by comparative genomics and functional analysis in these areas are presented here.

  16. JGI Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor V.

    2011-03-14

    Genomes of energy and environment fungi are in focus of the Fungal Genomic Program at the US Department of Energy Joint Genome Institute (JGI). Its key project, the Genomics Encyclopedia of Fungi, targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts), and explores fungal diversity by means of genome sequencing and analysis. Over 50 fungal genomes have been sequenced by JGI to date and released through MycoCosm (www.jgi.doe.gov/fungi), a fungal web-portal, which integrates sequence and functional data with genome analysis tools for user community. Sequence analysis supported by functional genomics leads to developing parts list for complex systems ranging from ecosystems of biofuel crops to biorefineries. Recent examples of such 'parts' suggested by comparative genomics and functional analysis in these areas are presented here

  17. The biological difference between CD13+CD133+ and CD13¬CD133¬liver cancer cells and its clinical significance

    Directory of Open Access Journals (Sweden)

    Shi-long JIN

    2013-09-01

    Full Text Available Objective To compare the biological difference between CD13+CD133+ and CD13-CD133- hepatocellular carcinoma (HCC cells in HuH7 cell line and its clinical significance. Methods The status of proliferation, phase of the cell cycle, tumor formation in vivo, differentiation, and their chemoresistance to 5-FU and pirarubicin of CD13+CD133+ and CD13-CD133-HCC cells were studied to analyze the clinical implication of CD13+CD133+HCC cell subset. Results The proliferation rate of CD13+CD133+HCC cells was significantly higher than that of CD13-CD133-HCC cells. The cell-cycle phase study showed that 78.45% of the CD13+CD133+HCC cells were in the G0/G1 phase, 2.19% in G2/M phase, and 19.36% in S phase, while 62.18% CD13-CD133-HCC cells were in the G0/G1 phase, 11.88% in G2/M phase, and 25.95% in S phase. Limiting dilution analysis of HuH7 cells revealed that 1×103 CD13+CD133+ cells could form the tumor, while 1×105 CD13-CD133- cells did. CD13+CD133+ cells showed chemoresistance to 5-FU and pirarubicin, while other three subsets succumbed to the drugs. Conclusion CD13+CD133+ cancer cells in HuH7 showed the characteristics of cancer stem cells (CSCs, which might contribute to the relapse and metastasis of liver cancer, and they may be the main target for chemotherapy in human liver cancer.

  18. Genetic Variance in Cadmium Tolerance and Accumulation in Wheat Materials Differing in Ploidy and Genome at Seedling Stage

    DEFF Research Database (Denmark)

    Ci, D; Jiang, D; Wollenweber, B;

    2010-01-01

    Cadmium (Cd) tolerance and accumulation in wheat varieties differing in ploidy and genome were investigated at seedling stage under controlled environmental conditions. The wheat varieties included six diploid, eight tetraploid, seven hexaploid and three octoploid species together with wheat rela...

  19. Syntheis and Photocurrent Performance of Graphene Oxide-CdTe/CdS Nanocomposite.

    Science.gov (United States)

    Ding, Liyun; Zhang, Bingyu; Li, Tao; Huang, Jun; Fan, Xiaochun

    2015-12-01

    Graphene with two-dimensional carbon nanostructures provides a potent strategy to enhance optoelectronic performance of semiconductor nanoparticles based light harvesting assemblies. Graphene oxide-CdTe/CdS (GO-CdTe/CdS) nanocomposites were successfully prepared by CdTe/CdS quantum dots (QDs) formed on the surface of graphene oxide sheets. The structure and optical properties of GO-CdTe/CdS nanocomposites were studied in detail. Photoluminescence measurements showed that the integration of CdTe/CdS QDs with graphene oxide significantly decreased its photoluminescence, which indicated effective transfer of photo-excited electrons from CdTe/CdS to graphene oxide. The generation of photocurrent on illumination of the GO-CdTe/CdS nanocomposite was studied. Significant enhancement in photocurrent induced by GO in CdTe/CdS QDs film had also been demonstrated due to increasing the charge separation and electron conduction.

  20. Differential number of CD34+, CD133+ and CD34+/CD133+ cells in peripheral blood of patients with congestive heart failure

    Directory of Open Access Journals (Sweden)

    Fritzenwanger M

    2009-03-01

    Full Text Available Abstract Background Endothelial progenitor cells (EPC which are characterised by the simulateous expression of CD34, CD133 and vascular endothelial growth receptor 2 (VEGF 2 are involved in the pathophysiology of congestive heart failure (CHF and their number and function is reduced in CHF. But so far our knowledge about the number of circulating hematopoietic stem/progenitor cells (CPC expressing the early hematopoietic marker CD133 and CD34 in CHF is spares and therefore we determined their number and correlated them with New York Heart Association (NYHA functional class. Methods CD34 and CD133 surface expression was quantified by flow cytometry in the peripheral venous blood of 41 healthy adults and 101 patients with various degrees of CHF. Results CD34+, CD133+ and CD34+/CD133+ cells correlated inversely with age. Both the number of CD34+ and of CD34+/CD133+ cells inversely correlated with NYHA functional class. The number of CD133+ cells was not affected by NYHA class. Furthermore the number of CD133+ cells did not differ between control and CHF patients. Conclusion In CHF the release of CD34+, CD133+ and CD34+/CD133+ cells from the bone marrow seems to be regulated differently. Modulating the releasing process in CHF may be a tool in CHF treatment.

  1. Recrystallization and sulfur diffusion in CdCl{sub 2}-treated CdTe/CdS thin films

    Energy Technology Data Exchange (ETDEWEB)

    McCandless, B.E.; Moulton, L.V.; Birkmire, R.W. [University of Delaware, Newark, DE (United States). Inst. of Energy Conversion

    1997-08-01

    The role of CdCl{sub 2} in prompting recrystallization, grain growth and interdiffusion between CdS and CdTe layers in physical vapor-deposited CdS/CdTe thin-film solar cells is presented. Several CdTe/CdS thin-film samples with different CdTe film thicknesses were treated in air at 415{sup o}C for different times with and without a surface coating of CdCl{sub 2}. The samples were characterized by scanning electron microscopy, transmission electron microscopy, energy dispersive x-ray spectroscopy, x-ray diffractometry and optical absorption. The results show that CdCl{sub 2} treatment enhances the recrystallization and diffusion processes, leading to a compositional variation within the CdTe layer due to diffusion of sulfur from the CdS. The highest sulfur concentrations observed after 30 min treatments with CdCl{sub 2} at 415{sup o}C are near the solubility limit for sulfur in CdTe. The compositional distributions indicated by x-ray diffraction measurements of samples with different CdTe thickness show that the S-rich CdTe{sub 1-x}S{sub x} region lies near the CdTe/CdS interface. A multiple-step mixing process must be inferred to account for the diffraction profiles obtained. (author)

  2. CD4+CD25+ regulatory T lymphocytes in tuberculous pleural effusion

    Institute of Scientific and Technical Information of China (English)

    QIN Xue-jun; SHI Huan-zhong; LIANG Qiu-li; HUANG Lu-ying; YANG Hai-bo

    2008-01-01

    Background Active suppression by CD4+CD25+ regulatory T lymphocytes plays an important role in the down-regulation of T cell responses to foreign and self-antigens.This study was conducted to analyze whether the CD4+CD25+ regulatory T cells exist and function normally in tuberculous pleural effusion.Methods The percentages of CD4+CD25+ T cells in pleural effusion and peripheral blood from patients with tuberculous pleurisy and peripheral blood from healthy control subjects were determined by flow cytometry.The expression of forkhead transcription factor Foxp3 was also examined.CD4+CD25+ and CD4+CD25- T cells from pleural effusion and blood were isolated,and were cultured to observe the effects Of CD4+CD25+ T cells on proliferation response of CD4+CD25- T cells in Vitro.Results There were increased numbers of CD4+CD25+ T cells in tuberculous pleural effusion compared with peripheral blood from both patients with tuberculous pleurisy and normal subjects,and these cells demonstrated a constitutive high-level expression of Foxp3.Moreover,CD4+CD25+ T cells mediated potent inhibition of proliferation response of CD4+CD25- T cells.Conclusion The increased CD4+CD25+ T cells in tuberculous pleu ral effusion express a high level of Foxp3 transcription factor,while potently suppressing the proliferation of CD4+CD25- T cells.

  3. Genomic Data Commons | Office of Cancer Genomics

    Science.gov (United States)

    The NCI’s Center for Cancer Genomics launches the Genomic Data Commons (GDC), a unified data sharing platform for the cancer research community. The mission of the GDC is to enable data sharing across the entire cancer research community, to ultimately support precision medicine in oncology.

  4. Directed genome engineering for genome optimization.

    Science.gov (United States)

    D'Halluin, Kathleen; Ruiter, Rene

    2013-01-01

    The ability to develop nucleases with tailor-made activities for targeted DNA double-strand break induction at will at any desired position in the genome has been a major breakthrough to make targeted genome optimization feasible in plants. The development of site specific nucleases for precise genome modification has expanded the repertoire of tools for the development and optimization of traits, already including mutation breeding, molecular breeding and transgenesis.Through directed genome engineering technology, the huge amount of information provided by genomics and systems biology can now more effectively be used for the creation of plants with improved or new traits, and for the dissection of gene functions. Although still in an early phase of deployment, its utility has been demonstrated for engineering disease resistance, herbicide tolerance, altered metabolite profiles, and for molecular trait stacking to allow linked transmission of transgenes. In this article, we will briefly review the different approaches for directed genome engineering with the emphasis on double strand break (DSB)-mediated engineering to-wards genome optimization for crop improvement and towards the acceleration of functional genomics.

  5. Comparative Genome Analysis and Genome Evolution

    NARCIS (Netherlands)

    Snel, Berend

    2003-01-01

    This thesis described a collection of bioinformatic analyses on complete genome sequence data. We have studied the evolution of gene content and find that vertical inheritance dominates over horizontal gene trasnfer, even to the extent that we can use the gene content to make genome phylogenies. Usi

  6. No association of polymorphisms in human endogenous retrovirus K18 and CD48 with schizophrenia

    DEFF Research Database (Denmark)

    Nyegaard, Mette; Demontis, Ditte; Thestrup, Britta Boserup;

    2012-01-01

    The human endogenous retrovirus HERV-K18 is located within intron 1 of CD48 on chromosome 1q and is still active in the human genome. Genetic variation in HERV-K18 single-nucleotide polymorphisms (SNPs) has previously been associated with an increased risk of schizophrenia (SZ) and with type 2...

  7. Stripe structure CdTe-CdZnTe-CdTe in a bulk single crystal

    Science.gov (United States)

    Azoulay, M.; Sinvani, M.; Mizrachi, M.; Feldstein, H.

    1994-03-01

    In this paper we present a study that was aimed at performing a selective diffusion of Zn into CdTe. A single crystal CdTe wafer fabricated into a "tooth-like" structure which was further subjected to high temperature annealing in the presence of Zn vapour. The sample was then cut parallel to the diffusion direction and a Zn concentration analysis, using an electron microprobe, was performed. As expected, the stripe structure CdTe-CdZnTe-CdTe has been confirmed. The Zn decay profiles were fitted to a modified diffusion model, suggesting a bulk diffusion mechanism coupled with a surface reaction. Practical implementation of this stripe structure for an infrared light waveguide is being evaluated.

  8. Genomic Data Commons launches

    Science.gov (United States)

    The Genomic Data Commons (GDC), a unified data system that promotes sharing of genomic and clinical data between researchers, launched today with a visit from Vice President Joe Biden to the operations center at the University of Chicago.

  9. Rat Genome Database (RGD)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Rat Genome Database (RGD) is a collaborative effort between leading research institutions involved in rat genetic and genomic research to collect, consolidate,...

  10. National Human Genome Research Institute

    Science.gov (United States)

    ... the Director Organization Reports & Publications Español The National Human Genome Research Institute conducts genetic and genomic research, funds ... Landscape Social Media Videos Image Gallery Fact Sheets Human Genome Project Clinical Studies Genomic Careers DNA Day Calendar ...

  11. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribut...

  12. Genomic Prediction in Barley

    DEFF Research Database (Denmark)

    Edriss, Vahid; Cericola, Fabio; Jensen, Jens D;

    2015-01-01

    Genomic prediction uses markers (SNPs) across the whole genome to predict individual breeding values at an early growth stage potentially before large scale phenotyping. One of the applications of genomic prediction in plant breeding is to identify the best individual candidate lines to contribut...

  13. Chicken's Genome Decoded

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ After completing the work on mapping chicken genome sequence and chicken genome variation in early March, 2004, two international research consortiums have made significant progress in reading the maps, shedding new light on the studies into the first bird as well as the first agricultural animal that has its genome sequenced and analyzed in the world.

  14. Different responses of low grain-Cd-accumulating and high grain-Cd-accumulating rice cultivars to Cd stress.

    Science.gov (United States)

    Wang, Feijuan; Wang, Min; Liu, Zhouping; Shi, Yan; Han, Tiqian; Ye, Yaoyao; Gong, Ning; Sun, Junwei; Zhu, Cheng

    2015-11-01

    Cadmium (Cd) is a major heavy metal pollutant which is highly toxic to plants and animals. The accumulation of Cd in rice grains is a major agricultural problem in regions with Cd pollution. A hydroponics experiment using low grain-Cd-accumulating rice (xiushui 11) and high grain-Cd-accumulating rice (xiushui 110) was carried out to characterize the different responses of rice cultivars to Cd stress. We found that xiushui 11 was more tolerant to Cd than xiushui 110, and xiushui 11 suffered less oxidative damage. Cell walls played an important role in limiting the amount of Cd that entered the protoplast, especially in xiushui 11. Cd stored in organelles as soluble fractions, leading to greater physiological stress of Cd detoxification. We found that Cd can disturb the ion homeostasis in rice roots because Cd(2+) and Ca(2+) may have a similar uptake route. Xiushui 11 had a faster root-to-shoot transport of Cd, and the expression level of OsPCR1 gene which was predicted related with Cd accumulation in rice was consist with the Cd transport of root-to-shoot in rice and maintain the greater Cd tolerance of xiushui 11. These results suggest there are different Cd detoxification and accumulation mechanisms in rice cultivars.

  15. Adsorption properties of CdS-CdTe system semiconductors

    Science.gov (United States)

    Kirovskaya, I. A.; Nor, P. E.

    2013-12-01

    The adsorption of carbon(II) oxide and ammonia on nanofilms of solid solutions and binary compounds of the CdS-CdTe system is studied by means of piezoquartz microweighing, FTIR IR, and measuring electroconductivity. Allowing for the conditions and composition of semiconductor systems, we determine the mechanisms and principles of adsorption processes by analyzing the α p = f( T), α T = f( p), and α T = f( t) experimental dependences; IR spectra; the thermodynamic and kinetic characteristics of adsorption; the acid-base, electrophysical, and other characteristics of adsorbents; the electron nature of adsorbate molecules; and the obtained acid-base characteristics: the composition and adsorption characteristics and composition state diagrams. Previous statements on the nature and retention of local active centers responsible for adsorption and catalytic processes upon changes in their habitus and composition (as components of systems of the AIIIBV-AIIBVI and AIIBVI-AIIBVI types) on the surface of diamond-like semiconductors are confirmed. Specific features of the behavior of (CdS) x (CdTe)1 - x solid solutions are identified in addition to general features with binary compounds (CdS, CdTe), as is demonstrated by the presence of critical points on acid-base characteristics-composition and adsorption characteristics-composition diagrams. On the basis of these diagrams, the most active adsorbents (with respect to CO and NH3) used in designing highly sensitive and selective sensors are identified.

  16. Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy

    Science.gov (United States)

    Sotillo, Elena; Barrett, David M.; Black, Kathryn L; Bagashev, Asen; Oldridge, Derek; Wu, Glendon; Sussman, Robyn; Lanauze, Claudia; Ruella, Marco; Gazzara, Matthew R.; Martinez, Nicole M.; Harrington, Colleen T.; Chung, Elaine Y.; Perazzelli, Jessica; Hofmann, Ted J.; Maude, Shannon L.; Raman, Pichai; Barrera, Alejandro; Gill, Saar; Lacey, Simon F.; Melenhorst, Jan J.; Allman, David; Jacoby, Elad; Fry, Terry; Mackall, Crystal; Barash, Yoseph; Lynch, Kristen W.; Maris, John M.; Grupp, Stephan A.; Thomas-Tikhonenko, Andrei

    2015-01-01

    The CD19 antigen, expressed on most B-cell acute lymphoblastic leukemias (B-ALL), can be targeted with chimeric antigen receptor–armed T cells (CART-19), but relapses with epitope loss occur in 10% to 20% of pediatric responders. We detected hemizygous deletions spanning the CD19 locus and de novo frameshift and missense mutations in exon 2 of CD19 in some relapse samples. However, we also discovered alternatively spliced CD19 mRNA species, including one lacking exon 2. Pull-down/siRNA experiments identified SRSF3 as a splicing factor involved in exon 2 retention, and its levels were lower in relapsed B-ALL. Using genome editing, we demonstrated that exon 2 skipping bypasses exon 2 mutations in B-ALL cells and allows expression of the N-terminally truncated CD19 variant, which fails to trigger killing by CART-19 but partly rescues defects associated with CD19 loss. Thus, this mechanism of resistance is based on a combination of deleterious mutations and ensuing selection for alternatively spliced RNA isoforms. Significance CART-19 yield 70% response rates in patients with B-ALL, but also produce escape variants. We discovered that the underlying mechanism is the selection for preexisting alternatively spliced CD19 isoforms with the compromised CART-19 epitope. This mechanism suggests a possibility of targeting alternative CD19 ectodomains, which could improve survival of patients with B-cell neoplasms. PMID:26516065

  17. Zebrafish CD59 has both bacterial-binding and inhibiting activities.

    Science.gov (United States)

    Sun, Chen; Wu, Jie; Liu, Shousheng; Li, Hongyan; Zhang, Shicui

    2013-10-01

    CD59, known as protectin, usually plays roles as a regulatory inhibitor of complement, but it also exhibits activities independent of its function as a complement inhibitor. This study reported the identification and characterization of an ortholog of mammalian cd59 from zebrafish Danio rerio, which is similar to known cd59 in terms of both amino acid sequence and genomic structure as well as synteny conservation. We showed that zebrafish cd59 was maternally expressed in early embryos and expressed in a tissue-specific manner, with most abundant expression in the brain. We further showed that recombinant zebrafish CD59 was capable of binding to both the Gram-negative and Gram-positive bacteria as well as the microbial signature molecules LPS and LTA. In addition we demonstrated that recombinant zebrafish CD59 displayed slight antimicrobial activity capable of inhibiting the growth of E. coli and S. aureus. All these data indicate that zebrafish CD59 can not only binds to the bacteria and their signature molecules LPS and LTA but can also inhibit their growth, a novel role assigned to CD59.

  18. [Genomics and functional genomics in microbiology].

    Science.gov (United States)

    Encarnación-Guevara, Sergio

    2006-01-01

    Functional genomics is changing our understanding of biology and changing our approach to biological research. It brings about concerted, high-throughput genetics with analyses of gene transcripts, proteins, and metabolites to answer the ultimate question posed by all genome-sequencing projects: what is the biological function of each and every gene? Functional genomics is stimulating a change in the research paradigm away from the analysis of single genes, proteins, or metabolites towards the analysis of each of these parameters on a global scale. By identifying and measuring several, if not the entire, molecular group of actors that take part in a given biological process, functional genomics offers the panorama of obtaining a truly holistic representation of life. Functional genomics methods are defined by high-throughput methods which are, not necessarily hypothesis-dependent. They offer insights into mRNA expression, protein expression, protein localization, and protein interactions and may cast light on the flow of information within signaling pathways. At its beginning, biology involved observing nature and experimenting on its isolated parts. Genomic research now generates new types of complex observational data derived from nature. This review describes the tools that are currently being used for functional genomics work and considers the impact that this new discipline on microbiology research.

  19. Genomic taxonomy of vibrios

    DEFF Research Database (Denmark)

    Thompson, Cristiane C.; Vicente, Ana Carolina P.; Souza, Rangel C.

    2009-01-01

    . RESULTS: We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide...... a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains...

  20. A genome blogger manifesto

    Directory of Open Access Journals (Sweden)

    Corpas Manuel

    2012-10-01

    Full Text Available Abstract Cheap prices for genomic testing have revolutionized consumers’ access to personal genomics. Exploration of personal genomes poses significant challenges for customers wishing to learn beyond provider customer reports. A vibrant community has spontaneously appeared blogging experiences and data as a way to learn about their personal genomes. No set of values has publicly been described to date encapsulating ideals and code of conduct for this community. Here I present a first attempt to address this vacuum based on my own personal experiences as genome blogger.

  1. Cis and trans acting factors involved in human cytomegalovirus experimental and natural latent infection of CD14 (+ monocytes and CD34 (+ cells.

    Directory of Open Access Journals (Sweden)

    Cyprian C Rossetto

    Full Text Available The parameters involved in human cytomegalovirus (HCMV latent infection in CD14 (+ and CD34 (+ cells remain poorly identified. Using next generation sequencing we deduced the transcriptome of HCMV latently infected CD14 (+ and CD34 (+ cells in experimental as well as natural latency settings. The gene expression profile from natural infection in HCMV seropositive donors closely matched experimental latency models, and included two long non-coding RNAs (lncRNAs, RNA4.9 and RNA2.7 as well as the mRNAs encoding replication factors UL84 and UL44. Chromatin immunoprecipitation assays on experimentally infected CD14 (+ monocytes followed by next generation sequencing (ChIP-Seq were employed to demonstrate both UL84 and UL44 proteins interacted with the latent viral genome and overlapped at 5 of the 8 loci identified. RNA4.9 interacts with components of the polycomb repression complex (PRC as well as with the MIE promoter region where the enrichment of the repressive H3K27me3 mark suggests that this lncRNA represses transcription. Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE, which identifies nucleosome-depleted viral DNA, was used to confirm that latent mRNAs were associated with actively transcribed, FAIRE analysis also showed that the terminal repeat (TR region of the latent viral genome is depleted of nucleosomes suggesting that this region may contain an element mediating viral genome maintenance. ChIP assays show that the viral TR region interacts with factors associated with the pre replication complex and a plasmid subclone containing the HCMV TR element persisted in latently infected CD14 (+ monocytes, strongly suggesting that the TR region mediates viral chromosome maintenance.

  2. Extensive Citrus Triploid Breeding by Crossing Monoembryonic Diploid Females with Allotetraploid Male Parents%单胚性二倍体为母本与异源四倍体杂交大规模创制柑橘三倍体

    Institute of Scientific and Technical Information of China (English)

    解凯东; 王惠芹; 王晓培; 梁武军; 谢宗周; 伊华林; 邓秀新; Grosser Jude W; 郭文武

    2013-01-01

    [目的]以单胚性的二倍体柑橘品种为母本与异源四倍体体细胞杂种杂交培育三倍体植株。[方法]选择亲本配置杂交组合进行人工授粉,授粉后70-100 d采幼果进行胚挽救,以流式细胞仪结合根尖染色体压片对再生植株进行倍性检测,最后进行SSR分子标记鉴定。[结果]2009-2012连续4年,以8个二倍体为母本、以4个异源四倍体体细胞杂种为父本,共配置14个倍性杂交组合,授粉花数3347朵,坐果数678个,平均坐果率20.26%。实施胚挽救的果实数505个,培养种子12357粒,经生芽、生根诱导培养共获得1022个株系。通过对再生植株的倍性检测,共获得三倍体植株755个株系,四倍体19个株系。对华农红柚× NH组合的三倍体、四倍体后代进行分子鉴定,表明三倍体和四倍体全部为双亲的有性杂种后代。[结论]本研究通过杂交获得的三倍体为我国无籽柑橘品种选育奠定了材料基础;同时获得的四倍体后代也为未来的柑橘三倍体育种提供了优良的亲本材料。%[Objective] The objective of this experiment is to produce citrus triploid hybrids by interploid crossing between elite monoembryonic diploid varieties as female parents and allotetraploid somatic hybrids.[Method]Pollinations were carried out between the selected male and female parents. Fruits were collected at 70-100 d after pollination and immature seeds were cultured in vitro. Ploidy level of the plantlets was determined by flow cytometry and chromosome counting. The genetic origin of triploids and tetraploids was analyzed by SSR markers.[Result] In successive four years from 2009 to 2012, 14 ploidy crosses using eight diploid cultivars as seed parents and four allotetraploid somatic hybrids as pollen parents, were carried out with a total of 3 347 flowers pollinated. With 678 fruits harvested, an average fruit set ratio of 20.26% was obtained. As a result, 1 022 plants were

  3. Initial viral load determines the magnitude of the human CD8 T cell response to yellow fever vaccination.

    Science.gov (United States)

    Akondy, Rama S; Johnson, Philip L F; Nakaya, Helder I; Edupuganti, Srilatha; Mulligan, Mark J; Lawson, Benton; Miller, Joseph D; Pulendran, Bali; Antia, Rustom; Ahmed, Rafi

    2015-03-10

    CD8 T cells are a potent tool for eliminating intracellular pathogens and tumor cells. Thus, eliciting robust CD8 T-cell immunity is the basis for many vaccines under development. However, the relationship between antigen load and the magnitude of the CD8 T-cell response is not well-described in a human immune response. Here we address this issue by quantifying viral load and the CD8 T-cell response in a cohort of 80 individuals immunized with the live attenuated yellow fever vaccine (YFV-17D) by sampling peripheral blood at days 0, 1, 2, 3, 5, 7, 9, 11, 14, 30, and 90. When the virus load was below a threshold (peak virus load < 225 genomes per mL, or integrated virus load < 400 genome days per mL), the magnitude of the CD8 T-cell response correlated strongly with the virus load (R(2) ∼ 0.63). As the virus load increased above this threshold, the magnitude of the CD8 T-cell responses saturated. Recent advances in CD8 T-cell-based vaccines have focused on replication-incompetent or single-cycle vectors. However, these approaches deliver relatively limited amounts of antigen after immunization. Our results highlight the requirement that T-cell-based vaccines should deliver sufficient antigen during the initial period of the immune response to elicit a large number of CD8 T cells that may be needed for protection.

  4. UCSC genome browser tutorial.

    Science.gov (United States)

    Zweig, Ann S; Karolchik, Donna; Kuhn, Robert M; Haussler, David; Kent, W James

    2008-08-01

    The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/.

  5. Effect of Homoharringtonine on Bone Morrow CD34+CD7+ Cells in Chronic Granulocytic Leukemia

    Institute of Scientific and Technical Information of China (English)

    LI Yu-feng; DENG Zhi-kui; XUAN Heng-bao; CHEN Bao-an

    2007-01-01

    Objective: To explore the effect of homoharringtonine (HHT) on bone morrow CD34+CD7+ cells in chronic granulocytic leukemia (CGL). Methods: The changes of bone morrow CD34+CD7+ cells were observed after the treatment of HHT in 23 cases with CGL. The proliferation and apoptosis of CD34+CD7+ cells treated with HHT in vitro were studied. Results: The proportion of CD34+CD7+ cells in CGL (0.145±0.021) was higher than that of normal control (0.052±0.013). The proportion of CD34+CD7+ cells in patients who got cytogenetic responses to HHT (0.072±0.020) decreased remarkably, but not in those patients who did not got cytogenetic responses to HHT, (0.137±0.023). the proliferation of CD34+ cells was inhibited and the proportion of CD34+CD7+ cells decreased after cultured with HHT (0.134 in 24 h, 0.126 in 48 h and 0.102 in 72). The apoptosis rate of CD34+CD7+ cells was higher than that in CD34+CD7- cells (35.39%±4.39% versus 24.57%(4.01%, P<0.05) 72 h after culture with HHT. Conclusion: The proportion of CD34+CD7+ cells in CGL was higher than that of normal control and HHT may inhibit the proliferation and induce apoptosis of bone marrow CD34+CD7+ cells.

  6. Impact of CdS annealing atmosphere on the performance of CdS–CdTe solar cell

    Energy Technology Data Exchange (ETDEWEB)

    Maticiuc, N., E-mail: nataliamaticiuc@yahoo.com; Spalatu, N.; Mikli, V.; Hiie, J.

    2015-09-30

    Highlights: • Annealed CdS films are used for CdTe based solar cells. • CdS–CdTe solar cell with air annealed CdS shows better performance. • The air annealed CdS brings the O{sub 2} and chloride at the place of junction formation. • H{sub 2} removes the oxygen containing compounds from CdS grain boundaries. - Abstract: CdS thin films obtained by chemical bath deposition and annealed in hydrogen and air ambients were combined with CdTe absorbers obtained by close spaced sublimation. CdS–CdTe solar cells in superstrate configuration were characterized by current–voltage and quantum efficiency measurements while the analysis of annealed CdS films was made by scanning electron microscopy, X-ray diffraction and UV–vis spectroscopy. It was found that in superstrate configuration, due to the big grains on CdS surface and gas emission from CdS film at high temperature deposition of the absorber, the delamination of layers take place. Annealing in H{sub 2} removes the oxygen compounds from CdS grain boundaries and opens them for formation of shortcutting through the CdS layer. The processing in air is most advantageous due to simultaneous presence of chloride and oxygen, contributing to the recrystallization and sintering of the highly textured columnar CdS. The direct influence of the CdS annealing on the solar cell parameters is shown for CdS–CdTe solar cell.

  7. Whole-exome/genome sequencing and genomics.

    Science.gov (United States)

    Grody, Wayne W; Thompson, Barry H; Hudgins, Louanne

    2013-12-01

    As medical genetics has progressed from a descriptive entity to one focused on the functional relationship between genes and clinical disorders, emphasis has been placed on genomics. Genomics, a subelement of genetics, is the study of the genome, the sum total of all the genes of an organism. The human genome, which is contained in the 23 pairs of nuclear chromosomes and in the mitochondrial DNA of each cell, comprises >6 billion nucleotides of genetic code. There are some 23,000 protein-coding genes, a surprisingly small fraction of the total genetic material, with the remainder composed of noncoding DNA, regulatory sequences, and introns. The Human Genome Project, launched in 1990, produced a draft of the genome in 2001 and then a finished sequence in 2003, on the 50th anniversary of the initial publication of Watson and Crick's paper on the double-helical structure of DNA. Since then, this mass of genetic information has been translated at an ever-increasing pace into useable knowledge applicable to clinical medicine. The recent advent of massively parallel DNA sequencing (also known as shotgun, high-throughput, and next-generation sequencing) has brought whole-genome analysis into the clinic for the first time, and most of the current applications are directed at children with congenital conditions that are undiagnosable by using standard genetic tests for single-gene disorders. Thus, pediatricians must become familiar with this technology, what it can and cannot offer, and its technical and ethical challenges. Here, we address the concepts of human genomic analysis and its clinical applicability for primary care providers.

  8. CdS/CdTe Solar Cells Containing Directly Deposited CdSxTe1-x Alloy Layers: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Duenow, J. N.; Dhere, R. G.; Moutinho, H. R.; To, B.; Pankow, J. W.; Kuciauskas, D.; Gessert, T. A.

    2011-07-01

    A CdSxTe1-x layer forms by interdiffusion of CdS and CdTe during the fabrication of thin-film CdTe photovoltaic (PV) devices. The CdSxTe1-x layer is thought to be important because it relieves strain at the CdS/CdTe interface that would otherwise exist due to the 10% lattice mismatch between these two materials. Our previous work [1] has indicated that the electrical junction is located in this interdiffused CdSxTe1-x region. Further understanding, however, is essential to predict the role of this CdSxTe1-x layer in the operation of CdS/CdTe devices. In this study, CdSxTe1-x alloy films were deposited by radio-frequency (RF) magnetron sputtering and co-evaporation from CdTe and CdS sources. Both RF-magnetron-sputtered and co-evaporated CdSxTe1-x films of lower S content (x<0.3) have a cubic zincblende (ZB) structure akin to CdTe, whereas those of higher S content have a hexagonal wurtzite (WZ) structure like that of CdS. Films become less preferentially oriented as a result of a CdCl2 heat treatment (HT) at ~400 degrees C for 5 min. Films sputtered in a 1% O2/Ar ambient are amorphous as deposited, but show CdTe ZB, CdS WZ, and CdTe oxide phases after a CdCl2 HT. Films sputtered in O2 partial pressure have a much wider bandgap than expected. This may be explained by nanocrystalline size effects seen previously [2] for sputtered oxygenated CdS (CdS:O) films. Initial PV device results show that the introduction of a directly-deposited CdSxTe1-x alloy layer into the device structure produces devices of comparable performance to those without the alloy layer when a CdCl2 HT is performed. Further investigation is required to determine whether the CdCl2 heat treatment step can be altered or eliminated through direct deposition of the alloy layer.

  9. Co-localization of Fyn with CD3 complex, CD45 or CD28 depends on different mechanisms.

    Science.gov (United States)

    zur Hausen, J D; Burn, P; Amrein, K E

    1997-10-01

    The Src family protein tyrosine kinase Fyn (p59fyn) plays an important role in thymocyte development and T cell receptor (TCR) signal transduction. Fyn has been shown to associate with the TCR-CD3 complex, the protein tyrosine phosphatase CD45 and several co-receptors such as CD28 which are crucial for initiating T cell activation and proliferation. The molecular basis of how Fyn is associated with these transmembrane proteins is largely unknown. To investigate the Fyn association with the TCR-CD3 complex, CD45 and CD28 at the molecular level, various Fyn/beta-galactosidase fusion proteins were constructed and expressed in Jurkat cells. Co-localization experiments applying antibody-induced co-capping and double immunofluorescence staining techniques were used to study the association of these fusion proteins with the TCR-CD3 complex, CD45 and CD28. Our results revealed that co-localization of Fyn with the TCR-CD3 complex requires the unique N terminus whereas co-localization with CD45 depends on the unique N terminus, the Src homology (SH)3- and a functional SH2 domain. CD28 co-localizes with Fyn molecules that contain the N terminus and a functional SH2 domain. These results suggest that Fyn association with the TCR-CD3 complex, CD45 and CD28 is mediated by different molecular mechanisms.

  10. The effect on CdS/CdTe solar cell conversion efficiency of the presence of fluorine in the usual CdCl2 treatment of CdTe

    OpenAIRE

    O. K. Echendu; Dharmadasa, I

    2015-01-01

    The addition of CdF2 to the CdCl2 solution used in the well-known CdCl2 treatment of CdS/CdTe solar cells has been observed to drastically improve the conversion efficiency of fully fabricated CdS/CdTe solar cells. The observed improvement is as a result of further enhancement of structural and optoelectronic properties of the CdCl2+CdF2-treated CdTe layers compared to the CdCl2-treated CdTe layers. A set of CdS/CdTe samples were grown by electrochemical deposition under different conditions ...

  11. Activation of Blood CD3+CD56+CD8+ T Cells during Pregnancy and Multiple Sclerosis

    Science.gov (United States)

    de Andrés, Clara; Fernández-Paredes, Lidia; Tejera-Alhambra, Marta; Alonso, Bárbara; Ramos-Medina, Rocío; Sánchez-Ramón, Silvia

    2017-01-01

    A striking common feature of most autoimmune diseases is their female predominance, with at least twice as common among women than men in relapsing–remitting multiple sclerosis (MS), the prevailing MS clinical form with onset at childbearing age. This fact, together with the protective effect on disease activity during pregnancy, when there are many biological changes including high levels of estrogens and progesterone, puts sex hormones under the spotlight. The role of natural killer (NK) and NKT cells in MS disease beginning and course is still to be elucidated. The uterine NK (uNK) cells are the most predominant immune population in early pregnancy, and the number and function of uNK cells infiltrating the endometrium are sex-hormones’ dependent. However, there is controversy on the role of estrogen or progesterone on circulating NK (CD56dim and CD56bright) and NKT cells’ subsets. Here, we show a significantly increased activation of CD3+CD56+CD8+ cells in pregnant MS women (MSP) compared with non-pregnant MS women (NPMS) (p pregnancy. Further studies on specific CD8+ NKT cells function and their role in pregnancy beneficial effects on MS are warranted to move forward more effective MS treatments. PMID:28280497

  12. Influence of CdS deposition technique for CdS/CdTe solar cells applications

    Science.gov (United States)

    Rubio, Sandra; Plaza, José Luis; Diéguez, Ernesto

    2014-09-01

    The manufacturing of an optimal window layer is essential for a high efficiency solar cell. CdS thin films were deposited on FTO commercial substrates by two different techniques: Chemical Bath Deposition (CBD), and Closed Space Sublimation (CSS) using SiC rods as electrical heating elements. The composition, morphology, and crystalline structure of the CdS thin films were analyzed by Energy Dispersive X-ray spectroscopy (EDX), Scanning Electron Microscope (SEM), and X-Ray Diffraction (XRD). CdS layers obtained by CSS have shown good stoichiometries of 51.07(Cd at %), and 48.93(S at %), with the presence of disordered microrods of hexagonal shape. The CdS films obtained by CBD exhibited certain contamination from the bath chemical components and a poor defined structure. In conclusion, the layers deposited by electric heating based CSS present a better morphology and crystal structure than the layers deposited by CBD. The CdTe absorber layer deposited by CSS electric heating also shows good cubic structure and morphology.

  13. Genome evolution of Oryza

    Directory of Open Access Journals (Sweden)

    Tieyan Liu

    2014-01-01

    Full Text Available The genus Oryza is composed of approximately 24 species. Wild species of Oryza contain a largely untapped resource of agronomically important genes. As an increasing number of genomes of wild rice species have been or will be sequenced, Oryza is becoming a model system for plant comparative, functional and evolutionary genomics studies. Comparative analyses of large genomic regions and whole-genome sequences have revealed molecular mechanisms involved in genome size variation, gene movement, genome evolution of polyploids, transition of euchromatin to heterochromatin and centromere evolution in the genus Oryza. Transposon activity and removal of transposable elements by unequal recombination or illegitimate recombination are two important factors contributing to expansion or contraction of Oryza genomes. Double-strand break repair mediated gene movement, especially non-homologous end joining, is an important source of non-colinear genes. Transition of euchromatin to heterochromatin is accompanied by transposable element amplification, segmental and tandem duplication of genic segments, and acquisition of heterochromatic genes from other genomic locations. Comparative analyses of multiple genomes dramatically improve the precision and sensitivity of evolutionary inference than single-genome analyses can provide. Further investigations on the impact of structural variation, lineage-specific genes and evolution of agriculturally important genes on phenotype diversity and adaptation in the genus Oryza should facilitate molecular breeding and genetic improvement of rice.

  14. CD4-regulatory cells in COPD patients

    DEFF Research Database (Denmark)

    Smyth, Lucy J C; Starkey, Cerys; Vestbo, Jørgen

    2007-01-01

    BACKGROUND: The numbers of airway CD8 and B lymphocytes are increased in COPD patients, suggesting an autoimmune process. CD4-regulatory T cells control autoimmunity but have not been studied in patients with COPD. OBJECTIVE: To compare T-regulatory cell numbers in the BAL from COPD patients......, smokers with normal lung function, and healthy nonsmokers (HNS). METHODS: BAL and peripheral blood mononuclear cell (PBMC) samples were obtained from 26 COPD patients, 19 smokers, and 8 HNS. Flow cytometry was performed for regulatory phenotypic markers. RESULTS: COPD patients had increased BAL CD8...... numbers compared to smokers and HNS. CD4 numbers were similar between groups. There was increased BAL CD4CD25(bright) expression in smokers (median 28.8%) and COPD patients (median 23.1%) compared to HNS (median 0%). Increased FoxP3 expression was confirmed in BAL CD4CD25(bright) cells. BAL CD4CD25 cells...

  15. Differential Diagnosis Value of CD117, CD13 and CD33 in Acute Myeloid Leukemia%CD117、CD13、CD33在鉴别诊断AML中的应用评价

    Institute of Scientific and Technical Information of China (English)

    郭冬芳

    2014-01-01

    目的:探讨CD117、CD13、CD33在鉴别诊断AML中的应用评价。方法:采用流式细胞术分析510例急性白血病患者骨髓或外周血标本的免疫表型。结果:在AML中CD117、CD13和CD33的表达率依次为91.9%、91.6%和94.4%。与急性淋巴细胞性白血病相比表达率高,有显著性意义(P<0.01)。结论:CD13、CD33和CD117在AML和ALL的鉴别诊断中具有重要意义。%Objectives:To study the differential diagnosis value of CD 117 、CD13 and CD33 in acute myeloid leukemia .Methods:The peripheral blood and bone marrow of 510 cases with acute myeloid leukemia was analyzed by flow cytometry .Results:In acute myeloid leu-kemia, the percent of expression in CD117,CD13 and CD33 was 91.9%、91.6%and 94.4%.These were significantly higher compared with acute lymphoblastic leukemia (P<0.01);Conclusion:CD117,CD13 and CD33 might be significant in differential diagnosis between acute myeloid leukemia and acute lymphoblastic leukemia .

  16. Percentages of CD4+CD161+ and CD4−CD8−CD161+ T Cells in the Synovial Fluid Are Correlated with Disease Activity in Rheumatoid Arthritis

    Directory of Open Access Journals (Sweden)

    Jinlin Miao

    2015-01-01

    Full Text Available Objective. CD161 has been identified as a marker of human IL-17-producing T cells that are implicated in the pathogenesis of rheumatoid arthritis (RA. This study aimed to investigate the potential link between the percentage of CD161+ T cells and disease activity in RA patients. Methods. Peripheral blood (PB from 54 RA patients and 21 healthy controls was evaluated. Paired synovial fluid (SF (n = 17 was analyzed. CD161 expression levels on CD4+, CD8+, and CD4−CD8− T cells were assessed by flow cytometry. Results. The percentage of CD4+CD161+ T cells in RA SF was higher than RA PB, and it was positively correlated with DAS28, erythrocyte sedimentation rate (ESR, and C-reactive protein (CRP. CD4−CD8−CD161+ T cell percentage was decreased in RA PB and was further reduced in RA SF, and its level in SF was inversely correlated with DAS28, ESR, and CRP. However, CD8+CD161+ T cell percentage was neither changed in RA PB and SF nor correlated with disease activity indices. Conclusion. An increased CD4+CD161+ T cell percentage and a decreased CD4−CD8−CD161+ T cell percentage are present in RA SF and are associated with disease activity, and the accumulation of CD4+CD161+ T cells in SF may contribute to the local inflammation of RA.

  17. An optimized multilayer structure of CdS layer for CdTe solar cells application

    Energy Technology Data Exchange (ETDEWEB)

    Han Junfeng, E-mail: pkuhjf@gmail.com [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Road Yiheyuan 5, Beijing 100871 (China); Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany); Liao Cheng, E-mail: Cliao@pku.edu.cn [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Road Yiheyuan 5, Beijing 100871 (China); Jiang Tao [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Road Yiheyuan 5, Beijing 100871 (China); Spanheimer, C.; Haindl, G.; Fu, Ganhua; Krishnakumar, V. [Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany); Zhao Kui [State Key Laboratory of Nuclear Physics and Technology, School of Physics, Peking University, Road Yiheyuan 5, Beijing 100871 (China); Klein, A.; Jaegermann, W. [Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany)

    2011-04-28

    Research highlights: > Two different methods to prepare CdS films for CdTe solar cells. > A new multilayer structure of window layer for the CdTe solar cell. > Thinner CdS window layer for the solar cell than the standard CdS layer. > Higher performance of solar cells based on the new multilayer structure. - Abstract: CdS layers grown by 'dry' (close space sublimation) and 'wet' (chemical bath deposition) methods are deposited and analyzed. CdS prepared with close space sublimation (CSS) has better crystal quality, electrical and optical properties than that prepared with chemical bath deposition (CBD). The performance of CdTe solar cell based on the CSS CdS layer has higher efficiency than that based on CBD CdS layer. However, the CSS CdS suffers from the pinholes. And consequently it is necessary to prepare a 150 nm thin film for CdTe/CdS solar cell. To improve the performance of CdS/CdTe solar cells, a thin multilayer structure of CdS layer ({approx}80 nm) is applied, which is composed of a bottom layer (CSS CdS) and a top layer (CBD CdS). That bi-layer film can allow more photons to pass through it and significantly improve the short circuit current of the CdS/CdTe solar cells.

  18. Highly luminescent CdTe/CdSe colloidal heteronanocrystals with temperature-dependent emission color

    NARCIS (Netherlands)

    Chin, P.T.K.; de Mello Donega, C.; van Bavel, S.S.; Meskers, S.C.J.; Sommerdijk, N.A.J.M.; Jansen, R.A.J.

    2007-01-01

    In this work we present the preparation of highly luminescent anisotropic CdTe/CdSe colloidal heteronanocrystals. The reaction conditions used (low temperature, slow precursor addition, and surfactant composition) resulted in a tunable shape from prolate to branched CdTe/CdSe nanocrystals. Upon CdSe

  19. Bioinformatics decoding the genome

    CERN Document Server

    CERN. Geneva; Deutsch, Sam; Michielin, Olivier; Thomas, Arthur; Descombes, Patrick

    2006-01-01

    Extracting the fundamental genomic sequence from the DNA From Genome to Sequence : Biology in the early 21st century has been radically transformed by the availability of the full genome sequences of an ever increasing number of life forms, from bacteria to major crop plants and to humans. The lecture will concentrate on the computational challenges associated with the production, storage and analysis of genome sequence data, with an emphasis on mammalian genomes. The quality and usability of genome sequences is increasingly conditioned by the careful integration of strategies for data collection and computational analysis, from the construction of maps and libraries to the assembly of raw data into sequence contigs and chromosome-sized scaffolds. Once the sequence is assembled, a major challenge is the mapping of biologically relevant information onto this sequence: promoters, introns and exons of protein-encoding genes, regulatory elements, functional RNAs, pseudogenes, transposons, etc. The methodological ...

  20. State of cat genomics.

    Science.gov (United States)

    O'Brien, Stephen J; Johnson, Warren; Driscoll, Carlos; Pontius, Joan; Pecon-Slattery, Jill; Menotti-Raymond, Marilyn

    2008-06-01

    Our knowledge of cat family biology was recently expanded to include a genomics perspective with the completion of a draft whole genome sequence of an Abyssinian cat. The utility of the new genome information has been demonstrated by applications ranging from disease gene discovery and comparative genomics to species conservation. Patterns of genomic organization among cats and inbred domestic cat breeds have illuminated our view of domestication, revealing linkage disequilibrium tracks consequent of breed formation, defining chromosome exchanges that punctuated major lineages of mammals and suggesting ancestral continental migration events that led to 37 modern species of Felidae. We review these recent advances here. As the genome resources develop, the cat is poised to make a major contribution to many areas in genetics and biology.

  1. Causes of genome instability

    DEFF Research Database (Denmark)

    Langie, Sabine A S; Koppen, Gudrun; Desaulniers, Daniel;

    2015-01-01

    chemicals present in our modern society could contribute to carcinogenesis by indirectly affecting genome stability. The selected chemicals with their mechanisms of action proposed to indirectly contribute to genome instability are: heavy metals (DNA repair, epigenetic modification, DNA damage signaling...... function, chromosome segregation, telomere length). The purpose of this review is to describe the crucial aspects of genome instability, to outline the ways in which environmental chemicals can affect this cancer hallmark and to identify candidate chemicals for further study. The overall aim is to make......Genome instability is a prerequisite for the development of cancer. It occurs when genome maintenance systems fail to safeguard the genome's integrity, whether as a consequence of inherited defects or induced via exposure to environmental agents (chemicals, biological agents and radiation). Thus...

  2. Genomics of oral bacteria.

    Science.gov (United States)

    Duncan, Margaret J

    2003-01-01

    Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.

  3. Reference Based Genome Compression

    CERN Document Server

    Chern, Bobbie; Manolakos, Alexandros; No, Albert; Venkat, Kartik; Weissman, Tsachy

    2012-01-01

    DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target genome, and then compresses this mapping with an entropy coder. As an illustration of the performance: applying our algorithm to James Watson's genome with hg18 as a reference, we are able to reduce the 2991 megabyte (MB) genome down to 6.99 MB, while Gzip compresses it to 834.8 MB.

  4. The effects of strain and spacer layer in CdSe/CdS/ZnS and CdSe/ZnS/CdS core/shell quantum dots

    Science.gov (United States)

    Pisheh, Hadi S.; Gheshlaghi, Negar; Ünlü, Hilmi

    2017-01-01

    The effects of lattice mismatch induced interface strain on the structural, optical and dielectric properties of CdSe based Cd(Zn)S shell and Cd(Zn)S/Zn(Cd)S multishell quantum dots (QDs) is studied. Introducing Zn(Cd)S spacer layer to the CdSe/Cd(Zn)S core/shell structure is found to influence induced interfacial strain through changing the lattice parameter, band gap and band offset of core/shell nanostructure. Lattice parameter of spacer layer affected by outer shell, changes the interface strain in the core region. Theoretically obtained strain in the core/shell(multishell) is used in the effective mass approximation (EMA) to determine the capped core diameter. We show that introducing ZnS spacer layer to the CdSe/CdS core/shell QDs rises the amount of strain and cause more decrease in the core size in CdSe/ZnS/CdS. Furthermore, CdS sandwiched between CdSe/ZnS decreases the amount of strain in crystal and suppresses the size decrease of the core in the CdSe/ZnS. Good agreement is found between the strain included EMA core size predictions in core/shell and multishell and observed size image from transmission electron microscopy (TEM) measurements of bare CdSe core nanocrystals.

  5. Selective regain of egfr gene copies in CD44+/CD24-/low breast cancer cellular model MDA-MB-468

    Directory of Open Access Journals (Sweden)

    Andreas Antje

    2010-03-01

    Full Text Available Abstract Background Increased transcription of oncogenes like the epidermal growth factor receptor (EGFR is frequently caused by amplification of the whole gene or at least of regulatory sequences. Aim of this study was to pinpoint mechanistic parameters occurring during egfr copy number gains leading to a stable EGFR overexpression and high sensitivity to extracellular signalling. A deeper understanding of those marker events might improve early diagnosis of cancer in suspect lesions, early detection of cancer progression and the prediction of egfr targeted therapies. Methods The basal-like/stemness type breast cancer cell line subpopulation MDA-MB-468 CD44high/CD24-/low, carrying high egfr amplifications, was chosen as a model system in this study. Subclones of the heterogeneous cell line expressing low and high EGF receptor densities were isolated by cell sorting. Genomic profiling was carried out for these by means of SNP array profiling, qPCR and FISH. Cell cycle analysis was performed using the BrdU quenching technique. Results Low and high EGFR expressing MDA-MB-468 CD44+/CD24-/low subpopulations separated by cell sorting showed intermediate and high copy numbers of egfr, respectively. However, during cell culture an increase solely for egfr gene copy numbers in the intermediate subpopulation occurred. This shift was based on the formation of new cells which regained egfr gene copies. By two parametric cell cycle analysis clonal effects mediated through growth advantage of cells bearing higher egfr gene copy numbers could most likely be excluded for being the driving force. Subsequently, the detection of a fragile site distal to the egfr gene, sustaining uncapped telomere-less chromosomal ends, the ladder-like structure of the intrachromosomal egfr amplification and a broader range of egfr copy numbers support the assumption that dynamic chromosomal rearrangements, like breakage-fusion-bridge-cycles other than proliferation drive the gain

  6. Detection and Significance of CD4+CD25+CD127dim Regulatory T Cells in Individuals with Severe Aplastic Anemia

    Directory of Open Access Journals (Sweden)

    Weiwei Qi

    2015-09-01

    Full Text Available Objective: To investigate the relationship between CD4+CD25+CD127dim regulatory T cells (Tregs and immune imbalance in acquired severe aplastic anemia (SAA. Materials and Methods: The quantity of CD4+CD25+CD127dim Tregs in 44 SAA patients and 23 normal controls was measured by flow cytometry. Correlations between Tregs and T cell subsets, dendritic cell (DC subsets, granulocyte counts, and percentage of reticulocytes (RET% were analyzed. Results: The percentage of CD4+CD25+CD127dim Tregs in peripheral blood lymphocytes (PBLs of untreated patients was lower than in recovery patients and normal controls (0.83±0.44% vs. 2.91±1.24% and 2.18±0.55%, respectively, p<0.05. The percentage of CD4+CD25+CD127dim Tregs in CD4+ T lymphocytes of recovery patients was higher than that of untreated patients and normal controls (9.39±3.51% vs. 7.61±5.3% and 6.83±1.4%, respectively, p<0.05. The percentage of CD4+ T lymphocytes in PBLs of untreated patients was lower than in recovery patients and normal controls (13.55±7.37% vs. 31.82±8.43% and 32.12±5.88%, respectively, p<0.05. T cell subset (CD4+/CD8+ ratio was 0.41±0.24 in untreated patients, which was lower than in recovery patients (1.2±0.4 and normal controls (1.11±0.23 (p<0.05. DC subset (myeloid DC/plasmacytoid DC ratio, DC1/DC2 ratio was 3.08±0.72 in untreated patients, which was higher than in recovery patients (1.61±0.49 and normal controls (1.39±0.36 (p<0.05. The percentage of CD4+CD25+CD127dim Tregs in PBLs was positively associated with T cell subset (r=0.955, p<0.01 and negatively associated with DC subset (r=-0.765, p<0.01. There were significant positive correlations between CD4+CD25+CD127dim Tregs/PBL and granulocyte counts and RET% (r=0.739 and r=0.749, respectively, p<0.01. Conclusion: The decrease of CD4+CD25+CD127dim Tregs in SAA patients may cause excessive functioning of T lymphocytes and thus lead to hematopoiesis failure in SAA.

  7. Querying genomic databases

    Energy Technology Data Exchange (ETDEWEB)

    Baehr, A.; Hagstrom, R.; Joerg, D.; Overbeek, R.

    1991-09-01

    A natural-language interface has been developed that retrieves genomic information by using a simple subset of English. The interface spares the biologist from the task of learning database-specific query languages and computer programming. Currently, the interface deals with the E. coli genome. It can, however, be readily extended and shows promise as a means of easy access to other sequenced genomic databases as well.

  8. Malaria Genome Sequencing Project

    Science.gov (United States)

    2004-01-01

    facts have stimulated efforts to develop an international, coordinated strategy for malaria research and control . Development of new drugs and...Interpolated Markov models for facilitate the development of new drugs and vaccines, the genome eukaryotic gene finding. Genomics 59, 24-31 (1999). of...Gardner, M. I. & Tettelin, H. Interpolated Markov models for facilitate the development of new drugs and vaccines, the genome eukaryotic gene finding

  9. Reference Based Genome Compression

    OpenAIRE

    Chern, Bobbie; Ochoa, Idoia; Manolakos, Alexandros; No, Albert; Venkat, Kartik; Weissman, Tsachy

    2012-01-01

    DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target gen...

  10. Concurrent hypermulticolor monitoring of CD31, CD34, CD45 and CD146 endothelial progenitor cell markers for acute myocardial infarction

    Energy Technology Data Exchange (ETDEWEB)

    Shim, Yumi [College of Pharmacy, Seoul National University, 1 Gwanak-Ro, Gwanak Gu, Seoul 151-742 (Korea, Republic of); Nam, Myung Hyun [Department of Laboratory Medicine, Korea University Ansan Hospital, Korea University College of Medicine (Korea, Republic of); Hyuk, Song Woo [Cardiology College of Medicine, Korea University (Korea, Republic of); Yoon, Soo Young [College of Medicine, Korea University, Seoul (Korea, Republic of); Song, Joon Myong, E-mail: jmsong@snu.ac.kr [College of Pharmacy, Seoul National University, 1 Gwanak-Ro, Gwanak Gu, Seoul 151-742 (Korea, Republic of)

    2015-01-01

    Highlights: • We observe EPCs and HPCs in patient for AMI diagnosis. • We detect two EPC subtypes using quantum dot and AOTF. • Quantum dot has narrower emission wavelength range than fluorescence dye. • AOTF provide smaller spectral interference than bandpass filters. • Quantum dot and AOTF are suitable for detecting large number of molecular markers concurrently. - Abstract: The circulating endothelial progenitor cells (EPCs) in blood of acute myocardial infarction (AMI) patient have been monitored in many previous studies. The number of circulating EPC increases in the blood of patients at onset of the AMI. EPC is originated from bone marrow. It performs vessel regeneration. There are many markers used for detecting EPC. Four of these markers, CD31, CD34, CD45, and CD146, were concurrently detected at the single cell level for the identification of EPC in the present preliminary study. The CD45 negative cell sorting was performed to peripheral blood mononuclear cells (PBMCs) acquired from four AMI patients with a magnetic bead sorter, since, EPCs expressed CD45 negative or dim. The resultant PBMC eluents were treated with quantum-antibody conjugates for the probing four different markers of EPCs and then applied to a high-content single cell imaging cytometer using acousto-optical tunable filter (AOTF). The use of quantum dot, with narrow emission wavelength range and AOTF enabling cellular image at a particular single wavelength, is very advantageous for accurate high-content AMI diagnosis based on simultaneous monitoring of many markers. The number of EPC increased as compared with control in three of four AMI patients. In this approach, two EPC subtypes were found, CD31(+), CD34(+), CD45(−/dim), CD146(−) as early outgrowth EPCs and CD31(+), CD34(+), CD45(−/dim), CD146(+) as late outgrowth EPCs. Patient 1 had CD31(+), CD34(+), CD45(−/dim), CD146(+) cells whose percentage was 4.21% of cells. Patient 2 had 2.38% of CD31(+), CD34(+), CD45(

  11. [Landscape and ecological genomics].

    Science.gov (United States)

    Tetushkin, E Ia

    2013-10-01

    Landscape genomics is the modern version of landscape genetics, a discipline that arose approximately 10 years ago as a combination of population genetics, landscape ecology, and spatial statistics. It studies the effects of environmental variables on gene flow and other microevolutionary processes that determine genetic connectivity and variations in populations. In contrast to population genetics, it operates at the level of individual specimens rather than at the level of population samples. Another important difference between landscape genetics and genomics and population genetics is that, in the former, the analysis of gene flow and local adaptations takes quantitative account of landforms and features of the matrix, i.e., hostile spaces that separate species habitats. Landscape genomics is a part of population ecogenomics, which, along with community genomics, is a major part of ecological genomics. One of the principal purposes of landscape genomics is the identification and differentiation of various genome-wide and locus-specific effects. The approaches and computation tools developed for combined analysis of genomic and landscape variables make it possible to detect adaptation-related genome fragments, which facilitates the planning of conservation efforts and the prediction of species' fate in response to expected changes in the environment.

  12. Between two fern genomes.

    Science.gov (United States)

    Sessa, Emily B; Banks, Jo Ann; Barker, Michael S; Der, Joshua P; Duffy, Aaron M; Graham, Sean W; Hasebe, Mitsuyasu; Langdale, Jane; Li, Fay-Wei; Marchant, D Blaine; Pryer, Kathleen M; Rothfels, Carl J; Roux, Stanley J; Salmi, Mari L; Sigel, Erin M; Soltis, Douglas E; Soltis, Pamela S; Stevenson, Dennis W; Wolf, Paul G

    2014-01-01

    Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.

  13. Fungal Genomics Program

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, Igor

    2012-03-12

    The JGI Fungal Genomics Program aims to scale up sequencing and analysis of fungal genomes to explore the diversity of fungi important for energy and the environment, and to promote functional studies on a system level. Combining new sequencing technologies and comparative genomics tools, JGI is now leading the world in fungal genome sequencing and analysis. Over 120 sequenced fungal genomes with analytical tools are available via MycoCosm (www.jgi.doe.gov/fungi), a web-portal for fungal biologists. Our model of interacting with user communities, unique among other sequencing centers, helps organize these communities, improves genome annotation and analysis work, and facilitates new larger-scale genomic projects. This resulted in 20 high-profile papers published in 2011 alone and contributing to the Genomics Encyclopedia of Fungi, which targets fungi related to plant health (symbionts, pathogens, and biocontrol agents) and biorefinery processes (cellulose degradation, sugar fermentation, industrial hosts). Our next grand challenges include larger scale exploration of fungal diversity (1000 fungal genomes), developing molecular tools for DOE-relevant model organisms, and analysis of complex systems and metagenomes.

  14. Genomic Database Searching.

    Science.gov (United States)

    Hutchins, James R A

    2017-01-01

    The availability of reference genome sequences for virtually all species under active research has revolutionized biology. Analyses of genomic variations in many organisms have provided insights into phenotypic traits, evolution and disease, and are transforming medicine. All genomic data from publicly funded projects are freely available in Internet-based databases, for download or searching via genome browsers such as Ensembl, Vega, NCBI's Map Viewer, and the UCSC Genome Browser. These online tools generate interactive graphical outputs of relevant chromosomal regions, showing genes, transcripts, and other genomic landmarks, and epigenetic features mapped by projects such as ENCODE.This chapter provides a broad overview of the major genomic databases and browsers, and describes various approaches and the latest resources for searching them. Methods are provided for identifying genomic locus and sequence information using gene names or codes, identifiers for DNA and RNA molecules and proteins; also from karyotype bands, chromosomal coordinates, sequences, motifs, and matrix-based patterns. Approaches are also described for batch retrieval of genomic information, performing more complex queries, and analyzing larger sets of experimental data, for example from next-generation sequencing projects.

  15. Genomics of Clostridium tetani.

    Science.gov (United States)

    Brüggemann, Holger; Brzuszkiewicz, Elzbieta; Chapeton-Montes, Diana; Plourde, Lucile; Speck, Denis; Popoff, Michel R

    2015-05-01

    Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies.

  16. GON4L Drives Cancer Growth through a YY1-Androgen Receptor-CD24 Axis.

    Science.gov (United States)

    Agarwal, Neeraj; Dancik, Garrett M; Goodspeed, Andrew; Costello, James C; Owens, Charles; Duex, Jason E; Theodorescu, Dan

    2016-09-01

    In principle, the inhibition of candidate gain-of-function genes defined through genomic analyses of large patient cohorts offers an attractive therapeutic strategy. In this study, we focused on changes in expression of CD24, a well-validated clinical biomarker of poor prognosis and a driver of tumor growth and metastasis, as a benchmark to assess functional relevance. Through this approach, we identified GON4L as a regulator of CD24 from screening a pooled shRNA library of 176 candidate gain-of-function genes. GON4L depletion reduced CD24 expression in human bladder cancer cells and blocked cell proliferation in vitro and tumor xenograft growth in vivo Mechanistically, GON4L interacted with transcription factor YY1, promoting its association with the androgen receptor to drive CD24 expression and cell growth. In clinical bladder cancer specimens, expression of GON4L, YY1, and CD24 was elevated compared with normal bladder urothelium. This pathway is biologically relevant in other cancer types as well, where CD24 and the androgen receptor are clinically prognostic, given that silencing of GON4L and YY1 suppressed CD24 expression and growth of human lung, prostate, and breast cancer cells. Overall, our results define GON4L as a novel driver of cancer growth, offering new biomarker and therapeutic opportunities. Cancer Res; 76(17); 5175-85. ©2016 AACR.

  17. CD27(-)CD45(+) γδ T cells can be divided into two populations, CD27(-)CD45(int) and CD27(-)CD45(hi) with little proliferation potential.

    Science.gov (United States)

    Odaira, Kosuke; Kimura, Shin-Nosuke; Fujieda, Nao; Kobayashi, Yukari; Kambara, Kaori; Takahashi, Takuya; Izumi, Takamichi; Matsushita, Hirokazu; Kakimi, Kazuhiro

    2016-09-23

    In addition to the majority of T cells which carry the αβ T cell receptor (TCR) for antigen, a distinct subset of about 1-5% of human peripheral blood T cells expressing the γδ TCR contributes to immune responses to infection, tissue damage and cancer. T cells with the Vδ2(+) TCR, usually paired with Vγ9, constitute the majority of these γδ T cells. Analogous to αβ T cells, they can be sorted into naive (CD27(+)CD45RA(+)), central memory (CD27(+)CD45RA(-)), effector memory (CD27(-)CD45RA(-)), and terminally-differentiated effector memory (CD27(-)CD45RA(+)) phenotypes. Here, we found that CD27(-)CD45RA(+) γδ T cells can be further divided into two populations based on the level of expression of CD45RA: CD27(-)CD45RA(int) and CD27(-)CD45RA(hi). Those with the CD27(-)CD45RA(hi) phenotype lack extensive proliferative capacity, while those with the CD27(-)CD45RA(int) phenotype can be easily expanded by culture with zoledronate and IL-2. These CD27(-)CD45RA(hi) potentially exhausted γδ T cells were found predominantly in cancer patients but also in healthy subjects. We conclude that γδ T cells can be divided into at least 5 subsets enabling discrimination of γδ T cells with poor proliferative capacity. It was one of our goals to predict the feasibility of γδ T cell expansion to sufficient amounts for adoptive immunotherapy without the necessity for conducting small-scale culture tests. Fulfilling the ≥1.5% criterion for γδ T cells with phenotypes other than CD27(-)CD45RA(hi), may help avoid small-scale culture testing and shorten the preparation period for adoptive γδ T cells by 10 days, which may be beneficial for patients with advanced cancer.

  18. MIPS plant genome information resources.

    Science.gov (United States)

    Spannagl, Manuel; Haberer, Georg; Ernst, Rebecca; Schoof, Heiko; Mayer, Klaus F X

    2007-01-01

    The Munich Institute for Protein Sequences (MIPS) has been involved in maintaining plant genome databases since the Arabidopsis thaliana genome project. Genome databases and analysis resources have focused on individual genomes and aim to provide flexible and maintainable data sets for model plant genomes as a backbone against which experimental data, for example from high-throughput functional genomics, can be organized and evaluated. In addition, model genomes also form a scaffold for comparative genomics, and much can be learned from genome-wide evolutionary studies.

  19. Photoluminescence properties of hybrid SiO2-coated CdTe/CdSe quantum dots.

    Science.gov (United States)

    Liu, Ning; Yang, Ping

    2014-09-01

    Hybrid SiO2-coated CdTe/CdSe quantum dots (QDs) were prepared using CdTe/CdSe QDs prepared by hydrothermal synthesis. A CdSe interlayer made CdTe/CdSe cores with unique type II heterostructures. The hybrid SiO2-coated CdTe/CdSe QDs revealed excellent photoluminescence (PL) properties compared with hybrid SiO2-coated CdTe QDs. Because of the existence of spatial separations of carriers in the type II CdTe/CdSe core/shell QDs, the hybrid QDs had a relatively extended PL lifetime and high stability in phosphate-buffered saline buffer solutions. This is ascribed to the unique components and stable surface state of hybrid SiO2-coated CdTe/CdSe QDs. During the stabilization test in phosphate-buffered saline buffer solutions, both static and dynamic quenching occurred. The quenching mechanism of the hybrid QDs was not suited with the Stern–Volmer equation. However, the relative stable surface of CdTe/CdSe QDs resulted in lower degradation and relative high PL quantum yields compared with hybrid SiO2-coated CdTe QDs. As a result, hybrid SiO2-coated CdTe/CdSe QDs can be used in bioapplications.

  20. CD-ROM-aided Databases

    Science.gov (United States)

    Nakaike, Shin'ichi; Tanaka, Masao

    The authors describe present status of patent information service by JAPIO, new on-line system project (PATOLIS-III), Paperless Project by the Patent Office and input of domestic gazettes for patent into optical disks. They also describe CD-ROM created by using image information of the gazettes for patent which is produced under the Paperless Project, its production method, and the terminals and their functions. Some problems found in CD-ROM of JAPIO, such as time lag for the issuance, treatment of the multiple copies, and countermeasures against them are mentioned.

  1. A model for the CdTe/CdS junction

    Energy Technology Data Exchange (ETDEWEB)

    Linam, David L; Singh, Vijay P; McClure, Jonh C; Lush, Gregory; Mathew, X [Centro de Investigacion en Energia, UNAM, Temixco, Morelos (Mexico)

    2000-07-01

    The saturation current and junction quality factor of a series of commercial CdTe/CdS solar cells have been measured. A high saturation current (compared to, for example, Si cells) is the primary cause of lower than theoretical efficiency. Furthermore, this current and the junction quality factor are functions of both light intensity and voltage bias level. It was found that tunneling is the predominant junction transport mechanism at high light levels and at low voltages while diffusion and regeneration/combination dominate at high voltage and low light levels. A model is presented to account for these observations. [Spanish] Se midieron las corrientes de saturacion y el factor de calidad de la union de una serie de celdas solares CdTe/CdS. Una corriente de saturacion alta (comparada por ejemplo a celdas de Si) es la causa primordial de eficiencia inferior a la teorica. Mas aun esta corriente y el factor de la calidad de la junta son funciones tanto de la intensidad de la luz y del nivel del voltaje de polarizacion. Se encontro que el paso a traves de una barrera de potencial (Tunneling) es el mecanismo de transporte predominate en la junta a altos niveles de luz y bajos voltajes mientras que la difusion y la regeneracion-combinacion predominaba a alto voltaje y bajos niveles de luz. Se presenta un modelo para tomar en cuenta estas observaciones.

  2. Association of BAP31 with CD11b/CD18. Potential role in intracellular trafficking of CD11b/CD18 in neutrophils.

    Science.gov (United States)

    Zen, Ke; Utech, Markus; Liu, Yuan; Soto, Illena; Nusrat, Asma; Parkos, Charles A

    2004-10-22

    The beta2 integrin CD11b/CD18 is an integral membrane protein that is present in the plasma membrane and secondary granules of neutrophils and functions as a major adhesion molecule. Upon cellular activation, there is translocation of intracellular pools of CD11b/CD18 to the plasma membrane in concert with enhanced cellular adhesion. Although much is known about the function of CD11b/CD18, how this protein is transported within the cell is less well defined. Here we report that CD11b/CD18 specifically binds to BAP31, a member of a novel class of sorting proteins regulating cellular anterograde transport. Through experiments aimed at identifying CD11b/CD18-binding proteins, we produced a monoclonal antibody termed E1B2 that recognizes a 28-kDa membrane protein that co-precipitates with CD11b/CD18. Microsequence analysis of the E1B2 antigen revealed that it is BAP31. Co-association of CD11b/CD18 and BAP31 was confirmed in co-immunoprecipitation and protein binding assays. Additional experiments revealed that the binding of BAP31 to CD11b/CD18 was not dependent on divalent cations nor mediated by the I-domain of CD11b. Using glutathione S-transferase fusion chimeras, we determined that binding of CD11b/CD18 to BAP31 is mediated through interactions with the cytoplasmic tail of BAP31. Immunolocalization studies revealed colocalization of BAP31 and CD11b/CD18 within neutrophil secondary granules. Subcellular fractionation studies in polymorphonuclear leukocytes (PMN) revealed similar patterns of redistribution of BAP31 and CD11b/CD18 from fractions enriched in secondary granules to the plasma membrane following stimulation with formylmethionylleucylphenylalanine (fMLP). Given the known sorting properties of BAP31, these findings suggest that BAP31 may play a role in regulating intracellular trafficking of CD11b/CD18 in neutrophils.

  3. Brief Guide to Genomics: DNA, Genes and Genomes

    Science.gov (United States)

    ... Breve guía de genómica A Brief Guide to Genomics DNA, Genes and Genomes Deoxyribonucleic acid (DNA) is ... genetic basis for health and disease. Implications of Genomics for Medical Science Virtually every human ailment has ...

  4. Complete genome sequence of Yersinia pestis strain 91001, an isolate avirulent to humans

    DEFF Research Database (Denmark)

    Song, Yajun; Tong, Zongzhong; Wang, Jin;

    2004-01-01

    -Microtus brandti. The genome of strain 91001 consists of one chromosome and four plasmids (pPCP1, pCD1, pMT1 and pCRY). The 9609-bp pPCP1 plasmid of strain 91001 is almost identical to the counterparts from reference strains (CO92 and KIM). There are 98 genes in the 70,159-bp range of plasmid pCD1. The 106,642-bp...

  5. Active RNA replication of hepatitis C virus downregulates CD81 expression.

    Science.gov (United States)

    Ke, Po-Yuan; Chen, Steve S-L

    2013-01-01

    So far how hepatitis C virus (HCV) replication modulates subsequent virus growth and propagation still remains largely unknown. Here we determine the impact of HCV replication status on the consequential virus growth by comparing normal and high levels of HCV RNA expression. We first engineered a full-length, HCV genotype 2a JFH1 genome containing a blasticidin-resistant cassette inserted at amino acid residue of 420 in nonstructural (NS) protein 5A, which allowed selection of human hepatoma Huh7 cells stably-expressing HCV. Short-term establishment of HCV stable cells attained a highly-replicating status, judged by higher expressions of viral RNA and protein as well as higher titer of viral infectivity as opposed to cells harboring the same genome without selection. Interestingly, maintenance of highly-replicating HCV stable cells led to decreased susceptibility to HCV pseudotyped particle (HCVpp) infection and downregulated cell surface level of CD81, a critical HCV entry (co)receptor. The decreased CD81 cell surface expression occurred through reduced total expression and cytoplasmic retention of CD81 within an endoplasmic reticulum -associated compartment. Moreover, productive viral RNA replication in cells harboring a JFH1 subgenomic replicon containing a similar blasticidin resistance gene cassette in NS5A and in cells robustly replicating full-length infectious genome also reduced permissiveness to HCVpp infection through decreasing the surface expression of CD81. The downregulation of CD81 surface level in HCV RNA highly-replicating cells thus interfered with reinfection and led to attenuated viral amplification. These findings together indicate that the HCV RNA replication status plays a crucial determinant in HCV growth by modulating the expression and intracellular localization of CD81.

  6. Active RNA replication of hepatitis C virus downregulates CD81 expression.

    Directory of Open Access Journals (Sweden)

    Po-Yuan Ke

    Full Text Available So far how hepatitis C virus (HCV replication modulates subsequent virus growth and propagation still remains largely unknown. Here we determine the impact of HCV replication status on the consequential virus growth by comparing normal and high levels of HCV RNA expression. We first engineered a full-length, HCV genotype 2a JFH1 genome containing a blasticidin-resistant cassette inserted at amino acid residue of 420 in nonstructural (NS protein 5A, which allowed selection of human hepatoma Huh7 cells stably-expressing HCV. Short-term establishment of HCV stable cells attained a highly-replicating status, judged by higher expressions of viral RNA and protein as well as higher titer of viral infectivity as opposed to cells harboring the same genome without selection. Interestingly, maintenance of highly-replicating HCV stable cells led to decreased susceptibility to HCV pseudotyped particle (HCVpp infection and downregulated cell surface level of CD81, a critical HCV entry (coreceptor. The decreased CD81 cell surface expression occurred through reduced total expression and cytoplasmic retention of CD81 within an endoplasmic reticulum -associated compartment. Moreover, productive viral RNA replication in cells harboring a JFH1 subgenomic replicon containing a similar blasticidin resistance gene cassette in NS5A and in cells robustly replicating full-length infectious genome also reduced permissiveness to HCVpp infection through decreasing the surface expression of CD81. The downregulation of CD81 surface level in HCV RNA highly-replicating cells thus interfered with reinfection and led to attenuated viral amplification. These findings together indicate that the HCV RNA replication status plays a crucial determinant in HCV growth by modulating the expression and intracellular localization of CD81.

  7. The analysis of CdS thin film at the processes of manufacturing CdS/CdTe solar cells

    Science.gov (United States)

    Chun, S.; Jung, Y.; Kim, J.; Kim, D.

    2011-07-01

    In sequence, the deposited CdS thin film had undergone physical and optical changes by the processes of manufacturing CdS/CdTe solar cells. CdS thin film was manufactured by the Chemical Bath Deposition (CBD) method. The aqueous solution was based on ammonia solution. The temperature of bath system was 75 °C and deposition time was 50 min. The thickness of deposited CdS thin film was about 200 nm. The substrate was the glass coated with SnO 2:F thin film. The following process was the deposition of CdTe thin film by the Closed-Space-Sublimation (CSS) method. The final process was the CdCl 2 heat treatment at N 2+O 2 atmosphere, and the contrast experiment progressed for CdCl 2-CdS thin film after CSS process at N 2 atmosphere. The phase transition of CdS thin film, stress relaxation and optical band gap narrowing were developed by each process. And so, the formation of cadmium oxide was detected after the CdCl 2 heat treatment. It influenced to increase the optical band gap of CdS thin film. The variation in the structure properties, optical properties and residual stresses of CdS thin film was analyzed by X-ray diffractometer (XRD), Raman spectroscopy and ultraviolet (UV)-visible (VIS) spectroscopy.

  8. Simulation of the Efficiency of CdS/CdTe Tandem Multi-Junction Solar Cells

    OpenAIRE

    Mirkamali, Ashrafalsadat S.; Muminov, Khikmat Kh.

    2016-01-01

    In this paper we study CdS/CdTe solar cells by means of AMPS-1D software. First we study the effect of thickness of semiconductor layers on the output parameters of the CdS/CdTe solar cell, such as density of short-circuit current, open circuit voltage, fill factor and efficiency. Numerical simulation shows that the highest efficiency of single-junction CdS/CdTe solar cell equal to 18.3% is achieved when the CdTe layer thickness is 1000 nm and a CdS layer is 60 nm. Then, in order to obtain th...

  9. The macrophage scavenger receptor CD163

    DEFF Research Database (Denmark)

    Nielsen, Marianne Jensby; Madsen, Mette; Møller, Holger J;

    2006-01-01

    CD163 is the monocyte/macrophage-specific receptor for haptoglobin-hemoglobin (Hp-Hb) complexes. The cytoplasmic tail of human CD163 exists as a short tail variant and two long tail variants. Reverse transcriptase-polymerase chain reaction analysis indicated that all three CD163 variants are subs......CD163 is the monocyte/macrophage-specific receptor for haptoglobin-hemoglobin (Hp-Hb) complexes. The cytoplasmic tail of human CD163 exists as a short tail variant and two long tail variants. Reverse transcriptase-polymerase chain reaction analysis indicated that all three CD163 variants...

  10. Breeding-assisted genomics.

    Science.gov (United States)

    Poland, Jesse

    2015-04-01

    The revolution of inexpensive sequencing has ushered in an unprecedented age of genomics. The promise of using this technology to accelerate plant breeding is being realized with a vision of genomics-assisted breeding that will lead to rapid genetic gain for expensive and difficult traits. The reality is now that robust phenotypic data is an increasing limiting resource to complement the current wealth of genomic information. While genomics has been hailed as the discipline to fundamentally change the scope of plant breeding, a more symbiotic relationship is likely to emerge. In the context of developing and evaluating large populations needed for functional genomics, none excel in this area more than plant breeders. While genetic studies have long relied on dedicated, well-structured populations, the resources dedicated to these populations in the context of readily available, inexpensive genotyping is making this philosophy less tractable relative to directly focusing functional genomics on material in breeding programs. Through shifting effort for basic genomic studies from dedicated structured populations, to capturing the entire scope of genetic determinants in breeding lines, we can move towards not only furthering our understanding of functional genomics in plants, but also rapidly improving crops for increased food security, availability and nutrition.

  11. Safeguarding genome integrity

    DEFF Research Database (Denmark)

    Sørensen, Claus Storgaard; Syljuåsen, Randi G

    2012-01-01

    Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with D...

  12. Unlocking the bovine genome

    Directory of Open Access Journals (Sweden)

    Worley Kim C

    2009-04-01

    Full Text Available Abstract The draft genome sequence of cattle (Bos taurus has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration involving more than 300 scientists from 25 different countries.

  13. Estimation of genome length

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The genome length is a fundamental feature of a species. This note outlined the general concept and estimation method of the physical and genetic length. Some formulae for estimating the genetic length were derived in detail. As examples, the genome genetic length of Pinus pinaster Ait. and the genetic length of chromosome Ⅵ of Oryza sativa L. were estimated from partial linkage data.

  14. Ensembl Genomes 2013

    DEFF Research Database (Denmark)

    Kersey, Paul Julian; Allen, James E; Christensen, Mikkel

    2014-01-01

    genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely...

  15. Genomic understanding of dinoflagellates.

    Science.gov (United States)

    Lin, Senjie

    2011-01-01

    The phylum of dinoflagellates is characterized by many unusual and interesting genomic and physiological features, the imprint of which, in its immense genome, remains elusive. Much novel understanding has been achieved in the last decade on various aspects of dinoflagellate biology, but most remarkably about the structure, expression pattern and epigenetic modification of protein-coding genes in the nuclear and organellar genomes. Major findings include: 1) the great diversity of dinoflagellates, especially at the base of the dinoflagellate tree of life; 2) mini-circularization of the genomes of typical dinoflagellate plastids (with three membranes, chlorophylls a, c1 and c2, and carotenoid peridinin), the scrambled mitochondrial genome and the extensive mRNA editing occurring in both systems; 3) ubiquitous spliced leader trans-splicing of nuclear-encoded mRNA and demonstrated potential as a novel tool for studying dinoflagellate transcriptomes in mixed cultures and natural assemblages; 4) existence and expression of histones and other nucleosomal proteins; 5) a ribosomal protein set expected of typical eukaryotes; 6) genetic potential of non-photosynthetic solar energy utilization via proton-pump rhodopsin; 7) gene candidates in the toxin synthesis pathways; and 8) evidence of a highly redundant, high gene number and highly recombined genome. Despite this progress, much more work awaits genome-wide transcriptome and whole genome sequencing in order to unfold the molecular mechanisms underlying the numerous mysterious attributes of dinoflagellates.

  16. Improved photoluminescence quantum yield and stability of CdSe-TOP, CdSe-ODA-TOPO, CdSe/CdS and CdSe/EP nanocomposites

    Science.gov (United States)

    Wei, Shutian; Zhu, Zhilin; Wang, Zhixiao; Wei, Gugangfen; Wang, Pingjian; Li, Hai; Hua, Zhen; Lin, Zhonghai

    2016-07-01

    Size-controllable monodisperse CdSe nanocrystals with different organic capping were prepared based on the hot-injection method. The effective separation of nucleation and growth was achieved by rapidly mixing two highly reactive precursors. As a contrast, we prepared CdSe/CdS nanocrystals (NCs) successfully based on the selective ion layer adsorption and reaction (SILAR) technique. This inorganic capping obtained higher photoluminescence quantum yield (PLQY) of 59.3% compared with organic capping of 40.8%. Furthermore, the CdSe-epoxy resin (EP) composites were prepared by adopting a flexible ex situ method, and showed excellent stability in the ambient environment for one year. So the composites with both high PLQY of nanocrystals and excellent stability are very promising to device application.

  17. Numerical modeling of CdS/CdTe and CdS/CdTe/ZnTe solar cells as a function of CdTe thickness

    Energy Technology Data Exchange (ETDEWEB)

    Amin, Nowshad [Department of Electrical, Electronic and System Engineering, Faculty of Engineering, National University of Malaysia (UKM), Bangi 43600, Selangor D.E (Malaysia); Sopian, Kamaruzzaman [Solar Energy Research Institute, National University of Malaysia (UKM), Bangi 43600, Selangor D.E (Malaysia); Konagai, Makoto [Department of Electrical and Electronic Engineering, Tokyo Institute of Technology, 2-12-1 O-okayama, Meguro-ku, Tokyo 152-8552 (Japan)

    2007-08-15

    CdTe-based solar cells have long been of interest for terrestrial usage because of their high potential conversion efficiency (in the range of 18-24%) with low-cost manufacturability and concern over environmental effects. In order to conserve material and address environmental pollution concerns as well as to reduce carrier recombination loss throughout the absorber layer, efforts have been carried out to decrease the thickness of the CdTe absorption layer to 1 {mu}m. As a result, to date, the experimental part of this study has realized cell efficiencies of 15.3% and 11.5% with 7 and 1.2-{mu}m-thick CdTe layers, grown by close-spaced sublimation (CSS) [N. Amin, T. Isaka, T. Okamoto, A. Yamada, M. Konagai, Jpn. J. Appl. Phys. 38 (8) (1999) 4666; N. Amin, T. Isaka, A. Yamada, M. Konagai, Sol. Energy Matter. Sol. Cells 67 (2001) 195]. Since some problems remain with such thin 1 {mu}m CdTe layers, possible methods to realize higher efficiency have been investigated using novel solar cell structures, with the help of numerical analyses tools. In the theory part of this study, numerical analysis with a 1-D simulation program named NSSP (Numerical Solar Cell Simulation Program) has been used to simulate these structures. We investigated the viability of CdTe thickness reduction to 1 {mu}m together with the insertion of higher band-gap materials (i.e., ZnTe) at the back contacts to reduce carrier recombination loss there. The study shows potential results of the thickness reduction of CdTe absorption layer for a conventional CdS/CdTe/Cu-doped C structure with around 16% efficiency for cells below 3 {mu}m CdTe. Decreases were found in spectral response that suggest from minority carrier recombination loss at the back contact interface. A higher band-gap material like ZnTe has been inserted to produce a back surface field (BSF) to inhibit the minority carrier loss at the back contact. An increase in the efficiency to about 20% has been found for a 1 {mu}m-thin CdTe cell

  18. Peripheral canine CD4(+)CD8(+) double-positive T cells - unique amongst others.

    Science.gov (United States)

    von Buttlar, Heiner; Bismarck, Doris; Alber, Gottfried

    2015-12-15

    T lymphocytes co-expressing CD4 and CD8 ("double-positive T cells") are commonly associated with a thymic developmental stage of T cells. Their first description in humans and pigs as extrathymic T cells with a memory phenotype almost 30 years ago came as a surprise. Meanwhile peripheral double-positive T cells have been described in a growing number of different species. In this review we highlight novel data from our very recent studies on canine peripheral double-positive T cells which point to unique features of double-positive T cells in the dog. In contrast to porcine CD4(+)CD8(+) T cells forming a homogenous cellular population based on their expression of CD4 and CD8α, canine CD4(+)CD8(+) T cells can be divided into three different cellular subsets with distinct expression levels of CD4 and CD8α. Double-positive T cells expressing CD8β are present in humans and dogs but absent in swine. Moreover, canine CD4(+)CD8(+) T cells can not only develop from CD4(+) single-positive T cells but also from CD8(+) single-positive T cells. Together, this places canine CD4(+)CD8(+) T cells closer to their human than porcine counterparts since human double-positive T cells also appear to be heterogeneous in their CD4 and CD8α expression and have both CD4(+) and CD8(+) T cells as progenitor cells. However, CD4(+) single-positive T cells are the more potent progenitors for canine double-positive T cells, whereas CD8(+) single-positive T cells are more potent progenitors for human double-positive T cells. Canine double-positive T cells have an activated phenotype and may have as yet unrecognized roles in vivo in immunity to infection or in inflammatory diseases such as chronic infection, autoimmunity, allergy, or cancer.

  19. CD49d- Treg Cells with High Suppressive Capacity are Remarkably Less Efficient on Activated CD45RA- than on Naive CD45RA+ Teff Cells

    Directory of Open Access Journals (Sweden)

    Britta Kraczyk

    2014-07-01

    Full Text Available Background: Impairment of regulatory T cells (Tregs in common autoimmune diseases seems likely. However, the extent of Treg deficiency (number, function or differential susceptibility of T effector cells (Teffs to suppression is not completely understood. We hypothesize that even in healthy individuals both cell populations are heterogeneous and differ in their suppressive capability and their susceptibility to suppression. Material and Methods: Lymphocytes were enriched by MACS for CD4+CD25+ Tregs or CD4+CD25- Teffs. After multicolour staining (anti-CD25, anti-CD127, anti-CD49d or anti-CD45RA highly purified Treg and Teff subpopulations were collected by FACS. Functional capacity of Tregs or suppressive susceptibility of Teffs was analyzed in an in vitro assay. Results: When CD4+CD25highCD127-/low CD49d- Tregs were tested on naive CD4+CD127+CD25-CD45RA+ Teffs (93.8 % suppression was almost complete, while the suppressive capacity of CD4+CD25highCD127-/low CD49d+ Tregs was significantly less (71.8 %. Suppressive activity was low when CD4+CD25highCD127-/low CD49d+ Tregs were analyzed on CD4+CD127+CD25-CD45RA- Teffs (48.7%. Conclusion: Although CD49d+ Tregs are functional, the suppressive capacity is significantly lower compared to CD49d- Tregs. CD45RA+ Teffs can be completely suppressed, while CD45RA- Teffs display relative resistance. Phenotypic and functional heterogeneity of Tregs as well as Teffs has to be considered when analyzing deficiencies in immune regulation.

  20. Electronic structure and properties of Cd4As2Br3 and Cd4Sb2I3, analogues of CdSe and CdTe

    Science.gov (United States)

    Roy, Anand; Suchitra; Manjunath, K.; Ahmad, Tokeer; Waghmare, Umesh V.; Rao, C. N. R.

    2017-04-01

    Substitution of aliovalent anions in metal oxides and chalcogenides significantly affects the electronic structure and properties of the materials. Thus, substitution of P3- and Cl- in CdS decreases the band gap and favorably influences the photocatalytic activity. Complete substitution of a trivalent (A3-) and a monovalent (B-) anions in a cadmium chalcogenides, CdX, should give rise to a material of the composition Cd A0.5B0.5 or Cd2AB, but a compound with the composition Cd4P2Cl3 (or Cd2PCl1.5) is obtained in the case of CdS. We have investigated the analogous compounds, Cd4As2Br3 and Cd4Sb2I3, wherein the anions in CdSe and CdTe are substituted by As, Br and Sb, I respectively. These compounds are direct band gap semiconductors with a band gap of 1.8-1.9 eV and a photoluminescence band in the visible region. First-principles calculations show both Cd4As2Br3 and Cd4Sb2I3 to be direct band gap semiconductors. The arsenic bromide is predicted to be photochemically more active for HER than the antimony iodide.

  1. Inflammation in disseminated lesions: an analysis of CD4+, CD20+, CD68+, CD31+ and vW+ cells in non-ulcerated lesions of disseminated leishmaniasis

    Directory of Open Access Journals (Sweden)

    Dayana Santos Mendes

    2013-02-01

    Full Text Available Disseminated leishmaniasis (DL differs from other clinical forms of the disease due to the presence of many non-ulcerated lesions (papules and nodules in non-contiguous areas of the body. We describe the histopathology of DL non-ulcerated lesions and the presence of CD4-, CD20-, CD68-, CD31- and von Willebrand factor (vW-positive cells in the inflamed area. We analysed eighteen biopsies from non-ulcerated lesions and quantified the inflamed areas and the expression of CD4, CD20, CD68, CD31 and vW using Image-Pro software (Media Cybernetics. Diffuse lymphoplasmacytic perivascular infiltrates were found in dermal skin. Inflammation was observed in 3-73% of the total biopsy area and showed a significant linear correlation with the number of vW+ vessels. The most common cells were CD68+ macrophages, CD20+ B-cells and CD4+ T-cells. A significant linear correlation between CD4+ and CD20+ cells and the size of the inflamed area was also found. Our findings show chronic inflammation in all DL non-ulcerated lesions predominantly formed by macrophages, plasmacytes and T and B-cells. As the inflamed area expanded, the number of granulomas and extent of the vascular framework increased. Thus, we demonstrate that vessels may have an important role in the clinical evolution of DL lesions.

  2. An increasing need for productive and stress resilient Festulolium amphiploids: what can be learnt from the stable genomic composition of Festuca pratensis subsp. apennina (De Not. Hegi?

    Directory of Open Access Journals (Sweden)

    David Kopecký

    2016-10-01

    Full Text Available Genome composition of Festuca pratensis subsp. apennina (De Not. Hegi, a tetraploid fescue species native to the tall forbs communities of south-eastern Europe at altitudes between 1100 and 2200m a.s.l. has been the subject of some debate by grass taxonomists. Our cytogenetic analyses including fluorescence in situ hybridisation with probes for genomic DNA and selected DNA repeats revealed the species to be allotetraploid and derived from interspecific hybridization between F. pratensis Huds., a species confined to grassland at lower altitudes, and a so far unknown Festuca species. Besides tetraploids, triploids and pentaploids were found growing in Alpine meadows in close association with F. pratensis subsp. apennina. Triploid cytotypes predominated at many sites in Switzerland and Romania, and in some localities, they were the only cytotypes observed. Cytogenetic analyses revealed the triploids to be hybrids between diploid F. pratensis and tetraploid Festuca pratensis subsp. apennina, while the pentaploid cytotypes originated from hybridization between F. pratensis subsp. apennina and hexaploid F. arundinacea Schreb., a closely-related species growing in a close vicinity to F. pratensis subsp. apennina. Parental genomes of F. pratensis subsp. apennina and of the triploid and pentaploid hybrids showed no evidence of homoeologous chromosome pairing and interspecific recombination, supporting previous observation of a disomic inheritance at meiosis, where chromosome pairing was restricted to bivalent associations. A hypothesis is presented that a chromosome pairing regulator(s, reported previously in other polyploid broad-leaved fescue species of the Festuca subg. Schedonorus, is present and functional in F. pratensis subsp. apennina. It is likely that a common ancestors’ genome that carries the chromosome pairing regulator(s is present in all polyploid broad-leaved fescue species, and its acquisition was a key event that enabled speciation

  3. Ultrafast charge carrier relaxation and charge transfer processes in CdS/CdTe thin films.

    Science.gov (United States)

    Pandit, Bill; Dharmadasa, Ruvini; Dharmadasa, I M; Druffel, Thad; Liu, Jinjun

    2015-07-14

    Ultrafast transient absorption pump-probe spectroscopy (TAPPS) has been employed to investigate charge carrier relaxation in cadmium sulfide/cadmium telluride (CdS/CdTe) nanoparticle (NP)-based thin films and electron transfer (ET) processes between CdTe and CdS. Effects of post-growth annealing treatments to ET processes have been investigated by carrying out TAPPS experiments on three CdS/CdTe samples: as deposited, heat treated, and CdCl2 treated. Clear evidence of ET process in the treated thin films has been observed by comparing transient absorption (TA) spectra of CdS/CdTe thin films to those of CdS and CdTe. Quantitative comparison between ultrafast kinetics at different probe wavelengths unravels the ET processes and enables determination of its rate constants. Implication of the photoinduced dynamics to photovoltaic devices is discussed.

  4. Electrodeposition, characterization and photo electrochemical properties of CdSe and CdTe

    Directory of Open Access Journals (Sweden)

    Atef Y. Shenouda

    2015-03-01

    Full Text Available CdSe and CdTe are electrodeposited using 0.1 M Cd2+ and different ion concentrations of Se and Te. The effect of the temperature on the electrodeposition process is also studied. The crystal structure of the deposited CdSe and CdTe is investigated by X-ray diffraction (XRD. Scanning electron microscopy (SEM of samples deposited at optimized parameters reveals that CdSe has spongy spherical grains while CdTe has coralloid morphology. Optical absorption shows the presence of direct transition with band gap energy 1.96 and 1.51 eV for CdSe and CdTe, respectively. The highest photo-conversion efficiencies of electrodeposited CdSe and CdTe films per unit area are 6% and 9.6%, respectively that achieved under simple laboratory conditions.

  5. CD4+ T Cells Expressing PD-1, TIGIT and LAG-3 Contribute to HIV Persistence during ART

    Science.gov (United States)

    Fromentin, Rémi; Bakeman, Wendy; Lawani, Mariam B.; Khoury, Gabriela; Hartogensis, Wendy; DaFonseca, Sandrina; Killian, Marisela; Epling, Lorrie; Hoh, Rebecca; Sinclair, Elizabeth; Hecht, Frederick M.; Bacchetti, Peter; Deeks, Steven G.; Lewin, Sharon R.; Sékaly, Rafick-Pierre; Chomont, Nicolas

    2016-01-01

    HIV persists in a small pool of latently infected cells despite antiretroviral therapy (ART). Identifying cellular markers expressed at the surface of these cells may lead to novel therapeutic strategies to reduce the size of the HIV reservoir. We hypothesized that CD4+ T cells expressing immune checkpoint molecules would be enriched in HIV-infected cells in individuals receiving suppressive ART. Expression levels of 7 immune checkpoint molecules (PD-1, CTLA-4, LAG-3, TIGIT, TIM-3, CD160 and 2B4) as well as 4 markers of HIV persistence (integrated and total HIV DNA, 2-LTR circles and cell-associated unspliced HIV RNA) were measured in PBMCs from 48 virally suppressed individuals. Using negative binomial regression models, we identified PD-1, TIGIT and LAG-3 as immune checkpoint molecules positively associated with the frequency of CD4+ T cells harboring integrated HIV DNA. The frequency of CD4+ T cells co-expressing PD-1, TIGIT and LAG-3 independently predicted the frequency of cells harboring integrated HIV DNA. Quantification of HIV genomes in highly purified cell subsets from blood further revealed that expressions of PD-1, TIGIT and LAG-3 were associated with HIV-infected cells in distinct memory CD4+ T cell subsets. CD4+ T cells co-expressing the three markers were highly enriched for integrated viral genomes (median of 8.2 fold compared to total CD4+ T cells). Importantly, most cells carrying inducible HIV genomes expressed at least one of these markers (median contribution of cells expressing LAG-3, PD-1 or TIGIT to the inducible reservoir = 76%). Our data provide evidence that CD4+ T cells expressing PD-1, TIGIT and LAG-3 alone or in combination are enriched for persistent HIV during ART and suggest that immune checkpoint blockers directed against these receptors may represent valuable tools to target latently infected cells in virally suppressed individuals. PMID:27415008

  6. CD4+ T Cells Expressing PD-1, TIGIT and LAG-3 Contribute to HIV Persistence during ART.

    Directory of Open Access Journals (Sweden)

    Rémi Fromentin

    2016-07-01

    Full Text Available HIV persists in a small pool of latently infected cells despite antiretroviral therapy (ART. Identifying cellular markers expressed at the surface of these cells may lead to novel therapeutic strategies to reduce the size of the HIV reservoir. We hypothesized that CD4+ T cells expressing immune checkpoint molecules would be enriched in HIV-infected cells in individuals receiving suppressive ART. Expression levels of 7 immune checkpoint molecules (PD-1, CTLA-4, LAG-3, TIGIT, TIM-3, CD160 and 2B4 as well as 4 markers of HIV persistence (integrated and total HIV DNA, 2-LTR circles and cell-associated unspliced HIV RNA were measured in PBMCs from 48 virally suppressed individuals. Using negative binomial regression models, we identified PD-1, TIGIT and LAG-3 as immune checkpoint molecules positively associated with the frequency of CD4+ T cells harboring integrated HIV DNA. The frequency of CD4+ T cells co-expressing PD-1, TIGIT and LAG-3 independently predicted the frequency of cells harboring integrated HIV DNA. Quantification of HIV genomes in highly purified cell subsets from blood further revealed that expressions of PD-1, TIGIT and LAG-3 were associated with HIV-infected cells in distinct memory CD4+ T cell subsets. CD4+ T cells co-expressing the three markers were highly enriched for integrated viral genomes (median of 8.2 fold compared to total CD4+ T cells. Importantly, most cells carrying inducible HIV genomes expressed at least one of these markers (median contribution of cells expressing LAG-3, PD-1 or TIGIT to the inducible reservoir = 76%. Our data provide evidence that CD4+ T cells expressing PD-1, TIGIT and LAG-3 alone or in combination are enriched for persistent HIV during ART and suggest that immune checkpoint blockers directed against these receptors may represent valuable tools to target latently infected cells in virally suppressed individuals.

  7. Phytozome Comparative Plant Genomics Portal

    Energy Technology Data Exchange (ETDEWEB)

    Goodstein, David; Batra, Sajeev; Carlson, Joseph; Hayes, Richard; Phillips, Jeremy; Shu, Shengqiang; Schmutz, Jeremy; Rokhsar, Daniel

    2014-09-09

    The Dept. of Energy Joint Genome Institute is a genomics user facility supporting DOE mission science in the areas of Bioenergy, Carbon Cycling, and Biogeochemistry. The Plant Program at the JGI applies genomic, analytical, computational and informatics platforms and methods to: 1. Understand and accelerate the improvement (domestication) of bioenergy crops 2. Characterize and moderate plant response to climate change 3. Use comparative genomics to identify constrained elements and infer gene function 4. Build high quality genomic resource platforms of JGI Plant Flagship genomes for functional and experimental work 5. Expand functional genomic resources for Plant Flagship genomes

  8. Improved flow cytometric identification of myelopoiesis by the simultaneous labelling with CD13, CD14 and CD66 monoclonal antibodies

    DEFF Research Database (Denmark)

    Bonde, J; Meyer, K; Broe, M K;

    1996-01-01

    The aim of the present study was to increase our knowledge of myelopoiesis evaluated by flow cytometry. We therefore designed a triple-marker assay employing monoclonal antibodies against the CD13 (immature), the CD14 (monocytic), and the CD66 (mature myeloid) antigens using three-colour immunofl...

  9. Characterization of CdS Thin-Film in High Efficient CdS/CdTe Solar Cells

    Science.gov (United States)

    Tsuji, Miwa; Aramoto, Tetsuya; Ohyama, Hideaki; Hibino, Takeshi; Omura, Kuniyoshi

    2000-07-01

    Cadmium sulfide (CdS) thin films are the most commonly used window materials for high efficient cadmium telluride (CdTe) and chalcopyrite polycrystalline thin-film photovoltaic devices. High efficient CdS/CdTe solar cells with thin CdS films have been developed using ultrathin CdS films with a thickness of less than 0.1 μm. CdS films were deposited on transparent conductive oxide (TCO)/glass substrates by the metal organic chemical vapor deposition (MOCVD) technique. CdTe films were subsequently deposited by the close-spaced sublimation (CSS) technique. The screen printing and sintering method fabricated carbon and silver electrodes. Cell performance depends primarily on the electrical and optical properties of CdS films. Therefore we started to develop higher-quality CdS films and found clear differences between high- and low-quality CdS films from the analyses of scanning electron microscope (SEM), atomic force microscope (AFM), secondary ion mass spectroscopy (SIMS), thermal desorption spectrometry (TDS) and Fourier transforms-infrared spectrometry (FT-IR) measurements. As a result of controlling the quality of CdS films, a photovoltaic conversion efficiency of 10.5% has been achieved for size of 1376 cm2 of the solar cells under the Air Mass (AM) 1.5 conditions of the Japan Quality Assurance Organization.

  10. Genetic determinism in the relationship between human CD4+ and CD8+ T lymphocyte populations?

    Science.gov (United States)

    Ahmadi, K R; Hall, M A; Norman, P; Vaughan, R W; Snieder, H; Spector, T D; Lanchbury, J S

    2001-11-01

    The adaptive immune system in mammals acts in a coordinated manner to eliminate environmentally derived pathogens. Humans, mice and rats show within species variation in the levels and ratios of their peripheral CD4+ and CD8+ T cells and to a significant degree this variation is under the control of polymorphic genes. Whether genes act separately to specify CD4+ and CD8+ subpopulation levels or whether CD8+ variation is controlled through gene and environmental action on CD4+ cells or vice versa, is not known. We use a quantitative modelling approach in identical and non-identical female human twins to delineate the lines of control which act upon and between CD4+ and CD8+ subsets. The major findings of the study are: (1) genetic variation controls CD8+ T cell levels through two major routes-the first is via an effect on CD4+ T cells which accounts for the observed co-variation between CD4+ and CD8+ T cells, the second is through direct action on CD8+ T cell levels. (2) No evidence of a gene effect from CD8+ T cells on CD4+ cells is observed. Our findings have implications for the evolution of the complex defence system of which CD4+ and CD8+ T cells are a crucial part and encourage further work towards locating common pleiotropic quantitative trait loci responsible for variation in numbers of T cells.

  11. Genetic Analysis of Triploid Progenies from Shatian Pummelo (2x) x Citrus Allotetraploid Somatic Hybrid NS (4x)%沙田柚(2x)×柑橘异源体细胞杂种NS(4x)的三倍体后代遗传分析

    Institute of Scientific and Technical Information of China (English)

    宋健坤; 朱世平; 谭美莲; 郭文武; 邓秀新

    2012-01-01

    Abstract: Two pairs of SSR (simple sequence repeat) primers TAA1 and TAA3 were used to detect the band patterns and segregation rations among the 79 triploid progenies derived from the sexual cross between diploid Citrus grandis (L.) Osbeck ' Shatian' pummelo and somatic hybrid NS [ ( C. reticulata Blanco×C. paradisi Macf. ) 'Nova' tangelo + C. sinensis (L.) Osbeck 'Succari' sweet orange] by embyo rescue technology. Five and four band patterns were generated from the TAA1 and TAA3 primers at the ratio of 4 : 1 : 1 : 5 : 1 and 2 : 2 : 1 : 1 respectively, as was in good accordance with the segregation ratio of amphidiploid deduced by the law of Mendel. The results preliminarily indicated that the meiosis behavior of citrus allotetraploid somatic hybrid was similar to that of the amphidiploid.%用两对SSR引物TAAl和TAA3对以二倍体沙田柚为母本,体细胞杂种NS(Nova橘柚+Succari甜橙)为父本,通过有性杂交和胚挽救获得的79株三倍体后代群体的带型和分离情况进行了分析。结果发现TAAl引物和TAA3引物在后代群体中分别扩增出5种带型和4种带型,子代带型分别符合4:1:1:5:1和2:2:1:1的分离比例,与根据孟德尔遗传规律推导的双二倍体的分离比例相吻合,初步表明柑橘异源四倍体体细胞杂种减数分裂行为类似于双二倍体。

  12. Hepatitis B Virus Replication in CD34+ Hematopoietic Stem Cells From Umbilical Cord Blood.

    Science.gov (United States)

    Huang, Yanxin; Yan, Qin; Fan, Rongshan; Song, Shupeng; Ren, Hong; Li, Yongguo; Lan, Yinghua

    2016-05-18

    BACKGROUND Hepatitis B virus (HBV) is a hepatotropic virus that can infect extrahepatic tissue. Whether hematopoietic stem cells (HSCs) can be infected by HBV and serve as a potential virus reservoir is still unknown. In this study, the susceptibility of CD34+ HSCs to HBV was investigated. MATERIAL AND METHODS Cord blood-derived CD34+ HSCs were exposed to HBV in vitro, and immunocytochemistry, transmission electron microscopy, and RT-PCR were used to identify viral-related proteins and specific viral genomic sequences. Then, CD34+ HSCs were challenged by different titers of HBV, and intracellular and supernatant HBV DNA, and hepatitis B surface antigen (HBsAg) levels, were examined. In addition, CD34+ peripheral blood stem cells (PBSCs) from chronic HBV carriers were isolated and cultured, and HBV DNA levels were measured. RESULTS HBV-infected CD34+ cells showed positive signals for HBsAg by DAB staining and TRITC staining, and HBV particles were identified. RT-PCR results showed that the 403 bp PCR products corresponding to the amplified hepatitis B S gene fragment were observed in CD34+ HSCs infected by HBV. In addition, supernatant and intracellular HBV DNA increased with the proliferation of CD34+ HSCs. Similar results were obtained from intracellular HBsAg quantification tests. In addition, HBV DNA levels both in cells and in supernatants of CD34+ PBSCs increased proportionally, and the increments of HBV DNA in the supernatants paralleled those found in cells. CONCLUSIONS HBV can replicate in CD34+ HSCs in cord blood or peripheral blood of chronic HBV carriers.

  13. Transcriptome Analysis of CD4+ T Cells in Coeliac Disease Reveals Imprint of BACH2 and IFNγ Regulation.

    Directory of Open Access Journals (Sweden)

    Emma M Quinn

    Full Text Available Genetic studies have to date identified 43 genome wide significant coeliac disease susceptibility (CD loci comprising over 70 candidate genes. However, how altered regulation of such disease associated genes contributes to CD pathogenesis remains to be elucidated. Recently there has been considerable emphasis on characterising cell type specific and stimulus dependent genetic variants. Therefore in this study we used RNA sequencing to profile over 70 transcriptomes of CD4+ T cells, a cell type crucial for CD pathogenesis, in both stimulated and resting samples from individuals with CD and unaffected controls. We identified extensive transcriptional changes across all conditions, with the previously established CD gene IFNy the most strongly up-regulated gene (log2 fold change 4.6; P(adjusted = 2.40x10(-11 in CD4+ T cells from CD patients compared to controls. We show a significant correlation of differentially expressed genes with genetic studies of the disease to date (P(adjusted = 0.002, and 21 CD candidate susceptibility genes are differentially expressed under one or more of the conditions used in this study. Pathway analysis revealed significant enrichment of immune related processes. Co-expression network analysis identified several modules of coordinately expressed CD genes. Two modules were particularly highly enriched for differentially expressed genes (P<2.2x10(-16 and highlighted IFNy and the genetically associated transcription factor BACH2 which showed significantly reduced expression in coeliac samples (log2FC -1.75; P(adjusted = 3.6x10(-3 as key regulatory genes in CD. Genes regulated by BACH2 were very significantly over-represented among our differentially expressed genes (P<2.2x10(-16 indicating that reduced expression of this master regulator of T cell differentiation promotes a pro-inflammatory response and strongly corroborates genetic evidence that BACH2 plays an important role in CD pathogenesis.

  14. Opposite activation of the Hedgehog pathway in CD138+ plasma cells and CD138-CD19+ B cells identifies two subgroups of patients with multiple myeloma and different prognosis.

    Science.gov (United States)

    Martello, M; Remondini, D; Borsi, E; Santacroce, B; Procacci, M; Pezzi, A; Dico, F A; Martinelli, G; Zamagni, E; Tacchetti, P; Pantani, L; Testoni, N; Marzocchi, G; Rocchi, S; Zannetti, B A; Mancuso, K; Cavo, M; Terragna, C

    2016-09-01

    Hyperactivation of the Hedgehog (Hh) pathway, which controls refueling of multiple myeloma (MM) clones, might be critical to disease recurrence. Although several studies suggest the Hh pathway is activated in CD138- immature cells, differentiated CD138+ plasma cells might also be able to self-renew by producing themselves the Hh ligands. We studied the gene expression profiles of 126 newly diagnosed MM patients analyzed in both the CD138+ plasma cell fraction and CD138-CD19+ B-cell compartment. Results demonstrated that an Hh-gene signature was able to cluster patients in two subgroups characterized by the opposite Hh pathway expression in mature plasma cells and their precursors. Strikingly, patients characterized by Hh hyperactivation in plasma cells, but not in their B cells, displayed high genomic instability and an unfavorable outcome in terms of shorter progression-free survival (hazard ratio: 1.92; 95% confidence interval: 1.19-3.07) and overall survival (hazard ratio: 2.61; 95% confidence interval: 1.26-5.38). These results suggest that the mechanisms triggered by the Hh pathway ultimately led to identify a more indolent vs a more aggressive biological and clinical subtype of MM. Therefore, patient stratification according to their molecular background might help the fine-tuning of future clinical and therapeutic studies.

  15. NCBI viral genomes resource.

    Science.gov (United States)

    Brister, J Rodney; Ako-Adjei, Danso; Bao, Yiming; Blinkova, Olga

    2015-01-01

    Recent technological innovations have ignited an explosion in virus genome sequencing that promises to fundamentally alter our understanding of viral biology and profoundly impact public health policy. Yet, any potential benefits from the billowing cloud of next generation sequence data hinge upon well implemented reference resources that facilitate the identification of sequences, aid in the assembly of sequence reads and provide reference annotation sources. The NCBI Viral Genomes Resource is a reference resource designed to bring order to this sequence shockwave and improve usability of viral sequence data. The resource can be accessed at http://www.ncbi.nlm.nih.gov/genome/viruses/ and catalogs all publicly available virus genome sequences and curates reference genome sequences. As the number of genome sequences has grown, so too have the difficulties in annotating and maintaining reference sequences. The rapid expansion of the viral sequence universe has forced a recalibration of the data model to better provide extant sequence representation and enhanced reference sequence products to serve the needs of the various viral communities. This, in turn, has placed increased emphasis on leveraging the knowledge of individual scientific communities to identify important viral sequences and develop well annotated reference virus genome sets.

  16. Human CD38hiCD138⁺ plasma cells can be generated in vitro from CD40-activated switched-memory B lymphocytes.

    Science.gov (United States)

    Maïga, Rayelle Itoua; Bonnaure, Guillaume; Rochette, Josiane Tremblay; Néron, Sonia

    2014-01-01

    B lymphocyte differentiation into long-lived plasma cells is the keystone event for the production of long-term protective antibodies. CD40-CD154 and CD27-CD70 interactions are involved in human B lymphocyte differentiation into CD38(hi)CD138(+) cells in vivo as well as in vitro. In this study, we have compared these interactions in their capacity to drive switched-memory B lymphocytes differentiation into CD38(hi)CD138(+) plasma cells. The targeted B lymphocytes were isolated from human peripheral blood, expanded for 19 days, and then submitted to CD70 or CD154 interactions for 14 days. The expanded B lymphocytes were constitutively expressing CD39, whereas CD31's expression was noticed only following the in vitro differentiation step (day 5) and was exclusively present on the CD38(hi) cell population. Furthermore, the generated CD38(hi)CD138(+) cells showed a higher proportion of CD31(+) cells than the CD38(hi)CD138(-) cells. Besides, analyses done with human blood and bone marrow plasma cells showed that in vivo and de novo generated CD38(hi)CD138(+) cells have a similar CD31 expression profile but are distinct according to their reduced CD39 expression level. Overall, we have evidences that in vitro generated plasma cells are heterogeneous and appear as CD39(+) precursors to the ones present in bone marrow niches.

  17. White-Light Diffraction with a CD

    Science.gov (United States)

    Ivanov, Dragia Trifonov; Nikolaev, Stefan

    2010-01-01

    Various wave optics experiments can be carried out using an ordinary compact disc. The CD is suitable for use as a diffraction grating. For instance, a standard CD (700 MB) has 625 lines/mm. In this article, the authors describe two white-light diffraction demonstrations for a large audience, realizable using a CD (as reflection or transmission…

  18. Biomaterials supported CdS nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Balu, Alina M. [Institute of Physical Chemistry ' Ilie Murgulescu' , Spl. Independentei 202, 060021 Bucharest (Romania); Departamento de Quimica Organica, Campus de Rabanales, Edificio Marie Curie, Ctra Nnal IV, Km 396, Universidad de Cordoba, E-14014 Cordoba (Spain); Campelo, Juan M. [Departamento de Quimica Organica, Campus de Rabanales, Edificio Marie Curie, Ctra Nnal IV, Km 396, Universidad de Cordoba, E-14014 Cordoba (Spain); Luque, Rafael, E-mail: q62alsor@uco.es [Departamento de Quimica Organica, Campus de Rabanales, Edificio Marie Curie, Ctra Nnal IV, Km 396, Universidad de Cordoba, E-14014 Cordoba (Spain); Rajabi, Fatemeh [Department of Science, Payame Noor University, PO Box 878, Qazvin (Iran, Islamic Republic of); Romero, Antonio A. [Departamento de Quimica Organica, Campus de Rabanales, Edificio Marie Curie, Ctra Nnal IV, Km 396, Universidad de Cordoba, E-14014 Cordoba (Spain)

    2010-11-01

    CdS quantum dot materials were prepared through a simple room temperature deposition of CdS nanocrystals on biomaterials including starch and chitosan. Materials obtained were found to contain differently distributed CdS nanocrystals on the surface of the biopolymers, making them potentially interesting for biomedical applications as contrast agents and/or in photocatalysis.

  19. Giant omental lipoblastoma and CD56 expression

    Directory of Open Access Journals (Sweden)

    Go Miyano

    2013-01-01

    Full Text Available We report a case of giant omental lipoblastoma in a 13-month-old boy, which was treated successfully by total excision. Tumor cells were positive for S100, CD34 and CD56. This is the first report of lipoblastoma expressing CD56, a fact that could be used to differentiate lipoblastoma from liposarcoma.

  20. Characterization of Foxp3+CD4+CD25+ and IL-10-secreting CD4+CD25+ T cells during cure of colitis.

    Science.gov (United States)

    Uhlig, Holm H; Coombes, Janine; Mottet, Christian; Izcue, Ana; Thompson, Claire; Fanger, Andrea; Tannapfel, Andrea; Fontenot, Jason D; Ramsdell, Fred; Powrie, Fiona

    2006-11-01

    CD4+CD25+ regulatory T cells can prevent and resolve intestinal inflammation in the murine T cell transfer model of colitis. Using Foxp3 as a marker of regulatory T cell activity, we now provide a comprehensive analysis of the in vivo distribution of Foxp3+CD4+CD25+ cells in wild-type mice, and during cure of experimental colitis. In both cases, Foxp3+CD4+CD25+ cells were found to accumulate in the colon and secondary lymphoid organs. Importantly, Foxp3+ cells were present at increased density in colon samples from patients with ulcerative colitis or Crohn's disease, suggesting similarities in the behavior of murine and human regulatory cells under inflammatory conditions. Cure of murine colitis was dependent on the presence of IL-10, and IL-10-producing CD4+CD25+ T cells were enriched within the colon during cure of colitis and also under steady state conditions. Our data indicate that although CD4+CD25+ T cells expressing Foxp3 are present within both lymphoid organs and the colon, subsets of IL-10-producing CD4+CD25+ T cells are present mainly within the intestinal lamina propria suggesting compartmentalization of the regulatory T cell response at effector sites.

  1. Genomic taxonomy of vibrios

    Directory of Open Access Journals (Sweden)

    Iida Tetsuya

    2009-10-01

    Full Text Available Abstract Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA, supertrees, Average Amino Acid Identity (AAI, genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.. A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in

  2. Human Genome Project

    Energy Technology Data Exchange (ETDEWEB)

    Block, S. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Cornwall, J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dally, W. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Dyson, F. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Fortson, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Joyce, G. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Kimble, H. J. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Lewis, N. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Max, C. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Prince, T. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Schwitters, R. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Weinberger, P. [The MITRE Corporation, McLean, VA (US). JASON Program Office; Woodin, W. H. [The MITRE Corporation, McLean, VA (US). JASON Program Office

    1998-01-04

    The study reviews Department of Energy supported aspects of the United States Human Genome Project, the joint National Institutes of Health/Department of Energy program to characterize all human genetic material, to discover the set of human genes, and to render them accessible for further biological study. The study concentrates on issues of technology, quality assurance/control, and informatics relevant to current effort on the genome project and needs beyond it. Recommendations are presented on areas of the genome program that are of particular interest to and supported by the Department of Energy.

  3. Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1993-01-01

    The DOE Human Genome program has grown tremendously, as shown by the marked increase in the number of genome-funded projects since the last workshop held in 1991. The abstracts in this book describe the genome research of DOE-funded grantees and contractors and invited guests, and all projects are represented at the workshop by posters. The 3-day meeting includes plenary sessions on ethical, legal, and social issues pertaining to the availability of genetic data; sequencing techniques, informatics support; and chromosome and cDNA mapping and sequencing.

  4. Genomic signal processing

    CERN Document Server

    Shmulevich, Ilya

    2007-01-01

    Genomic signal processing (GSP) can be defined as the analysis, processing, and use of genomic signals to gain biological knowledge, and the translation of that knowledge into systems-based applications that can be used to diagnose and treat genetic diseases. Situated at the crossroads of engineering, biology, mathematics, statistics, and computer science, GSP requires the development of both nonlinear dynamical models that adequately represent genomic regulation, and diagnostic and therapeutic tools based on these models. This book facilitates these developments by providing rigorous mathema

  5. Center for Cancer Genomics | Office of Cancer Genomics

    Science.gov (United States)

    The Center for Cancer Genomics (CCG) was established to unify the National Cancer Institute's activities in cancer genomics, with the goal of advancing genomics research and translating findings into the clinic to improve the precise diagnosis and treatment of cancers. In addition to promoting genomic sequencing approach

  6. Reactivity of naive CD4+CD25- T cells against gut microflora in healthy mice

    DEFF Research Database (Denmark)

    Gad, Monika; Lundsgaard, Dorthe; Kjellev, Stine

    2006-01-01

    . Upon enteroantigen activation, the CD4+ CD25- T cells secrete IL-4, IL-5, IL-10, granulocyte macrophage colony-stimulating factor, tumor necrosis factor-alpha and IFN-gamma. Clonotype mapping of the TCRBV regions 1-18 of enteroantigen-reactive CD4+ CD25- T cells by TCR clonotype mapping revealed...

  7. Isolation and identification of CD4+CD25+ regulatory T cells in rat

    Institute of Scientific and Technical Information of China (English)

    Ling Lü; Feng Zhang; Liyong Pu; Chao Jiang

    2006-01-01

    Objective: To establish a stable and high efficient method for collection of CD4+CD25+ regulatory T cells from rats in vitro. Methods: CD4+CD25+ regulatory T cells were isolated from the rat splenic cells through two steps by magic cell sorting (MACS) system. The first step was negative selection of CD4+ T cells by cocktail antibodies and anti-IgG magic microbeads, and the second step was positive selection of CD25+ T cells by anti-CD25 PE and anti-PE magic microbeads. The purity and viability of separated cells were measured by flow cytometry (FACS) and Trypan blue staining. The suppressive ability of seperated cells on the proliferation of CD4+CD25- T cells was assessed by cell proliferation assay. Results: The purity of negatively enriched CD4+ T cells was 79%-87% (83.6% ± 2.5%) , and the purity of positively enriched CD4+CD25+ T cells was 86%-93% ( 90.2 ± 1.8%) with the viability of 92%-95% (92.8% ± 3.4%). The enriched cells significantly suppressed the proliferation of CD4+CD25- T cells in mixed lymphocyte culture (P < 0.05). Conclusion: An effective method can be established for enrichment of CD4+CD25+ regulatory T cells in two steps by MACS, with satisfied cell purity, viability and function.

  8. Regulation and gene expression profiling of NKG2D positive human cytomegalovirus-primed CD4+ T-cells.

    Directory of Open Access Journals (Sweden)

    Helle Jensen

    Full Text Available NKG2D is a stimulatory receptor expressed by natural killer (NK cells, CD8(+ T-cells, and γδ T-cells. NKG2D expression is normally absent from CD4(+ T-cells, however recently a subset of NKG2D(+ CD4(+ T-cells has been found, which is specific for human cytomegalovirus (HCMV. This particular subset of HCMV-specific NKG2D(+ CD4(+ T-cells possesses effector-like functions, thus resembling the subsets of NKG2D(+ CD4(+ T-cells found in other chronic inflammations. However, the precise mechanism leading to NKG2D expression on HCMV-specific CD4(+ T-cells is currently not known. In this study we used genome-wide analysis of individual genes and gene set enrichment analysis (GSEA to investigate the gene expression profile of NKG2D(+ CD4(+ T-cells, generated from HCMV-primed CD4(+ T-cells. We show that the HCMV-primed NKG2D(+ CD4(+ T-cells possess a higher differentiated phenotype than the NKG2D(- CD4(+ T-cells, both at the gene expression profile and cytokine profile. The ability to express NKG2D at the cell surface was primarily determined by the activation or differentiation status of the CD4(+ T-cells and not by the antigen presenting cells. We observed a correlation between CD94 and NKG2D expression in the CD4(+ T-cells following HCMV stimulation. However, knock-down of CD94 did not affect NKG2D cell surface expression or signaling. In addition, we show that NKG2D is recycled at the cell surface of activated CD4(+ T-cells, whereas it is produced de novo in resting CD4(+ T-cells. These findings provide novel information about the gene expression profile of HCMV-primed NKG2D(+ CD4(+ T-cells, as well as the mechanisms regulating NKG2D cell surface expression.

  9. CD4/CD8 double negative mycosis fungoides with PD-1 (CD279) expression--a disease of follicular helper T-cells?

    OpenAIRE

    Kempf, Werner; Dmitry V. Kazakov; Cipolat, Claudio; Kutzner, Heinz; Roncador, Giovanna; Tomasini, Dario

    2012-01-01

    CD4/CD8 double negative mycosis fungoides (MF) is a rare phenotypic variant of this epidermotropic cutaneous T-cell lymphoma. Clinically, this MF form manifests with unusual appearances such as annular lesions confined to one body region as in our patient in whom the lesions were found on the left lower leg. The cellular origin of CD4/CD8 double negative MF is unknown. In our case, the intraepidermal CD4/CD8 double negative clonal T-lymphocytes (CD2+, CD4-, CD8-, CD30-, beta-F1+) expressed pr...

  10. Restrictions to HIV-1 replication in resting CD4+T lymphocytes

    Institute of Scientific and Technical Information of China (English)

    Xiaoyu Pan; Hanna-Mari Baldauf; Oliver T Keppler; Oliver T Fackler

    2013-01-01

    CD4+ T lymphocytes represent the main target cell population of human immunodeficiency virus (HIV).In an activated state,CD4+ T cells residing in lymphoid organs are a major reservoir of ongoing HIV-1 replication in infected individuals.In contrast,resting CD4+ T cells are highly resistant to productive HIV-1 infection,yet are massively depleted during disease progression and represent a substantial latent reservoir for the virus in vivo.Barriers preventing replication of HIV-1 in resting CD4+ T cells include a rigid layer of cortical actin and,early after HIV-1entry,a block that limits reverse transcription of incoming viral RNA genomes.Defining the molecular bases of these restrictions has remained one of the central open questions in HIV research.Recent advances unraveled mechanisms by which HIV-1 bypasses the entry block and established the host cell restriction factor SAMHD1,a deoxynucleoside triphosphate triphosphohydrolase,as a central determinant of the cellular restriction to HIV-1 reverse transcription in resting CD4+ T cells.This review summarizes our current molecular and pathophysiological understanding of the multi-faceted interactions of HIV-1 with resting CD4+ T lymphocytes.

  11. Analysis of circulating regulatory T cells (CD4+CD25+CD127-) after cryosurgery in prostate cancer

    Institute of Scientific and Technical Information of China (English)

    Tong-Guo Si; Jun-Ping Wang; Zhi Guo

    2013-01-01

    This study was performed to assess the response of regulatory T cells (Tregs) following cryosurgery in prostate cancer (PCa) patients by measuring their frequency and immune function.Blood was collected prior to and at 4 and 8 weeks after treatment in 30 patients with high-risk PCa who underwent cryosurgery and from 15 healthy volunteers.Circulating CD4+CD25+CD127-Tregs were isolated.Their frequency was detected by flow cytometry,and immune suppressive function was evaluated by measuring the proliferation of CD4+CD25-T cells cocultured with Tregs.The results showed that the percentage of circulating CD4+CD25+CD127-Tregs was increased in PCa patients compared to healthy volunteers (7.6%±0.73% vs.5.8%±-0.54%,P<0.001).The frequency of circulating CD4+CD25+CD127-Tregs was reduced 4 weeks after cryosurgery compared to before surgery (6.3%±0.58% vs.7.6%±0.73%,P<0.001),and the decrease persisted for 8 weeks.However,the suppressive function of Tregs was increased in eight of 12 patients,which might contribute to cancer recurrence.Then the response of circulating rregs is complicated after cryosurgery for PCa,and further studies are warranted.

  12. Characterization of CdS thin film in high efficient CdS/CdTe solar cells

    Science.gov (United States)

    Tsuji, Miwa; Aramoto, Tetsuya; Ohyama, Hideaki; Hibino, Takeshi; Omura, Kuniyoshi

    2000-06-01

    Cadmium sulfide (CdS) thin film is the most commonly used window material for high-efficient cadmium telluride (CdTe) thin-film photovoltaic devices. High-efficient CdS/CdTe solar cells have been developed using ultra-thin CdS films having a thickness of below 0.1 μm. CdS film is deposited on transparent conductive oxide (TCO) film coated glass substrates by the metal organic chemical vapor deposition (MOCVD) technique, CdTe film is subsequently deposited by the close-spaced sublimation (CSS) technique. Finally, carbon and Ag-In electrodes are fabricated by the screen printing and sintering method. Cell performance depends primarily on the electrical and optical properties of CdS film, and hence we started to develop higher quality CdS film and found out clear differences between high- and low-quality CdS films from various analyses: SEM, AFM, SIMS, TDS and FT-IR. As a result of controlling qualities of CdS films, photovoltaic conversion efficiency of 10.5% has been achieved for a size of 1376 cm 2 of the solar module under air mass (AM) 1.5 conditions by the Japan Quality Assurance Organization (JQA).

  13. Genomic libraries: I. Construction and screening of fosmid genomic libraries.

    Science.gov (United States)

    Quail, Mike A; Matthews, Lucy; Sims, Sarah; Lloyd, Christine; Beasley, Helen; Baxter, Simon W

    2011-01-01

    Large insert genome libraries have been a core resource required to sequence genomes, analyze haplotypes, and aid gene discovery. While next generation sequencing technologies are revolutionizing the field of genomics, traditional genome libraries will still be required for accurate genome assembly. Their utility is also being extended to functional studies for understanding DNA regulatory elements. Here, we present a detailed method for constructing genomic fosmid libraries, testing for common contaminants, gridding the library to nylon membranes, then hybridizing the library membranes with a radiolabeled probe to identify corresponding genomic clones. While this chapter focuses on fosmid libraries, many of these steps can also be applied to bacterial artificial chromosome libraries.

  14. Cu-Doped-CdS/In-Doped-CdS Cosensitized Quantum Dot Solar Cells

    Directory of Open Access Journals (Sweden)

    Lin Li

    2014-01-01

    Full Text Available Cu-doped-CdS and In-doped-CdS cosensitized (Cu-doped-CdS/In-doped-CdS quantum dot solar cells (QDSCs are introduced here. Different cosensitized sequences, doping ratios, and the thickness (SILAR cycles of Cu-doped-CdS and In-doped-CdS are discussed. Compared with undoped CdS QDSCs, the short circuit current density, UV-Vis absorption spectra, IPCE (monochromatic incident photon-to-electron conversion, open circuit voltage, and so on are all improved. The photoelectric conversion efficiency has obviously improved from 0.71% to 1.28%.

  15. Soluble CD36- a marker of the (pathophysiological) role of CD36 in the metabolic syndrome?

    DEFF Research Database (Denmark)

    Koonen, Debby P Y; Jensen, Majken K; Handberg, Aase

    2011-01-01

    associated with obesity and lipid components of the metabolic syndrome, with risk of heart disease and type 2 diabetes. Recently, non-cell bound CD36 was identified in human plasma and was termed soluble CD36 (sCD36). In this review we will describe the functions of CD36 in tissues and address the role of s......CD36 is a class B scavenger receptor observed in many cell types and tissues throughout the body. Recent literature has implicated CD36 in the pathogenesis of metabolic dysregulation such as found in obesity, insulin resistance, and atherosclerosis. Genetic variation at the CD36 loci have been...

  16. Challenges and Prospects for Developing CdS/CdTe Substrate Solar Cells on Mo foils

    OpenAIRE

    Williams, Ben; Major, Jonathan; Bowen, Leon; Phillips, Laurie; Zoppi, Guillaume; Forbes, Ian; Durose, Ken

    2014-01-01

    ITO/ZnO/CdS/CdTe/Mo solar cells have been grown in the substrate configuration by a combination of close-space sublimation and RF sputtering. A peak efficiency of 8.01% was achieved. A two stage CdCl2 annealing process was developed, with the first stage contributing to CdTe doping and the second being linked to CdTe/CdS interdiffusion by secondary ion mass spectrometry analysis. The inclusion of a ZnO layer between CdS and ITO layers improved performance significantly (from η=6% to η=8%) by ...

  17. Electrodeposition, characterization and photo electrochemical properties of CdSe and CdTe

    OpenAIRE

    Atef Y. Shenouda; El Sayed, El Sayed M.

    2015-01-01

    CdSe and CdTe are electrodeposited using 0.1 M Cd2+ and different ion concentrations of Se and Te. The effect of the temperature on the electrodeposition process is also studied. The crystal structure of the deposited CdSe and CdTe is investigated by X-ray diffraction (XRD). Scanning electron microscopy (SEM) of samples deposited at optimized parameters reveals that CdSe has spongy spherical grains while CdTe has coralloid morphology. Optical absorption shows the presence of direct transition...

  18. Evaluation of Stem Cell Markers, CD44/CD24 in Breast Cancer Cell Lines

    Directory of Open Access Journals (Sweden)

    Masoud Hashemi Arabi

    2014-05-01

    Four breast cancer cell lines, MCF-7 ، T47D ، MDA-MB231 and MDA-MB468 were purchased from National cell Bank of Iran based in Iran Pasture Institute and were cultured in high glucose DMEM supplemented with 10% FCS. Cells were stained with antiCD44-PE and antiCD24-FITC antibodies and Status of CD44 and CD24 as markers of breast cancer stem cells were evaluated using flow cytometer and fluorescent microscopy.Evaluation of CD44 and CD24 as markers of breast cancer stem cells showed that MDA-MB231 with 97±1.2% CD44+/CD24-/low cells is significantly different from the others that they were mainly CD44 and CD24 positive cells(p

  19. High-Efficiency Photochemical Water Splitting of CdZnS/CdZnSe Nanostructures

    OpenAIRE

    2013-01-01

    We have prepared and employed TiO2/CdZnS/CdZnSe electrodes for photochemical water splitting. The TiO2/CdZnS/CdZnSe electrodes consisting of sheet-like CdZnS/CdZnSe nanostructures (8–10 μm in length and 5–8 nm in width) were prepared through chemical bath deposition on TiO2 substrates. The TiO2/CdZnS/CdZnSe electrodes have light absorption over the wavelength 400–700 nm and a band gap of 1.87 eV. Upon one sun illumination of 100 mW cm−2, the TiO2/CdZnS/CdZnSe electrodes provide a significant ...

  20. Photovoltaic properties of sintered CdS/CdTe solar cells doped with Cu

    Science.gov (United States)

    Park, J. W.; Ahn, B. T.; Im, H. B.; Kim, C. S.

    1992-11-01

    The effect of Cu doping before sintering on the photovoltaic properties of sintered CdS/CdTe solar cells were investigated by putting various amounts of CuCl2 either into the CdTe layer or into the back contact carbon layer. It was found that, as the amount of CuCl2 in the CdTe layers increased up to 25 ppm, the cell parameters of the sintered CdS/CdTe solar cells remained at about the same values, and then decreased sharply with further increase of CuCl2. The decreases in cell parameters are caused mainly by the increase in the resistivity of CdS and CdTe layer and the decrease in the optical transmission of CdS due to Cu doping from the CdTe.

  1. CD44+/CD24- Cancer Stem Cells Are Associated With Higher Grade of Canine Mammary Carcinomas.

    Science.gov (United States)

    Im, K S; Jang, Y G; Shin, J I; Kim, N H; Lim, H Y; Lee, S M; Kim, J H; Sur, J H

    2015-11-01

    The CD44+/CD24- phenotype identifies cancer stem cell (CSC) properties in canine mammary carcinoma (MC); however, the histopathological features associated with this phenotype remain to be elucidated. Here, we determined whether the CD44+/CD24- phenotype was associated with hormonal receptor (HR; estrogen receptor [ER] and/or progesterone receptor [PR]) status and/or triple (ER, PR, and human epithelial growth factor receptor 2)-negative (TN) subtype; conventional histological evaluation was also performed. We found that, as single markers, both CD44+ and CD24+ were associated with less aggressive histological types, low grade, and a non-TN subtype; both markers were associated with HR positivity. On the other hand, a CD44+/CD24- phenotype was associated with higher grade of carcinoma. Therefore, our results suggest that immunohistochemical phenotyping for CD44/CD24 is useful for the evaluation of tumor behavior as well as CSC-like properties in canine MCs.

  2. Expression of CD133 in acute leukemia.

    Science.gov (United States)

    Tolba, Fetnat M; Foda, Mona E; Kamal, Howyda M; Elshabrawy, Deena A

    2013-06-01

    There have been conflicting results regarding a correlation between CD133 expression and disease outcome. To assess CD133 expression in patients with acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) and to evaluate its correlation with the different clinical and laboratory data as well as its relation to disease outcome, the present study included 60 newly diagnosed acute leukemic patients; 30 ALL patients with a male to female ratio of 1.5:1 and their ages ranged from 9 months to 48 years, and 30 AML patients with a male to female ratio of 1:1 and their ages ranged from 17 to 66 years. Flow cytometric assessment of CD133 expression was performed on blast cells. In ALL, no correlations were elicited between CD133 expression and some monoclonal antibodies, but in AML group, there was a significant positive correlation between CD133 and HLA-DR, CD3, CD7 and TDT, CD13 and CD34. In ALL group, patients with negative CD133 expression achieved complete remission more than patients with positive CD133 expression. In AML group, there was no statistically significant association found between positive CD133 expression and treatment outcome. The Kaplan-Meier curve illustrated a high significant negative correlation between CD133 expression and the overall survival of the AML patients. CD133 expression is an independent prognostic factor in acute leukemia, especially ALL patients and its expression could characterize a group of acute leukemic patients with higher resistance to standard chemotherapy and relapse. CD133 expression was highly associated with poor prognosis in acute leukemic patients.

  3. Mouse Genome Informatics (MGI)

    Data.gov (United States)

    U.S. Department of Health & Human Services — MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human...

  4. Epidemiology & Genomics Research Program

    Science.gov (United States)

    The Epidemiology and Genomics Research Program, in the National Cancer Institute's Division of Cancer Control and Population Sciences, funds research in human populations to understand the determinants of cancer occurrence and outcomes.

  5. Yeast genome sequencing:

    DEFF Research Database (Denmark)

    Piskur, Jure; Langkjær, Rikke Breinhold

    2004-01-01

    For decades, unicellular yeasts have been general models to help understand the eukaryotic cell and also our own biology. Recently, over a dozen yeast genomes have been sequenced, providing the basis to resolve several complex biological questions. Analysis of the novel sequence data has shown...... of closely related species helps in gene annotation and to answer how many genes there really are within the genomes. Analysis of non-coding regions among closely related species has provided an example of how to determine novel gene regulatory sequences, which were previously difficult to analyse because...... they are short and degenerate and occupy different positions. Comparative genomics helps to understand the origin of yeasts and points out crucial molecular events in yeast evolutionary history, such as whole-genome duplication and horizontal gene transfer(s). In addition, the accumulating sequence data provide...

  6. The Lotus japonicus genome

    DEFF Research Database (Denmark)

    This book provides insights into some of the key achievements made in the study of Lotus japonicus (birdsfoot trefoil), as well as a timely overview of topics that are pertinent for future developments in legume genomics. Key topics covered include endosymbiosis, development, hormone regulation......, carbon/nitrogen and secondary metabolism, as well as advances made in high-throughput genomic and genetic approaches. Research focusing on model plants has underpinned the recent growth in plant genomics and genetics and provided a basis for investigations of major crop species. In the legume family...... Fabaceae, groundbreaking genetic and genomic research has established a significant body of knowledge on Lotus japonicus, which was adopted as a model species more than 20 years ago. The diverse nature of legumes means that such research has a wide potential and agricultural impact, for example...

  7. Lophotrochozoan mitochondrial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Yvonne; Boore, Jeffrey L.

    2005-10-01

    Progress in both molecular techniques and phylogeneticmethods has challenged many of the interpretations of traditionaltaxonomy. One example is in the recognition of the animal superphylumLophotrochozoa (annelids, mollusks, echiurans, platyhelminthes,brachiopods, and other phyla), although the relationships within thisgroup and the inclusion of some phyla remain uncertain. While much ofthis progress in phylogenetic reconstruction has been based on comparingsingle gene sequences, we are beginning to see the potential of comparinglarge-scale features of genomes, such as the relative order of genes.Even though tremendous progress is being made on the sequencedetermination of whole nuclear genomes, the dataset of choice forgenome-level characters for many animals across a broad taxonomic rangeremains mitochondrial genomes. We review here what is known aboutmitochondrial genomes of the lophotrochozoans and discuss the promisethat this dataset will enable insight into theirrelationships.

  8. The genomics of adaptation.

    Science.gov (United States)

    Radwan, Jacek; Babik, Wiesław

    2012-12-22

    The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

  9. Mouse genome database 2016.

    Science.gov (United States)

    Bult, Carol J; Eppig, Janan T; Blake, Judith A; Kadin, James A; Richardson, Joel E

    2016-01-01

    The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these data to human biology and disease. As the cost of genome-scale sequencing continues to decrease and new technologies for genome editing become widely adopted, the laboratory mouse is more important than ever as a model system for understanding the biological significance of human genetic variation and for advancing the basic research needed to support the emergence of genome-guided precision medicine. Recent enhancements to MGD include new graphical summaries of biological annotations for mouse genes, support for mobile access to the database, tools to support the annotation and analysis of sets of genes, and expanded support for comparative biology through the expansion of homology data.

  10. Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

    OpenAIRE

    Jaffe, David B.; Butler, Jonathan; Gnerre, Sante; Mauceli, Evan; Lindblad-Toh, Kerstin; Jill P. Mesirov; Michael C Zody; Lander, Eric S.

    2003-01-01

    We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Three principal changes were simultaneously made and applied to the assembly of the mouse genome, during a six-month period of development: (1) Supercontigs (scaffolds) were iteratively broken and rej...

  11. Construction of recombinant eukaryotic expression plasmid containing murine CD40 ligand gene and its expression in H22 cells

    Institute of Scientific and Technical Information of China (English)

    Yong-Fang Jiang; Yan He; Guo-Zhong Gong; Jun Chen; Chun-Yan Yang; Yun Xu

    2005-01-01

    AIM: To construct a recombinant murine CD40 ligand (mCD40L) eukaryotic expression vector for gene therapy and target therapy of hepatocellular carcinoma (HCC).METHODS: mCD40L cDNA was synthesized by RT-PCR with the specific primers and directly cloned into T vector to generate middle recombinant. After digestion with restriction endonuclease, the target fragment was subcloned into the multi-clone sites of the eukaryotic vector. The constructed vector was verified by enzyme digestion and sequencing,and the product expressed was detected by RT-PCR and immunofluorescence methods.RESULTS: The full-length mCD40L-cDNA was successfully cloned into the eukaryotic vector through electrophoresis,and mCD40L gene was integrated into the genome of infected H22 cells by RT-PCR. Murine CD40L antigen molecule was observed in the plasma of mCD40L-H22 by indirect immuno-fluorescence staining.CONCLUSION: The recombined mCD40L eukaryotic expression vector can be expressed in H22 cell line. It providesexperimental data for gene therapy and target therapy ofhepatocellular carcinoma.

  12. Spectral response of CdS/CdTe solar cells obtained with different S/Cd ratios for the CdS chemical bath

    Energy Technology Data Exchange (ETDEWEB)

    Vigil-Galan, O.; Sastre-Hernandez, J.; Contreras-Puente, G.; Tufino-Velazquez, M. [Escuela Superior de Fisica y Matematicas, Instituto Politecnico Nacional, 07738 Mexico D. F. (Mexico); Arias-Carbajal, A. [Facultad de Quimica, IMRE, Universidad de La Habana, 10400 La Habana (Cuba); Mendoza-Perez, R. [Universidad Autonoma de la Ciudad de Mexico, 09970 Mexico, D. F. (Mexico); Santana, G. [Instituto de Investigacion en Materiales, UNAM, 04510 Mexico, D. F. (Mexico); Morales-Acevedo, A. [Departamento de Ingenieria Electrica, CINVESTAV-IPN, 07360 Mexico, D. F. (Mexico)

    2006-09-22

    In this work, the influence of the variation of chemical bath thiourea concentration in the solution for depositing CdS layers upon the spectral response of chemical bath deposition (CBD)-CdS/CdTe solar cells is studied. Although changes in the short and long wavelength range for the spectral response of the cells were observed in dependence of the thiourea concentration, no significant changes were observed in the diffusion length of minority carriers in the CdTe layer, as determined from the constant photocurrent method, when the thiourea concentration is increased in the CdS deposition solution. (author)

  13. An Introduction to Genome Annotation.

    Science.gov (United States)

    Campbell, Michael S; Yandell, Mark

    2015-12-17

    Genome projects have evolved from large international undertakings to tractable endeavors for a single lab. Accurate genome annotation is critical for successful genomic, genetic, and molecular biology experiments. These annotations can be generated using a number of approaches and available software tools. This unit describes methods for genome annotation and a number of software tools commonly used in gene annotation.

  14. Decoding the human genome

    CERN Document Server

    CERN. Geneva. Audiovisual Unit; Antonerakis, S E

    2002-01-01

    Decoding the Human genome is a very up-to-date topic, raising several questions besides purely scientific, in view of the two competing teams (public and private), the ethics of using the results, and the fact that the project went apparently faster and easier than expected. The lecture series will address the following chapters: Scientific basis and challenges. Ethical and social aspects of genomics.

  15. Molluscan Evolutionary Genomics

    Energy Technology Data Exchange (ETDEWEB)

    Simison, W. Brian; Boore, Jeffrey L.

    2005-12-01

    In the last 20 years there have been dramatic advances in techniques of high-throughput DNA sequencing, most recently accelerated by the Human Genome Project, a program that has determined the three billion base pair code on which we are based. Now this tremendous capability is being directed at other genome targets that are being sampled across the broad range of life. This opens up opportunities as never before for evolutionary and organismal biologists to address questions of both processes and patterns of organismal change. We stand at the dawn of a new 'modern synthesis' period, paralleling that of the early 20th century when the fledgling field of genetics first identified the underlying basis for Darwin's theory. We must now unite the efforts of systematists, paleontologists, mathematicians, computer programmers, molecular biologists, developmental biologists, and others in the pursuit of discovering what genomics can teach us about the diversity of life. Genome-level sampling for mollusks to date has mostly been limited to mitochondrial genomes and it is likely that these will continue to provide the best targets for broad phylogenetic sampling in the near future. However, we are just beginning to see an inroad into complete nuclear genome sequencing, with several mollusks and other eutrochozoans having been selected for work about to begin. Here, we provide an overview of the state of molluscan mitochondrial genomics, highlight a few of the discoveries from this research, outline the promise of broadening this dataset, describe upcoming projects to sequence whole mollusk nuclear genomes, and challenge the community to prepare for making the best use of these data.

  16. MIR retrotransposon sequences provide insulators to the human genome.

    Science.gov (United States)

    Wang, Jianrong; Vicente-García, Cristina; Seruggia, Davide; Moltó, Eduardo; Fernandez-Miñán, Ana; Neto, Ana; Lee, Elbert; Gómez-Skarmeta, José Luis; Montoliu, Lluís; Lunyak, Victoria V; Jordan, I King

    2015-08-11

    Insulators are regulatory elements that help to organize eukaryotic chromatin via enhancer-blocking and chromatin barrier activity. Although there are several examples of transposable element (TE)-derived insulators, the contribution of TEs to human insulators has not been systematically explored. Mammalian-wide interspersed repeats (MIRs) are a conserved family of TEs that have substantial regulatory capacity and share sequence characteristics with tRNA-related insulators. We sought to evaluate whether MIRs can serve as insulators in the human genome. We applied a bioinformatic screen using genome sequence and functional genomic data from CD4(+) T cells to identify a set of 1,178 predicted MIR insulators genome-wide. These predicted MIR insulators were computationally tested to serve as chromatin barriers and regulators of gene expression in CD4(+) T cells. The activity of predicted MIR insulators was experimentally validated using in vitro and in vivo enhancer-blocking assays. MIR insulators are enriched around genes of the T-cell receptor pathway and reside at T-cell-specific boundaries of repressive and active chromatin. A total of 58% of the MIR insulators predicted here show evidence of T-cell-specific chromatin barrier and gene regulatory activity. MIR insulators appear to be CCCTC-binding factor (CTCF) independent and show a distinct local chromatin environment with marked peaks for RNA Pol III and a number of histone modifications, suggesting that MIR insulators recruit transcriptional complexes and chromatin modifying enzymes in situ to help establish chromatin and regulatory domains in the human genome. The provisioning of insulators by MIRs across the human genome suggests a specific mechanism by which TE sequences can be used to modulate gene regulatory networks.

  17. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  18. Human Genome Annotation

    Science.gov (United States)

    Gerstein, Mark

    A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. My talk will focus on annotating the 99% of the genome that does not code for canonical genes, concentrating on intergenic features such as structural variants (SVs), pseudogenes (protein fossils), binding sites, and novel transcribed RNAs (ncRNAs). In particular, I will describe how we identify regulatory sites and variable blocks (SVs) based on processing next-generation sequencing experiments. I will further explain how we cluster together groups of sites to create larger annotations. Next, I will discuss a comprehensive pseudogene identification pipeline, which has enabled us to identify >10K pseudogenes in the genome and analyze their distribution with respect to age, protein family, and chromosomal location. Throughout, I will try to introduce some of the computational algorithms and approaches that are required for genome annotation. Much of this work has been carried out in the framework of the ENCODE, modENCODE, and 1000 genomes projects.

  19. Human social genomics.

    Directory of Open Access Journals (Sweden)

    Steven W Cole

    2014-08-01

    Full Text Available A growing literature in human social genomics has begun to analyze how everyday life circumstances influence human gene expression. Social-environmental conditions such as urbanity, low socioeconomic status, social isolation, social threat, and low or unstable social status have been found to associate with differential expression of hundreds of gene transcripts in leukocytes and diseased tissues such as metastatic cancers. In leukocytes, diverse types of social adversity evoke a common conserved transcriptional response to adversity (CTRA characterized by increased expression of proinflammatory genes and decreased expression of genes involved in innate antiviral responses and antibody synthesis. Mechanistic analyses have mapped the neural "social signal transduction" pathways that stimulate CTRA gene expression in response to social threat and may contribute to social gradients in health. Research has also begun to analyze the functional genomics of optimal health and thriving. Two emerging opportunities now stand to revolutionize our understanding of the everyday life of the human genome: network genomics analyses examining how systems-level capabilities emerge from groups of individual socially sensitive genomes and near-real-time transcriptional biofeedback to empirically optimize individual well-being in the context of the unique genetic, geographic, historical, developmental, and social contexts that jointly shape the transcriptional realization of our innate human genomic potential for thriving.

  20. CD160-associated CD8 T-cell functional impairment is independent of PD-1 expression.

    Directory of Open Access Journals (Sweden)

    Selena Viganò

    2014-09-01

    Full Text Available Expression of co-inhibitory molecules is generally associated with T-cell dysfunction in chronic viral infections such as HIV or HCV. However, their relative contribution in the T-cell impairment remains unclear. In the present study, we have evaluated the impact of the expression of co-inhibitory molecules such as 2B4, PD-1 and CD160 on the functions of CD8 T-cells specific to influenza, EBV and CMV. We show that CD8 T-cell populations expressing CD160, but not PD-1, had reduced proliferation capacity and perforin expression, thus indicating that the functional impairment in CD160(+ CD8 T cells may be independent of PD-1 expression. The blockade of CD160/CD160-ligand interaction restored CD8 T-cell proliferation capacity, and the extent of restoration directly correlated with the ex vivo proportion of CD160(+ CD8 T cells suggesting that CD160 negatively regulates TCR-mediated signaling. Furthermore, CD160 expression was not up-regulated upon T-cell activation or proliferation as compared to PD-1. Taken together, these results provide evidence that CD160-associated CD8 T-cell functional impairment is independent of PD-1 expression.

  1. Cd4As2Br3

    Directory of Open Access Journals (Sweden)

    Mohammed Kars

    2014-03-01

    Full Text Available Single crystals of Cd4As2Br3 (tetracadmium biarsenide tribromide were grown by a chemical transport reaction. The structure is isotypic with the members of the cadmium and mercury pnictidohalides family with general formula M4A2X3 (M = Cd, Hg; A = P, As, Sb; X = Cl, Br, I and contains two independent As atoms on special positions with site symmetry -3 and two independent Cd atoms, of which one is on a special position with site symmetry -3. The Cd4As2Br3 structure consists of AsCd4 tetrahedra sharing vertices with isolated As2Cd6 octahedra that contain As–As dumbbells in the centre of the octahedron. The Br atoms are located in the voids of this three-dimensional arrangement and bridge the different polyhedra through Cd...Br contacts.

  2. Synthesis and photoelectrochemical properties of CdWO{sub 4} and CdS/CdWO{sub 4} nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Weina [Department of Applied Physics, Chongqing University, Chongqing 400044 (China); Zheng, Chunhua [Department of Applied Physics, Chongqing University, Chongqing 400044 (China); Department of Mathematics and Physics, Officer College of the Chinese People' s Armed Police Forces, Chengdu 610213 (China); Hua, Hao; Yang, Qi; Chen, Lin [Department of Applied Physics, Chongqing University, Chongqing 400044 (China); Xi, Yi, E-mail: yxi6@cqu.edu.cn [Department of Applied Physics, Chongqing University, Chongqing 400044 (China); Hu, Chenguo, E-mail: hucg@cqu.edu.cn [Department of Applied Physics, Chongqing University, Chongqing 400044 (China)

    2015-02-01

    Graphical abstract: - Highlights: • A facile CHM strategy is employed for the first time to synthesize CdWO{sub 4} nanowire and nanoflower arrays on cadmium foils. • The photoelectrochemical (PEC) properties are measured on the electrodes made of the CdWO{sub 4} nanowire and nanoflower arrays. • The photocurrent density of the nanowire electrode reaches 0.35 mA/cm{sup 2}, which is 3 times as much as that of the nanoflower electrode. • CdS nanoparticles are deposited on CdWO{sub 4} nanowire arrays to form a CdS/CdWO{sub 4} heterojunction to improve the PEC properties. • The remarkably enhanced photoresponse is achieved on the CdS/CdWO{sub 4} which is twice as much as that on the pure CdWO{sub 4} electrode. - Abstract: A facile composite-salt-mediated strategy is employed for the first time to synthesize CdWO{sub 4} nanowire and nanoflower arrays on cadmium foil substrates. The photoelectrochemical (PEC) properties are measured on the electrodes made of the CdWO{sub 4} nanowire and nanoflower arrays under the simulated sunlight illumination. Both electrodes display high sensitive response and photocurrent stability. The photocurrent density of the nanowire arrays electrode reach 0.35 mA/cm{sup 2}, which is about 3 times as much as that of the nanoflower array electrode. To improve the visible light photocurrent response, CdS nanoparticles are deposited on the CdWO{sub 4} nanowire arrays to form a CdS/CdWO{sub 4} heterojunction. Remarkably enhanced photoresponse is observed on the CdS/CdWO{sub 4} heterostructure and the photocurrent intensity is about twice as much as that of the electrode made of the pure CdWO{sub 4} nanowire arrays. The photoelectric mechanism is also discussed by the crystal structure and morphology characterization, optical band gap and carrier mobility analysis. This work presents a new design of a photoelectrochemical device for possible applications in photoelectrolysis of water and solar cells or highly sensitive light detection.

  3. 喉癌Hep-2细胞CD44+CD133+生物学特性研究%Research on the biological characteristics of CD44+CD133+of human laryngeal carcinoma Hep-2 cells

    Institute of Scientific and Technical Information of China (English)

    孔令帅; 温树信; 高伟; 王珏; 付荣; 杨丽娟; 李飞; 杨雨燕

    2016-01-01

    Objective To isolate, culture and identify laryngeal cancer stem cells from laryngeal carcinoma Hep-2 cell line and observe its biological characteristics in vitro. Methods Isolated, cultured and indentified human laryngeal carcinoma Hep-2 cells by MACS to obtain CD44+CD133+,CD44+CD133-,CD44-CD133+,CD44-CD133-four subsets of stem cells and plot-ted, the growth curves of four kinds of cells. The positive rate was detected by flow cytometry. The transwell chamber invasion assay, cell adhesion experiment and cloneformation assay were performed to evaluate the invasive capability, adhesion ability and the cloneforming ability respectively. The drug resistance was detected by CCK8 method. Results The biological charac-teristics of the five kinds of cells in Hep-2, CD44+CD133+, CD44+CD133-, CD44-CD133+and CD44-CD133-were analyzed. The ability of proliferation, invasion, adhesion, clone formation and drug resistance of CD44+CD133+cell subsets were higher than those of other four. CD44+CD133+>CD44-CD133+>Hep2>CD44+CD133->CD44-CD133-. Conclusion MACS is an effective method for sorting CD44+CD133+ cells. CD44+CD133+ cell subsets have obvious characteristics of cancer stem cells , and may make some new exploration for the high expression markers of laryngeal cancer cells.%目的:分选培养和鉴定人喉癌Hep-2细胞珠,并研究其体外生物学特性。方法通过磁珠细胞分选(mag-netic bead cell sorting,MACS)方法,分选培养和鉴定CD44+CD133+喉癌干细胞,应用免疫磁珠分选技术分选CD44+CD133+、CD44+CD133-、CD44-CD133+、CD44-CD133-4种亚群,对4种细胞绘制生长曲线,应用流式细胞仪检测其阳性率,应用侵袭实验、黏附实验和克隆形成实验评价其侵袭能力、黏附能力和克隆形成能力,用CCK8法检测其耐药性。结果对Hep-2、CD44+CD133+亚群、CD44+CD133-亚群、CD44-CD133+亚群、CD44-CD133-亚群5种细胞进行生物学特性研究,CD44+CD133+细胞亚群的增殖、侵

  4. Evaluation of CD45 protein expression and transcript in canine small clear cell/T zone lymphoma.

    Directory of Open Access Journals (Sweden)

    Marzia Cozzi

    2015-07-01

    Full Text Available Canine small clear cell lymphoma is a peculiar lymphoma entity with T-zone histopathological pattern andindolent clinical course. From an immunophenotypic point of view the main feature is the lack of CD45 staining by flow-cytometry (FC, which accounts for >95% of cases. Underlying mechanisms have never been investigated.Aim of this work was to evaluate CD45 protein and mRNA expression in small clear cell lymphoma.Lymph nodes of 18 cases and 11 controls, with either reactive hyperplasia or CD45-positive high grade T-cell lymphoma, were investigated. FC was performed on lymph node fine needle aspiration and CD45 median fluorescence intensity (MFI was then evaluated on small clear cells and normal residual T-lymphocytes. CD45 surface expression was also evaluated by immunohistochemical reaction on paraffin wax-embedded lymph node sections.Quantitative real-time RT-PCR was performed on cases and controls. Total RNA was isolated from cell suspension in RNA later. The generated CD45cDNA was amplified and ΔΔCt method was used for the relative mRNA quantification.CD45-MFI in neoplastic cells was <1% compared to normal residual T-lymphocytes in the same sample. Cells were also negative for CD45 stain on histopathological preparations. RT-PCR showed a significantly lower amount of CD45 transcript in neoplastic samples compared to controls, likely due to the residual population.Results showed the lack of CD45 surface antigen and the virtually absence of CD45-mRNA in small clear cell lymphoma. We hypothesize a possible genomic/epigenomic aberration; further studies are in progress to investigate the pathogenesis of this aberrancy and the possible linkage to lymphomagenesis.

  5. CD

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    Future Orients《Running》从去年开始,一支名为The Eat的乐队开始在各家livehouse的舞台上崭露头角。而这支刚刚被人所熟知的新乐队却在今年的第一天,更名为了更具辨识度的“Future Orients”,目前成员包括王英男(主唱、吉他手)、郭震(吉他手)、彭超(贝斯手、)张永郭(鼓手)。这支名字略怪的乐队成立于2012年,那段时间正是北京新乐队的”断档期”。秉持着低调的行事风格,他们直到成立两年后,才正式出现在人们的视线中。

  6. CD

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    1 Maia Vidal《Love Song》Maia Vidal用小提琴、手风琴、吉他和玩具钢琴写歌,同时也是一位视觉艺术家。她的嗓音甜美静谧,每首歌都好像是一个童话故事。Maia Vidal于2011年10月

  7. CD

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    来自北京的Elenore乐队成立于2009年,他们于2015年在树音乐旗下发布了首张全长专辑《马戏团的国王》。专辑中收录了乐队从将近20首成型作品中精选出的12首歌,延续了首张EP《迷失的女皇》中混合着英式摇滚律动、布鲁斯吉他、凶狠的贝斯线条以及大气的弦乐铺陈的风格。这首《Elenore)作为乐队最早创作的作品之一,此番也经过了重新编排与录制,显示出乐队日渐成熟的音乐态度和不断提升的掌控力。

  8. CD4+CD25+Treg细胞与支气管哮喘%CD4+ CD25+ Treg cells and bronchial asthma

    Institute of Scientific and Technical Information of China (English)

    鞠云飞; 孙立锋; 胡华

    2011-01-01

    The main function of CD4+ CD25+ Treg cells are immunological anergy and inhibition,which is essential to the maintenance of immunological tolerance in the host.CD4+ CD25+ Treg cells produce inhibitory cytokines (TGF-β and IL-10),express membrane molecules (CTLA-4,GITR,etc) and Foxp3.There are abnormal in function and quantity of CD4+ CD25+ Treg cells of peripheral blood from asthmatic patients,which maybe one of the pathogenesis of asthma.Glucocorticoids can inhibit the airway inflamation of asthma by impacting CD4+ CD25+ Treg cells.%CD4+ CD25+ Treg细胞的主要作用表现为免疫无能性和免疫抑制性,是外周免疫耐受形成机制的主要组成部分.其主要作用机制为分泌抑制性细胞因子(IL-10和TGF-β)、表达细胞表面分子(CTLA-4、GITR等)及Foxp3等.支气管哮喘患者外周血CD4+ CD25+ Treg功能及数量存在异常,这可能是支气管哮喘发病机制之一.糖皮质激素可以通过影响CD4+ CD25+ Treg的状态起到抑制支气管哮喘气道炎症的作用.

  9. Evolution of small prokaryotic genomes

    OpenAIRE

    Martínez-Cano, David J.; Reyes-Prieto, Mariana; Martínez-Romero, Esperanza; Partida-Martínez, Laila P.; Latorre, Amparo; Moya, Andrés; Delaye, Luis

    2015-01-01

    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent ...

  10. Evolution of small prokaryotic genomes

    OpenAIRE

    David José Martínez-Cano; Mariana eReyes-Prieto; Esperanza eMartinez-Romero; Laila Pamela Partida-Martinez; Amparo eLatorre; Andres eMoya; Luis eDelaye

    2015-01-01

    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent ...

  11. Effects of in vivo injection of anti-chicken CD25 monoclonal antibody on regulatory T cell depletion and CD4+CD25- T cell properties in chickens.

    Science.gov (United States)

    Shanmugasundaram, Revathi; Selvaraj, Ramesh K

    2012-03-01

    Regulatory T cells (Tregs) are defined as CD4(+)CD25(+) cells in chickens. This study examined the effects of an anti-chicken CD25 monoclonal antibody injection (0.5 mg/bird) on in vivo depletion of Tregs and the properties of CD4(+)CD25(-) cells in Treg-depleted birds. The CD4(+)CD25(+) cell percentage in the blood was lower at 8 d post injection than at 0 d. Anti-CD25-mediated CD4(+)CD25(+) cell depletion in blood was maximum at 12 d post injection. The anti-CD25 antibody injection depleted CD4(+)CD25(+) cells in the spleen and cecal tonsils, but not in the thymus, at 12 d post antibody injection. CD4(+)CD25(-) cells from the spleen and cecal tonsils of birds injected with the anti-chicken CD25 antibody had higher proliferation and higher IL-2 and IFNγ mRNA amounts than the controls at 12 d post injection. At 20 d post injection, CD4(+)CD25(+) cell percentages in the blood, spleen and thymus were comparable to that of the 0 d post injection. It could be concluded that anti-chicken CD25 injection temporarily depleted Treg population and increased and IL-2 and IFNγ mRNA amounts in CD4(+)CD25(-) cells at 12d post injection.

  12. La Doping of CdS for Enhanced CdS/CdSe Quantum Dot Cosensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Xiaolei Qi

    2015-01-01

    Full Text Available CdS/CdSe system of quantum dot cosensitized solar cells (QDCSCs is one of the most attractive structures for high-efficiency due to its effect of level adjusting. However, the stepwise structure formed between levels of CdS and CdSe has a limitation for enhancing the efficiencies. Metal ions doping in quantum dots have emerged as a common way for changing the Fermi level, band gap, and conductance. Here we report an innovative concept for the rare earth materials La-doped of the CdS layer in the CdS/CdSe QDCSCs by means of the successive ionic layer adsorption and reaction (SILAR. Then we tested that La doped quantum dots can help more electrons accumulate in CdS film, which makes the Fermi level shift up and form a stepped structure. This method leads to enhanced absorption intensity, obviously increasing current density in CdS/CdSe QDCSCs. Our research is a new exploration for improving efficiencies of quantum dot sensitized solar cells.

  13. Can arbuscular mycorrhizal fungi reduce Cd uptake and alleviate Cd toxicity of Lonicera japonica grown in Cd-added soils?

    Science.gov (United States)

    Jiang, Qiu-Yun; Zhuo, Feng; Long, Shi-Hui; Zhao, Hai-Di; Yang, Dan-Jing; Ye, Zhi-Hong; Li, Shao-Shan; Jing, Yuan-Xiao

    2016-02-01

    A greenhouse pot experiment was conducted to study the impact of arbuscular mycorrhizal fungi‑Glomus versiforme (Gv) and Rhizophagus intraradices (Ri) on the growth, Cd uptake, antioxidant indices [glutathione reductase (GR), ascorbate peroxidase (APX), superoxide dismutase (SOD), catalase (CAT), ascorbate (ASA), glutathione (GSH) and malonaldehyde (MDA)] and phytochelatins (PCs) production of Lonicera japonica in Cd-amended soils. Gv and Ri significantly increased P acquisition, biomass of shoots and roots at all Cd treatments. Gv significantly decreased Cd concentrations in shoots and roots, and Ri also obviously reduced Cd concentrations in shoots but increased Cd concentrations in roots. Meanwhile, activities of CAT, APX and GR, and contents of ASA and PCs were remarkably higher in Gv/Ri-inoculated plants than those of uninoculated plants, but lower MDA and GSH contents in Gv/Ri-inoculated plants were found. In conclusion, Gv and Ri symbiosis alleviated Cd toxicity of L. japonica through the decline of shoot Cd concentrations and the improvement of P nutrition, PCs content and activities of GR, CAT, APX in inoculated plants, and then improved plant growth. The decrease of shoot Cd concentrations in L. japonica inoculated with Gv/Ri would provide a clue for safe production of this plant from Cd-contaminated soils.

  14. Establishment and Identification of Chinese Hamster Ovary Cell Lines with Stable Expression of Soluble CD40 Ligands

    Directory of Open Access Journals (Sweden)

    JIANG Hua-wei

    2014-09-01

    Full Text Available Objective: To establish the Chinese Hamster Ovary (CHO cell lines with stable expression of soluble CD40 ligands (sCD40L. Methods: Recombinant plasmid pIRES2-EGFP-sCD40L, enzyme digestion and sequencing identification were obtained by cloning sCD40L coding sequences into eukaryotic expression vector pIRES2-EGFP from carrier pDC316-sCD40 containing sCD40L. CHO cells were transfected by electroporation, followed by screening of resistant clones with G418, after which monoclones were obtained by limited dilution assay and multiply cultured. Flow cytometer and reverted fluorescence microscope were applied to observe the expression of green fluorescent protein, while sCD40L expression was detected by polymerase chain reaction (PCR, reverse transcription-polymerase chain reaction (RT-PCR and enzyme-linked immunosorbent assay (ELISA from aspects of deoxyribose nucleic acid (DNA, messenger ribonucleic acid (mRNA and protein, respectively. CHO-sCD40L was cultured together with MDA-MB-231 cells to compare the expression changes of surface molecule fatty acid synthase (Fas by flow cytometer and observe the apoptosis of MDA-MB-231 cells after Fas activated antibodies (CH-11 were added 24 h later. Results: Plasmid pIRES2-EGFP-sCD40L was successfully established, and cell lines with stable expression of sCD40L were obtained with cloned culture after CHO cell transfection, which was named as B11. Flow cytometer and reverted fluorescence microscope showed >90% expression of green fluorescent protein, while PCR, RT-PCR and ELISA suggested integration of sCD40L genes into cell genome DNA, transcription of sCD40L mRNA and sCD40L protein expression being (4.5±2.1 ng/mL in the supernatant of cell culture, respectively. After co-culture of B11 and MDA-MB-231 cells, the surface Fas expression of MDA-MB-231 cells was increased from (3±1.02 % to (34.8±8.75%, while the apoptosis rate 24 h after addition of CH11 from (5.4±1.32% to (20.7±5.24%, and the differences

  15. CD4+CD25high Regulatory Cells in Peripheral Blood of NSCLC Patients

    Institute of Scientific and Technical Information of China (English)

    LIU Li; YAO Junxia; DING Qian; HUANG Shiang

    2006-01-01

    The proportion and changes of CD4+CD25high regulatory T cells (Trs) in peripheral blood of non-small cell lung cancer (NSCLC) patients were analyzed and their clinical significance explored. The peripheral blood was collected from 61 patients with NSCLC and 15 healthy controls. By using monoclonal antibodies, the blood samples were evaluated with the flow cytometry for lymphocyte subsets (CD3+, CD4+ and CD8+) and CD4+CD25high Tr cells. The results showed that the proportion of CD4+CD25high Tr cells in NSCLC group was significantly higher than in control group [(4.36±2.07) % vs (2.04±1.03) %, P<0.01]. The proportion of CD4+CD25 high Tr cells in late stage was higher than that in early stage [stages Ⅰ + Ⅱ (2.26±0.6) %; stage Ⅲ (3.28±1.38) %; stage Ⅳ(6.06±4.08) %] (P<0.05). Kaplan-Meier survival analysis revealed that the prognosis of the patients who had higher proportion of CD4+CD25high Tr cells in peripheral blood was worse (P=0.0026). In conclusion, the relative increase in CD4+CD25high Tr cells in peripheral blood may be related to immunosuppression and tumor progression in patients with NSCLC. This finding suggests that CD4+CD25+high Tr cells in peripheral blood of NSCLC may be positive for prognosis analysis. The use of depletion of the CD4+CD25high Tr cell therapy to treat NSCLC patients may be an effective strategy.

  16. Association of CD40 with rheumatoid arthritis confirmed in a large UK case-control study

    Science.gov (United States)

    Orozco, Gisela; Eyre, Steve; Hinks, Anne; Ke, Xiayi; Wilson, Anthony G; Bax, Deborah E; Morgan, Ann W; Emery, Paul; Steer, Sophia; Hocking, Lynne; Reid, David M; Wordsworth, Paul; Harrison, Pille; Thomson, Wendy; Barton, Anne; Worthington, Jane

    2010-01-01

    Objective A recent meta-analysis of published genome-wide association studies (GWAS) in populations of European descent reported novel associations of markers mapping to the CD40, CCL21 and CDK6 genes with rheumatoid arthritis (RA) susceptibility while a large-scale, case-control association study in a Japanese population identified association with multiple single nucleotide polymorphisms (SNPs) in the CD244 gene. The aim of the current study was to validate these potential RA susceptibility markers in a UK population. Methods A total of 4 SNPs (rs4810485 in CD40, rs2812378 in CCL21, rs42041 in CDK6 and rs6682654 in CD244) were genotyped in a UK cohort comprising 3962 UK patients with RA and 3531 healthy controls using the Sequenom iPlex platform. Genotype counts in patients and controls were analysed with the χ2 test using Stata. Results Association to the CD40 gene was robustly replicated (p=2×10−4, OR 0.86, 95% CI 0.79 to 0.93) and modest evidence was found for association with the CCL21 locus (p=0.04, OR 1.08, 95% CI 1.01 to 1.16). However, there was no evidence for association of rs42041 (CDK6) and rs6682654 (CD244) with RA susceptibility in this UK population. Following a meta-analysis including the original data, association to CD40 was confirmed (p=7.8×10−8, OR 0.87 (95% CI 0.83 to 0.92). Conclusion In this large UK cohort, strong association of the CD40 gene with susceptibility to RA was found, and weaker evidence for association with RA in the CCL21 locus. PMID:19435719

  17. Pathogenic roles of CD14, galectin-3, and OX40 during experimental cerebral malaria in mice.

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    Miranda S Oakley

    Full Text Available An in-depth knowledge of the host molecules and biological pathways that contribute towards the pathogenesis of cerebral malaria would help guide the development of novel prognostics and therapeutics. Genome-wide transcriptional profiling of the brain tissue during experimental cerebral malaria (ECM caused by Plasmodium berghei ANKA parasites in mice, a well established surrogate of human cerebral malaria, has been useful in predicting the functional classes of genes involved and pathways altered during the course of disease. To further understand the contribution of individual genes to the pathogenesis of ECM, we examined the biological relevance of three molecules -- CD14, galectin-3, and OX40 that were previously shown to be overexpressed during ECM. We find that CD14 plays a predominant role in the induction of ECM and regulation of parasite density; deletion of the CD14 gene not only prevented the onset of disease in a majority of susceptible mice (only 21% of CD14-deficient compared to 80% of wildtype mice developed ECM, p<0.0004 but also had an ameliorating effect on parasitemia (a 2 fold reduction during the cerebral phase. Furthermore, deletion of the galectin-3 gene in susceptible C57BL/6 mice resulted in partial protection from ECM (47% of galectin-3-deficient versus 93% of wildtype mice developed ECM, p<0.0073. Subsequent adherence assays suggest that galectin-3 induced pathogenesis of ECM is not mediated by the recognition and binding of galectin-3 to P. berghei ANKA parasites. A previous study of ECM has demonstrated that brain infiltrating T cells are strongly activated and are CD44(+CD62L(- differentiated memory T cells [1]. We find that OX40, a marker of both T cell activation and memory, is selectively upregulated in the brain during ECM and its distribution among CD4(+ and CD8(+ T cells accumulated in the brain vasculature is approximately equal.

  18. A Review on Genomics APIs

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    Rajeswari Swaminathan

    2016-01-01

    Full Text Available The constant improvement and falling prices of whole human genome Next Generation Sequencing (NGS has resulted in rapid adoption of genomic information at both clinics and research institutions. Considered together, the complexity of genomics data, due to its large volume and diversity along with the need for genomic data sharing, has resulted in the creation of Application Programming Interface (API for secure, modular, interoperable access to genomic data from different applications, platforms, and even organizations. The Genomics APIs are a set of special protocols that assist software developers in dealing with multiple genomic data sources for building seamless, interoperable applications leading to the advancement of both genomic and clinical research. These APIs help define a standard for retrieval of genomic data from multiple sources as well as to better package genomic information for integration with Electronic Health Records. This review covers three currently available Genomics APIs: a Google Genomics, b SMART Genomics, and c 23andMe. The functionalities, reference implementations (if available and authentication protocols of each API are reviewed. A comparative analysis of the different features across the three APIs is provided in the Discussion section. Though Genomics APIs are still under active development and have yet to reach widespread adoption, they hold the promise to make building of complicated genomics applications easier with downstream constructive effects on healthcare.

  19. Studies of CdS/CdTe interface: Comparison of CdS films deposited by close space sublimation and chemical bath deposition techniques

    Energy Technology Data Exchange (ETDEWEB)

    Han, Jun-feng, E-mail: pkuhjf@bit.edu.cn [Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44322 Nantes Cedex 3 (France); Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany); School of Physics, Beijing Institute of Technology, Beijing 100081 (China); Fu, Gan-hua; Krishnakumar, V.; Schimper, Hermann-Josef [Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany); Liao, Cheng [Department of Physics, Peking University, Beijing 100871 (China); Jaegermann, Wolfram [Institute of Materials Science, Darmstadt University of Technology, Petersenstr. 23, 64287 Darmstadt (Germany); Besland, M.P. [Institut des Matériaux Jean Rouxel (IMN), Université de Nantes, UMR CNRS 6502, 2 rue de la Houssinière, BP 32229, 44322 Nantes Cedex 3 (France)

    2015-05-01

    The CdS layers were deposited by two different methods, close space sublimation (CSS) and chemical bath deposition (CBD) technique. The CdS/CdTe interface properties were investigated by transmission electron microscope (TEM) and X-ray photoelectron spectroscopy (XPS). The TEM images showed a large CSS-CdS grain size in the range of 70-80 nm. The interface between CSS-CdS and CdTe were clear and sharp, indicating an abrupt hetero-junction. On the other hand, CBD-CdS layer had much smaller grain size in the 5-10 nm range. The interface between CBD-CdS and CdTe was not as clear as CSS-CdS. With the stepwise coverage of CdTe layer, the XPS core levels of Cd 3d and S 2p in CSS-CdS had a sudden shift to lower binding energies, while those core levels shifted gradually in CBD-CdS. In addition, XPS depth profile analyses indicated a strong diffusion in the interface between CBD-CdS and CdTe. The solar cells prepared using CSS-CdS yielded better device performance than the CBD-CdS layer. The relationships between the solar cell performances and properties of CdS/CdTe interfaces were discussed. - Highlights: • Studies of CdS deposited by close space sublimation and chemical bath deposition • An observation of CdS/CdTe interface by transmission electron microscope • A careful investigation of CdS/CdTe interface by X ray photoelectron spectra • An easier diffusion at the chemical bath deposition CdS and CdTe interface.

  20. An update on MyoD evolution in teleosts and a proposed consensus nomenclature to accommodate the tetraploidization of different vertebrate genomes.

    Directory of Open Access Journals (Sweden)

    Daniel J Macqueen

    Full Text Available BACKGROUND: MyoD is a muscle specific transcription factor that is essential for vertebrate myogenesis. In several teleost species, including representatives of the Salmonidae and Acanthopterygii, but not zebrafish, two or more MyoD paralogues are conserved that are thought to have arisen from distinct, possibly lineage-specific duplication events. Additionally, two MyoD paralogues have been characterised in the allotetraploid frog, Xenopus laevis. This has lead to a confusing nomenclature since MyoD paralogues have been named outside of an appropriate phylogenetic framework. METHODS AND PRINCIPAL FINDINGS: Here we initially show that directly depicting the evolutionary relationships of teleost MyoD orthologues and paralogues is hindered by the asymmetric evolutionary rate of Acanthopterygian MyoD2 relative to other MyoD proteins. Thus our aim was to confidently position the event from which teleost paralogues arose in different lineages by a comparative investigation of genes neighbouring myod across the vertebrates. To this end, we show that genes on the single myod-containing chromosome of mammals and birds are retained in both zebrafish and Acanthopterygian teleosts in a striking pattern of double conserved synteny. Further, phylogenetic reconstruction of these neighbouring genes using Bayesian and maximum likelihood methods supported a common origin for teleost paralogues following the split of the Actinopterygii and Sarcopterygii. CONCLUSION: Our results strongly suggest that myod was duplicated during the basal teleost whole genome duplication event, but was subsequently lost in the Ostariophysi (zebrafish and Protacanthopterygii lineages. We propose a sensible consensus nomenclature for vertebrate myod genes that accommodates polyploidization events in teleost and tetrapod lineages and is justified from a phylogenetic perspective.

  1. Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?

    Science.gov (United States)

    Moustafa, Ibrahim M; Gohara, David W; Uchida, Akira; Yennawar, Neela; Cameron, Craig E

    2015-11-23

    The genomes of RNA viruses are relatively small. To overcome the small-size limitation, RNA viruses assign distinct functions to the processed viral proteins and their precursors. This is exemplified by poliovirus 3CD protein. 3C protein is a protease and RNA-binding protein. 3D protein is an RNA-dependent RNA polymerase (RdRp). 3CD exhibits unique protease and RNA-binding activities relative to 3C and is devoid of RdRp activity. The origin of these differences is unclear, since crystal structure of 3CD revealed "beads-on-a-string" structure with no significant structural differences compared to the fully processed proteins. We performed molecular dynamics (MD) simulations on 3CD to investigate its conformational dynamics. A compact conformation of 3CD was observed that was substantially different from that shown crystallographically. This new conformation explained the unique properties of 3CD relative to the individual proteins. Interestingly, simulations of mutant 3CD showed altered interface. Additionally, accelerated MD simulations uncovered a conformational ensemble of 3CD. When we elucidated the 3CD conformations in solution using small-angle X-ray scattering (SAXS) experiments a range of conformations from extended to compact was revealed, validating the MD simulations. The existence of conformational ensemble of 3CD could be viewed as a way to expand the poliovirus proteome, an observation that may extend to other viruses.

  2. Label Free Detection of CD4+ and CD8+ T Cells Using the Optofluidic Ring Resonator

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    John T. Gohring

    2010-06-01

    Full Text Available We have demonstrated label free detection of CD4+ and CD8+ T-Lymphocyte whole cells and CD4+ T-Lymphocyte cell lysis using the optofluidic ring resonator (OFRR sensor. The OFRR sensing platform incorporates microfluidics and photonics in a setup that utilizes small sample volume and achieves a fast detection time. In this work, white blood cells were isolated from healthy blood and the concentrations were adjusted to match T-Lymphocyte levels of individuals infected with HIV. Detection was accomplished by immobilizing CD4 and CD8 antibodies on the inner surface of the OFRR. Sensing results show excellent detection of CD4+ and CD8+ T-Lymphocyte cells at medically significant concentrations with a detection time of approximately 30 minutes. This work will lead to a rapid and low-cost sensing device that can provide a CD4 and CD8 count as a measure of HIV progression.

  3. CD152 (CTLA-4) regulates effector functions of CD8+ T lymphocytes by repressing Eomesodermin.

    Science.gov (United States)

    Hegel, Johannes K; Knieke, Karin; Kolar, Paula; Reiner, Steven L; Brunner-Weinzierl, Monika C

    2009-03-01

    CD8(+) T lymphocytes are required for effective host defense against pathogens and also for mediating effector responses against uncontrolled proliferating self-tissues. In this study, we determine that individual CD8(+) T cells are tightly controlled in their effector functions by CD152 (CTLA-4). We demonstrate that signals induced by CD152 reduce the frequency of IFN-gamma and granzyme B expressing CD8(+) T cells independently of the transcription factors T-bet or cKrox by selectively inhibiting accumulation of Eomesodermin mRNA and protein. Ectopic expression of Eomesodermin reversed the CD152-mediated inhibition of effector molecule production. Additionally, enhanced cytotoxicity of individual CD8(+) T cells differentiated in the absence of CD152 signaling was determined in vivo. These novel insights extend our understanding of how immune responses of CD8(+) T cells are selectively modulated.

  4. Adoptive immunotherapy of cancer with polyclonal, 108-fold hyperexpanded, CD4+ and CD8+ T cells

    Directory of Open Access Journals (Sweden)

    Kim Julian A

    2004-11-01

    Full Text Available Abstract T cell-mediated cancer immunotherapy is dose dependent and optimally requires participation of antigen-specific CD4+ and CD8+ T cells. Here, we isolated tumor-sensitized T cells and activated them in vitro using conditions that led to greater than 108-fold numerical hyperexpansion of either the CD4+ or CD8+ subset while retaining their capacity for in vivo therapeutic efficacy. Murine tumor-draining lymph node (TDLN cells were segregated to purify the CD62Llow subset, or the CD4+ subset thereof. Cells were then propagated through multiple cycles of anti-CD3 activation with IL-2 + IL-7 for the CD8+ subset, or IL-7 + IL-23 for the CD4+ subset. A broad repertoire of TCR Vβ families was maintained throughout hyperexpansion, which was similar to the starting population. Adoptive transfer of hyper-expanded CD8+ T cells eliminated established pulmonary metastases, in an immunologically specific fashion without the requirement for adjunct IL-2. Hyper-expanded CD4+ T cells cured established tumors in intracranial or subcutaneous sites that were not susceptible to CD8+ T cells alone. Because accessibility and antigen presentation within metastases varies according to anatomic site, maintenance of a broad repertoire of both CD4+ and CD8+ T effector cells will augment the overall systemic efficacy of adoptive immunotherapy.

  5. Involvement of CD4+CD25+ regulatory T cells in the pathogenesis of polycythaemia vera

    Institute of Scientific and Technical Information of China (English)

    ZHAO Wen-bo; LI Ying; LIU Xin; ZHANG Ling-yan; WANG Xin

    2008-01-01

    Background Regulatory T cells (Treg) have been shown to play an important role in the regulation of hematopoietic activity. However, there is no information about the effect of Treg cells in the pathogenesis of polycythaemia vera (PV).Methods In this study, we investigated the percentage and function of Treg cells in the peripheral blood of 21 PV patients and 25 healthy donors. Treg cells were identified and characterized as CD4+CD25+FOXP3+ by flow cytometry.The suppressive activity of CD4+CD25+ Treg cells was assessed by the proliferation and cytokine secretion of the co-cultured CD4+CD25- fractions.Results The results showed that the percentage of Treg cells in the peripheral blood of PV patients significantly increased compared to healthy controls ((10.93±4.02)% vs (5.86±1.99)%, P <0.05). Moreover, the mRNA and protein expression of FOXP3 was higher in CD4+CD25+ Treg cells. Coordinately, when co-cultured with the activated CD4+CD25-cells, the CD4+CD25+ Treg cells showed enhanced suppressive function in PV. Yet, the underlying mechanism for the increased frequency and function of CD4+CD25+ Treg cells is still to be clarified.Conclusion Treg cells expansion might account for the abnormal T cell immunity in PV patients and thus contribute to the pathogenesis of PV.

  6. Thin film CdS/CdTe solar cells fabricated by electrodeposition

    Science.gov (United States)

    Kim, D.; Pozder, S.; Qi, B.; Zhu, Y.; Furtak, T. E.; Williamson, D. L.; Trefny, J. U.

    1994-06-01

    CdTe cells with efficiencies up to 9.58% were fabricated by electrodeposition. The minority-carrier lifetime in the CdTe measured by time-resolved photoluminescence was 2.39 ns. A first method to characterize CdS microstructure by small-angle x-ray scattering method has been made. Scanning tunneling microscopy performed on 1000 Å thick CdS films made by chemical bath deposition revealed a thickness fluctuation of 500 Å. Annealing of the CdS films followed by a CdCl2 treatment did not reduce the roughness, but drastically changed the contour of the grains. Some of the CdCl2-treated CdS showed white spots with diameters ranging from about 0.5 mm to 5 mm. These spots are conglomerates of dendritic patterns of either Cd metal or some Cd-rich phase. Optical transmittance of CdS films with various thicknesses (170 Å-2400 Å) showed a good correlation between thickness and transmittance for photon energies above the bandgap. The effect of CdCl2 treatment and annealing on transmittance was either negligible or slightly deleterious. CdTe films made by electrodeposition showed a dense, faceted surface morphology and films were under compressive stress after CdCl2 treatment and annealing.

  7. CdS/CdTe interface analysis by transmission electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Dhere, R. G. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States); Al-Jassim, M. M. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States); Yan, Y. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States); Jones, K. M. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States); Moutinho, H. R. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States); Gessert, T. A. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States); Sheldon, P. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States); Kazmerski, L. L. [National Renewable Energy Laboratory, 1617 Cole Boulevard, Golden, Colorado 80401 (United States)

    2000-07-01

    CdTe-based polycrystalline solar cells are leading candidates for terrestrial photovoltaic applications. High efficiency devices have been obtained despite large lattice mismatch between hexagonal CdS and cubic CdTe. In the present work, CdS was deposited by chemical bath deposition on Si substrates, and CdTe was deposited by close spaced sublimation. The chemical nature of the CdS/CdTe interface, structural properties, and their dependence on the fabrication parameters, e.g., substrate temperature (475-600 degree sign C) and postdeposition CdCl{sub 2} heat treatment, were analyzed. In addition, the effects of crystallinity of CdS on the interface structural defects were examined. Small spot energy dispersive spectroscopy of the interface revealed a considerable amount of sulfur in CdTe. The concentration of sulfur, in general, was higher in the grains with higher density of structural defects and at the grain boundaries. The planar defect density in CdTe films increased with substrate temperature, whereas the threading dislocation density decreased. Interface analysis showed that the majority of the crystalline defects in the CdTe films deposited on CdS were generated at the interface. The crystallinity of CdS did not have a major influence on the interface defect generation. (c) 2000 American Vacuum Society.

  8. CD70-expressing CD4 T cells produce IFN-γ and IL-17 in rheumatoid arthritis

    NARCIS (Netherlands)

    Park, Jin Kyun; Han, Bobby Kwanghoon; Park, Ji Ah; Woo, Youn Jung; Kim, So Young; Lee, Eun Young; Lee, Eun Bong; Chalan, Paulina; Boots, Annemieke M.; Song, Yeong Wook

    2014-01-01

    OBJECTIVE: CD70-expressing CD4 T cells are enriched in RA and promote autoimmunity via co-stimulatory CD70-CD27 interaction. This study aimed to explore the phenotype and cytokine production of CD70(+) CD4 T cells in RA. METHODS: Peripheral blood mononuclear cells from 32 RA patients were isolated a

  9. Photoluminescence of Cu-doped CdTe and related stability issues in CdS/CdTe solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Grecu, D. [University of Toledo, Toledo, Ohio 43606-3390 (United States); Compaan, A. D. [University of Toledo, Toledo, Ohio 43606-3390 (United States); Young, D. [National Renewable Energy Laboratory, Golden, Colorado 80401 (United States); Jayamaha, U. [First Solar LLC., Perrysburg, Ohio 43551 (United States); Rose, D. H. [First Solar LLC., Perrysburg, Ohio 43551 (United States)

    2000-09-01

    We explore Cu electronic states in CdTe using photoluminescence as the main investigative method. Our results are consistent with some Cu atoms occupying substitutional positions on the Cd sublattice and with others forming Frenkel pairs of the type Cu{sub i}{sup +}-V{sub Cd}{sup -} involving an interstitial Cu and a Cd vacancy. In addition, we find that Cu-doped CdTe samples exhibit a significant ''aging'' behavior, attributable to the instability of Cu acceptor states as verified by our Hall measurements. The aging appears to be reversible by a 150-200 degree sign C anneal. Our results are used to explain efficiency degradation of some CdTe solar-cell devices which use Cu for the formation of a backcontact. (c) 2000 American Institute of Physics.

  10. Translational genomics for plant breeding with the genome sequence explosion.

    Science.gov (United States)

    Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Jeong, Haneul; Satyawan, Dani; Kim, Moon Young; Lee, Suk-Ha

    2016-04-01

    The use of next-generation sequencers and advanced genotyping technologies has propelled the field of plant genomics in model crops and plants and enhanced the discovery of hidden bridges between genotypes and phenotypes. The newly generated reference sequences of unstudied minor plants can be annotated by the knowledge of model plants via translational genomics approaches. Here, we reviewed the strategies of translational genomics and suggested perspectives on the current databases of genomic resources and the database structures of translated information on the new genome. As a draft picture of phenotypic annotation, translational genomics on newly sequenced plants will provide valuable assistance for breeders and researchers who are interested in genetic studies.

  11. NUP98/11p15 translocations affect CD34+ cells in myeloid and T lymphoid leukemias.

    Science.gov (United States)

    Crescenzi, Barbara; Nofrini, Valeria; Barba, Gianluca; Matteucci, Caterina; Di Giacomo, Danika; Gorello, Paolo; Beverloo, Berna; Vitale, Antonella; Wlodarska, Iwona; Vandenberghe, Peter; La Starza, Roberta; Mecucci, Cristina

    2015-07-01

    We assessed lineage involvement by NUP98 translocations in myelodysplastic syndromes (MDS), acute myeloid leukaemia (AML), and T-cell acute lymphoblastic leukaemia (T-ALL). Single cell analysis by FICTION (Fluorescence Immunophenotype and Interphase Cytogenetics as a Tool for Investigation of Neoplasms) showed that, despite diverse partners, i.e. NSD1, DDX10, RAP1GDS1, and LNP1, NUP98 translocations always affected a CD34+/CD133+ hematopoietic precursor. Interestingly the abnormal clone included myelomonocytes, erythroid cells, B- and T- lymphocytes in MDS/AML and only CD7+/CD3+ cells in T-ALL. The NUP98-RAP1GDS1 affected different hematopoietic lineages in AML and T-ALL. Additional specific genomic events, were identified, namely FLT3 and CEBPA mutations in MDS/AML, and NOTCH1 mutations and MYB duplication in T-ALL.

  12. Involvement of CD244 in regulating CD4+ T cell immunity in patients with active tuberculosis.

    Directory of Open Access Journals (Sweden)

    Bingfen Yang

    Full Text Available CD244 (2B4 is a member of the signaling lymphocyte activation molecule (SLAM family of immune cell receptors and it plays an important role in modulating NK cell and CD8(+ T cell immunity. In this study, we investigated the expression and function of CD244/2B4 on CD4(+ T cells from active TB patients and latent infection individuals. Active TB patients had significantly elevated CD244/2B4 expression on M. tuberculosis antigen-specific CD4(+ T cells compared with latent infection individuals. The frequencies of CD244/2B4-expressing antigen-specific CD4(+ T cells were significantly higher in retreatment active TB patients than in new active TB patients. Compared with CD244/2B4-dull and -middle CD4(+ T cells, CD244/2B4-bright CD4(+ T cell subset had significantly reduced expression of IFN-γ, suggesting that CD244/2B4 expression may modulate IFN-γ production in M. tuberculosis antigen-responsive CD4(+ T cells. Activation of CD244/2B4 signaling by cross-linking led to significantly decreased production of IFN-γ. Blockage of CD244/2B4 signaling pathway of T cells from patients with active TB resulted in significantly increased production of IFN-γ, compared with isotype antibody control. In conclusion, CD244/2B4 signaling pathway has an inhibitory role on M. tuberculosis antigen-specific CD4(+ T cell function.

  13. Effects of estrogen on CD4+CD25+ regulatory T cell in peripheral blood during pregnancy

    Institute of Scientific and Technical Information of China (English)

    Yuan-Huan Xiong; Zhen Yuan; Li He

    2013-01-01

    Objective:To investigate the effects of estrogen (E2) level on regulatory T cells (Treg) in peripheral blood during pregnancy. Methods:A total of 30 healthy non-pregnant women were selected as control group, 90 pregnant women of early, middle and late pregnancy and 30 postpartum women at 1 month after parturition were selected as experimental groups including early pregnancy group, middle pregnancy group and late pregnancy group;the proportions of CD4+CD25+Treg and CD4+CD25+CD127-Treg among CD4+T cells were detected by flow cytometry;the serum estrogen content in peripheral blood was detected by electrochemical immune luminescence method. Results: E2 level was coincident with the change of Tregs number during pregnancy. The estrogen content in peripheral blood increased gradually from early pregnancy to late pregnancy, then decreased significantly after parturition, and the level at 1 month after parturition down to the level in non-pregnancy group (P>0.05);the level of E2 in pregnancy groups were significantly higher than those in non-pregnancy group (P0.05);the proportions in middle and late pregnancy groups were significantly higher than those in early pregnancy group (P0.05). There was correlation between Tregs number with estrogen level during pregnancy. The proportion of CD4+CD25+ Treg and CD4+CD25+CD127- Treg were positively correlated with estrogen level. Conclusions:High proportion of CD4+CD25+Treg and CD4+CD25+CD127-Treg is closely related to the high level of E2 during pregnancy. It suggested that high level of estrogen may induce an increase of CD4+CD25+Treg in peripheral blood, and then influence the immune function of pregnant women. The results of this experiment might play an important role of estrogen in immune-modulation during pregnancy.

  14. In situ identification of CD44+/CD24- cancer cells in primary human breast carcinomas.

    Directory of Open Access Journals (Sweden)

    Giuseppe Perrone

    Full Text Available Breast cancer cells with the CD44+/CD24- phenotype have been reported to be tumourigenic due to their enhanced capacity for cancer development and their self-renewal potential. The identification of human tumourigenic breast cancer cells in surgical samples has recently received increased attention due to the implications for prognosis and treatment, although limitations exist in the interpretation of these studies. To better identify the CD44+/CD24- cells in routine surgical specimens, 56 primary breast carcinoma cases were analysed by immunofluorescence and confocal microscopy, and the results were compared using flow cytometry analysis to correlate the amount and distribution of the CD44+/CD24- population with clinicopathological features. Using these methods, we showed that the breast carcinoma cells displayed four distinct sub-populations based on the expression pattern of CD44 and CD24. The CD44+/CD24- cells were found in 91% of breast tumours and constituted an average of 6.12% (range, 0.11%-21.23% of the tumour. A strong correlation was found between the percentage of CD44+/CD24- cells in primary tumours and distant metastasis development (p = 0.0001; in addition, there was an inverse significant association with ER and PGR status (p = 0.002 and p = 0.001, respectively. No relationship was evident with tumour size (T and regional lymph node (N status, differentiation grade, proliferative index or HER2 status. In a multivariate analysis, the percentage of CD44+/CD24- cancer cells was an independent factor related to metastasis development (p = 0.004. Our results indicate that confocal analysis of fluorescence-labelled breast cancer samples obtained at surgery is a reliable method to identify the CD44+/CD24- tumourigenic cell population, allowing for the stratification of breast cancer patients into two groups with substantially different relapse rates on the basis of CD44+/CD24- cell percentage.

  15. TWEAK inhibits TRAF2-mediated CD40 signaling by destabilization of CD40 signaling complexes.

    Science.gov (United States)

    Salzmann, Steffen; Lang, Isabell; Rosenthal, Alevtina; Schäfer, Viktoria; Weisenberger, Daniela; Carmona Arana, José Antonio; Trebing, Johannes; Siegmund, Daniela; Neumann, Manfred; Wajant, Harald

    2013-09-01

    We found recently that TNF-like weak inducer of apoptosis (TWEAK) and fibroblast growth factor-inducible-14 (Fn14) by virtue of their strong capability to reduce the freely available cytoplasmic pool of TNFR-associated factor (TRAF)2 and cellular inhibitors of apoptosis (cIAPs) antagonize the functions of these molecules in TNFR1 signaling, resulting in sensitization for apoptosis and inhibition of classical NF-κB signaling. In this study, we demonstrate that priming of cells with TWEAK also interferes with activation of the classical NF-κB pathway by CD40. Likewise, there was strong inhibition of CD40 ligand (CD40L)-induced activation of MAPKs in TWEAK-primed cells. FACS analysis and CD40L binding studies revealed unchanged CD40 expression and normal CD40L-CD40 interaction in TWEAK-primed cells. CD40L immunoprecipitates, however, showed severely reduced amounts of CD40 and CD40-associated proteins, indicating impaired formation or reduced stability of CD40L-CD40 signaling complexes. The previously described inhibitory effect of TWEAK on TNFR1 signaling has been traced back to reduced activity of the TNFR1-associated TRAF2-cIAP1/2 ubiquitinase complex and did not affect the stability of the immunoprecipitable TNFR1 receptor complex. Thus, the inhibitory effect of TWEAK on CD40 signaling must be based at least partly on other mechanisms. In line with this, signaling by the CD40-related TRAF2-interacting receptor TNFR2 was also attenuated but still immunoprecipitable in TWEAK-primed cells. Collectively, we show that Fn14 activation by soluble TWEAK impairs CD40L-CD40 signaling complex formation and inhibits CD40 signaling and thus identify the Fn14-TWEAK system as a potential novel regulator of CD40-related cellular functions.

  16. CD25+CD127+Foxp3- Cells Represent a Major Subpopulation of CD8+ T Cells in the Eye Chambers of Normal Mice

    Science.gov (United States)

    Ziółkowska, Natalia; Ziółkowski, Hubert; Małaczewska, Joanna

    2017-01-01

    The aim of this study has been to determine whether eye chambers constitute part of the normal migratory pathway of naive CD4+ and CD8+ T cells in mouse and if natural CD4+CD25+Foxp3+ and CD8+CD25+Foxp3+ regulatory T cells are present within these eye compartments. To this aim, the cells obtained from aqueous humor (AH) of normal mice were phenotyped in terms of the expression CD4, CD8, CD25, CD127 and transcription factor Foxp3. The mean percentage of CD8+ T cells in the total AH lymphocyte population was as high as 28.69%; the mean percentage of CD8high and CD8low cells in this population was 34.09% and 65.91%, respectively. The presence of cells with the regulatory phenotype, i.e. CD25+Foxp3+ cells, constituted only 0.32% of CD8+ T cell subset. Regarding the expression of CD25, AH CD8+ T cells were an exceptional population in that nearly 85% of these cells expressed this molecule without concomitant Foxp3 expression. Despite having this phenotype, they should not be viewed as activated cells because most of them co-expressed CD127, which indicates that they are naive lymphocytes. With regard to the markers applied in the present research, CD8+CD25+CD127+Foxp3- T cells represent the most numerous subset of AH CD8+ cells. The results suggest that eye chambers in mice are an element in the normal migratory pathway of naive CD8+ T cells. The study presented herein demonstrated only trace presence of CD4+ cells in the eye chambers, as the mean percentage of these cells was just 0.56. Such selective and specific homing of CD8+ and CD4+ cells to the eye chambers is most clearly engaged in the induction and maintenance of ocular immune privilege. PMID:28081241

  17. Genomes to Proteomes

    Energy Technology Data Exchange (ETDEWEB)

    Panisko, Ellen A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Grigoriev, Igor [USDOE Joint Genome Inst., Walnut Creek, CA (United States); Daly, Don S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Webb-Robertson, Bobbie-Jo [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Baker, Scott E. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-03-01

    Biologists are awash with genomic sequence data. In large part, this is due to the rapid acceleration in the generation of DNA sequence that occurred as public and private research institutes raced to sequence the human genome. In parallel with the large human genome effort, mostly smaller genomes of other important model organisms were sequenced. Projects following on these initial efforts have made use of technological advances and the DNA sequencing infrastructure that was built for the human and other organism genome projects. As a result, the genome sequences of many organisms are available in high quality draft form. While in many ways this is good news, there are limitations to the biological insights that can be gleaned from DNA sequences alone; genome sequences offer only a bird's eye view of the biological processes endemic to an organism or community. Fortunately, the genome sequences now being produced at such a high rate can serve as the foundation for other global experimental platforms such as proteomics. Proteomic methods offer a snapshot of the proteins present at a point in time for a given biological sample. Current global proteomics methods combine enzymatic digestion, separations, mass spectrometry and database searching for peptide identification. One key aspect of proteomics is the prediction of peptide sequences from mass spectrometry data. Global proteomic analysis uses computational matching of experimental mass spectra with predicted spectra based on databases of gene models that are often generated computationally. Thus, the quality of gene models predicted from a genome sequence is crucial in the generation of high quality peptide identifications. Once peptides are identified they can be assigned to their parent protein. Proteins identified as expressed in a given experiment are most useful when compared to other expressed proteins in a larger biological context or biochemical pathway. In this chapter we will discuss the automatic

  18. Genomic Feature Models

    DEFF Research Database (Denmark)

    Sørensen, Peter; Edwards, Stefan McKinnon; Rohde, Palle Duun

    Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available in many populations. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non-additive g......Whole-genome sequences and multiple trait phenotypes from large numbers of individuals will soon be available in many populations. Well established statistical modeling approaches enable the genetic analyses of complex trait phenotypes while accounting for a variety of additive and non......-additive genetic mechanisms. These modeling approaches have proven to be highly useful to determine population genetic parameters as well as prediction of genetic risk or value. We present a series of statistical modelling approaches that use prior biological information for evaluating the collective action...... of sets of genetic variants. We have applied these approaches to whole genome sequences and a complex trait phenotype resistance to starvation collected on inbred lines from the Drosophila Genome Reference Panel population. We identified a number of genomic features classification schemes (e.g. prior QTL...

  19. Rf sputtering of CdTE and CdS for thin film PV

    Energy Technology Data Exchange (ETDEWEB)

    Compaan, A.D.; Tabory, C.N.; Shao, M.; Fischer, A.; Feng, Z.; Bohn, R.G. (Department of Physics and Astronomy, University of Toledo, Toledo, Ohio 43606 (United States))

    1994-06-30

    In late 1992 we demonstrated the first rf sputtered CdS/CdTe photovoltaic cell with efficiency exceeding 10%. In this cell both CdS and CdTe layers were deposited by rf sputtering. In this paper we report preliminary measurements of (1) optical emission spectroscopy of the rf plasma, (2) the width of the phonon Raman line as a function of deposition temperature for CdS, and (3) studies of oxygen doping during pulsed laser deposition of CdTe.

  20. Increased plasma levels of microparticles expressing CD39 and CD133 in acute liver injury

    DEFF Research Database (Denmark)

    Schmelzle, Moritz; Splith, Katrin; Wiuff Andersen, Lars;

    2013-01-01

    BACKGROUND: We have previously demonstrated that CD133 and CD39 are expressed by hematopoietic stem cells (HSC), which are mobilized after liver injury and target sites of injury, limit vascular inflammation, and boost hepatic regeneration. Plasma microparticles (MP) expressing CD39 can block...... endothelial activation. Here, we tested whether CD133 MP might be shed in a CD39-dependent manner in a model of liver injury and could potentially serve as biomarkers of liver failure in the clinic. METHODS: Wild-type and Cd39-null mice were subjected to acetaminophen-induced liver injury. Mice were...

  1. Induction of cytotoxic CD8+CD56+ T cells from human thymocytes by interleukin-15

    DEFF Research Database (Denmark)

    Thulesen, S; Nissen, Mogens Holst; Ødum, N;

    2001-01-01

    CD8(+) CD56(+) cells isolated from human peripheral blood lymphocytes have been shown recently to represent a population of cytotoxic active T cells. However, it is not known if these cells are intrathymically or extrathymically developed or how these cells are influenced by growth factors...... of thymocytes. The majority of the IL-15-grown CD8(+) CD56(+) cells were CD45R0(+), representing a memory phenotype, and showed high expression of the IL-15R-complex and high numbers of CD69(+) cells. Moreover, cytotoxic activity was confined to this cell population....

  2. Increased T cell expression of CD154 (CD40-ligand) in multiple sclerosis

    DEFF Research Database (Denmark)

    Jensen, J; Krakauer, M; Sellebjerg, F

    2001-01-01

    CD154 (CD40-ligand, gp39), expressed on activated T cells, is crucial in T cell-dependent immune responses and may be involved in the pathogenesis of multiple sclerosis (MS). We studied cerebro-spinal fluid and peripheral blood T cell expression of CD154 in MS by flow cytometry. Patients with sec......CD154 (CD40-ligand, gp39), expressed on activated T cells, is crucial in T cell-dependent immune responses and may be involved in the pathogenesis of multiple sclerosis (MS). We studied cerebro-spinal fluid and peripheral blood T cell expression of CD154 in MS by flow cytometry. Patients...

  3. Achievements and Challenges of CdS/CdTe Solar Cells

    Directory of Open Access Journals (Sweden)

    Zhou Fang

    2011-01-01

    Full Text Available Thin film CdS/CdTe has long been regarded as one promising choice for the development of cost-effective and reliable solar cells. Efficiency as high as 16.5% has been achieved in CdS/CdTe heterojunction structure in laboratory in 2001, and current techniques for CdS/CdTe solar cells gradually step toward commercialization. This paper reviews some novel techniques mainly within two years to solve this problem from aspects of promotion of fabrication technology, structural modification, and choice of back contact materials.

  4. Achievements and Challenges of CdS/CdTe Solar Cells

    OpenAIRE

    Zhou Fang; Xiao Chen Wang; Hong Cai Wu; Ce Zhou Zhao

    2011-01-01

    Thin film CdS/CdTe has long been regarded as one promising choice for the development of cost-effective and reliable solar cells. Efficiency as high as 16.5% has been achieved in CdS/CdTe heterojunction structure in laboratory in 2001, and current techniques for CdS/CdTe solar cells gradually step toward commercialization. This paper reviews some novel techniques mainly within two years to solve this problem from aspects of promotion of fabrication technology, structural modification, and cho...

  5. Roles of 1,25(OH2D3 and Vitamin D Receptor in the Pathogenesis of Rheumatoid Arthritis and Systemic Lupus Erythematosus by Regulating the Activation of CD4+ T Cells and the PKCδ/ERK Signaling Pathway

    Directory of Open Access Journals (Sweden)

    Xiao-Jie He

    2016-12-01

    Full Text Available Background/Aims: The study aims to elucidate the roles of 1,25(OH2D3 and vitamin D receptor (VDR in the pathogenesis of rheumatoid arthritis (RA and systemic lupus erythematosus (SLE by regulating the activation of CD4+ T cells and the PKCδ/ERK signaling pathway. Methods: From January 2013 to December 2015, a total of 130 SLE patients, 137 RA patients and 130 healthy controls were selected in this study. Serum levels of 1,25(OH2D3 and VDR mRNA expression were detected by ELISA and real-time fluorescence quantitative PCR (RT-qPCR. Density gradient centrifugation was performed to separate peripheral blood mononuclear cells (PBMCs. CD4+ T cells were separated using magnetic activated cell sorting (MACS. CD4+T cells in logarithmic growth phase were collected and assigned into 9 groups: the normal control group, the normal negative control (NC group, the VDR siRNA group, the RA control group, the RA NC group, the VDR over-expressed RA group, the SLE control group, the SLE NC group, and the VDR over-expressed SLE group. The mRNA and protein expressions of VDR, PKCδ, ERK1/2, CD11a, CD70 and CD40L were detected by RT-qPCR and Western blotting. Bisulfite genomic sequencing was conducted to monitor the methylation status of CD11a, CD70 and CD40L. Results: Compared with healthy controls, serum 1,25(OH2D3 level and VDR mRNA expression in peripheral blood were decreased in SLE patients and RA patients. With the increase of concentrations of 1,25(OH2D3 treatment, the VDR mRNA expression and DNA methylation levels of CD11a, CD70 and CD40L were declined, while the expressions of PKCδ, ERK1/2, CD11a, CD70 and CD40L were elevated in SLE, RA and normal CD4+T cells. Compared with the SLE contro, RA control, SLE NC and RA NC groups, the expressions of PKCδ, ERK1/2, CD11a, CD70 and CD40L decreased but DNA methylation levels of CD11a, CD70 and CD40L increased in the VDR over-expressed SLE group and VDR over-expressed RA group. However, compared with the normal

  6. Comparative genomics of Escherichia coli isolated from patients with inflammatory bowel disease

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk; Hancock, Viktoria; Petersen, Andreas M.;

    2011-01-01

    Background: Inflammatory bowel disease (IBD) is used to describe a state of idiopathic, chronic inflammation of the gastrointestinal tract. The two main phenotypes of IBD are Crohn's disease (CD) and ulcerative colitis (UC). The major cause of IBD-associated mortality is colorectal cancer. Although...... both host-genetic and exogenous factors have been found to be involved, the aetiology of IBD is still not well understood. In this study we characterized thirteen Escherichia coli strains from patients with IBD by comparative genomic hybridization employing a microarray based on 31 sequenced E. coli...... genomes from a wide range of commensal and pathogenic isolates. Results: The IBD isolates, obtained from patients with UC and CD, displayed remarkably heterogeneous genomic profiles with little or no evidence of group-specific determinants. No IBD-specific genes were evident when compared...

  7. CD8{sup +}CD25{sup +} T cells reduce atherosclerosis in apoE(−/−) mice

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jianchang; Dimayuga, Paul C.; Zhao, Xiaoning; Yano, Juliana; Lio, Wai Man; Trinidad, Portia; Honjo, Tomoyuki; Cercek, Bojan; Shah, Prediman K.; Chyu, Kuang-Yuh, E-mail: Chyuk@cshs.org

    2014-01-17

    Highlights: •The role of a sub-population of CD8{sup +} T cells with suppressor functions was investigated in atherosclerosis. •CD8{sup +}CD25{sup +} T cells from adult apoE(−/−) mice had phenotype characteristics of T suppressor cells. •These CD8{sup +}CD25{sup +} T cells reduced CD4{sup +} T cell proliferation and CD8{sup +} cytotoxic activity in vitro. •Adoptive transfer of CD8{sup +}CD25{sup +} T cells significantly reduced atherosclerosis. •CD8{sup +}CD25{sup +} T cells have a suppressive function in atherosclerosis. -- Abstract: Background: It is increasingly evident that CD8{sup +} T cells are involved in atherosclerosis but the specific subtypes have yet to be defined. CD8{sup +}CD25{sup +} T cells exert suppressive effects on immune signaling and modulate experimental autoimmune disorders but their role in atherosclerosis remains to be determined. The phenotype and functional role of CD8{sup +}CD25{sup +} T cells in experimental atherosclerosis were investigated in this study. Methods and results: CD8{sup +}CD25{sup +} T cells were observed in atherosclerotic plaques of apoE(−/−) mice fed hypercholesterolemic diet. Characterization by flow cytometric analysis and functional evaluation using a CFSE-based proliferation assays revealed a suppressive phenotype and function of splenic CD8{sup +}CD25{sup +} T cells from apoE(−/−) mice. Depletion of CD8{sup +}CD25{sup +} from total CD8{sup +} T cells rendered higher cytolytic activity of the remaining CD8{sup +}CD25{sup −} T cells. Adoptive transfer of CD8{sup +}CD25{sup +} T cells into apoE(−/−) mice suppressed the proliferation of splenic CD4{sup +} T cells and significantly reduced atherosclerosis in recipient mice. Conclusions: Our study has identified an athero-protective role for CD8{sup +}CD25{sup +} T cells in experimental atherosclerosis.

  8. Genomic dairy cattle breeding

    DEFF Research Database (Denmark)

    Mark, Thomas; Sandøe, Peter

    2010-01-01

    The aim of this paper is to discuss the potential consequences of modern dairy cattle breeding for the welfare of dairy cows. The paper focuses on so-called genomic selection, which deploys thousands of genetic markers to estimate breeding values. The discussion should help to structure...... the thoughts of breeders and other stakeholders on how to best make use of genomic breeding in the future. Intensive breeding has played a major role in securing dramatic increases in milk yield since the Second World War. Until recently, the main focus in dairy cattle breeding was on production traits......, unfavourable genetic trends for metabolic, reproductive, claw and leg diseases indicate that these attempts have been insufficient. Today, novel genome-wide sequencing techniques are revolutionising dairy cattle breeding; these enable genetic changes to occur at least twice as rapidly as previously. While...

  9. Genomics and drug discovery.

    Science.gov (United States)

    Haseltine, W A

    2001-09-01

    Genomics, the systematic study of all the genes of an organism, offers a new and much-needed source of systematic productivity for the pharmaceutical industry. The isolation of the majority of human genes in their most useful form is leading to the creation of new drugs based on human proteins, antibodies, peptides, and genes. Human Genome Sciences, Inc, was the first company to use the systematic, genomics approach to discovering drugs, and we have placed 4 of these in clinical trials. Two are described: repifermin (keratinocyte growth factor-2, KGF-2) for wound healing and treatment of mucositis caused by cancer therapy, and B lymphocyte stimulator (BLyS) for stimulation of the immune system. An anti-BLyS antibody drug is in advanced preclinical development for treatment of autoimmune diseases.

  10. Genomics of Salmonella Species

    Science.gov (United States)

    Canals, Rocio; McClelland, Michael; Santiviago, Carlos A.; Andrews-Polymenis, Helene

    Progress in the study of Salmonella survival, colonization, and virulence has increased rapidly with the advent of complete genome sequencing and higher capacity assays for transcriptomic and proteomic analysis. Although many of these techniques have yet to be used to directly assay Salmonella growth on foods, these assays are currently in use to determine Salmonella factors necessary for growth in animal models including livestock animals and in in vitro conditions that mimic many different environments. As sequencing of the Salmonella genome and microarray analysis have revolutionized genomics and transcriptomics of salmonellae over the last decade, so are new high-throughput sequencing technologies currently accelerating the pace of our studies and allowing us to approach complex problems that were not previously experimentally tractable.

  11. Screening of genomic libraries.

    Science.gov (United States)

    Novelli, Valdenice M; Cristofani-Yaly, Mariângela; Bastianel, Marinês; Palmieri, Dario A; Machado, Marcos A

    2013-01-01

    Microsatellites, or simple sequence repeats (SSRs), have proven to be an important molecular marker in plant genetics and breeding research. The main strategies to obtain these markers can be through genomic DNA and from expressed sequence tags (ESTs) from mRNA/cDNA libraries. Genetic studies using microsatellite markers have increased rapidly because they can be highly polymorphic, codominant markers and they show heterozygous conserved sequences. Here, we describe a methodology to obtain microsatellite using the enrichment library of DNA genomic sequences. This method is highly efficient to development microsatellite markers especially in plants that do not have available ESTs or genome databases. This methodology has been used to enrich SSR marker libraries in Citrus spp., an important tool to genotype germplasm, to select zygotic hybrids, and to saturate genetic maps in breeding programs.

  12. Domestication and plant genomes.

    Science.gov (United States)

    Tang, Haibao; Sezen, Uzay; Paterson, Andrew H

    2010-04-01

    The techniques of plant improvement have been evolving with the advancement of technology, progressing from crop domestication by Neolithic humans to scientific plant breeding, and now including DNA-based genotyping and genetic engineering. Archeological findings have shown that early human ancestors often unintentionally selected for and finally fixed a few major domestication traits over time. Recent advancement of molecular and genomic tools has enabled scientists to pinpoint changes to specific chromosomal regions and genetic loci that are responsible for dramatic morphological and other transitions that distinguish crops from their wild progenitors. Extensive studies in a multitude of additional crop species, facilitated by rapid progress in sequencing and resequencing(s) of crop genomes, will further our understanding of the genomic impact from both the unusual population history of cultivated plants and millennia of human selection.

  13. Genomics of Preterm Birth

    Science.gov (United States)

    Swaggart, Kayleigh A.; Pavlicev, Mihaela; Muglia, Louis J.

    2015-01-01

    The molecular mechanisms controlling human birth timing at term, or resulting in preterm birth, have been the focus of considerable investigation, but limited insights have been gained over the past 50 years. In part, these processes have remained elusive because of divergence in reproductive strategies and physiology shown by model organisms, making extrapolation to humans uncertain. Here, we summarize the evolution of progesterone signaling and variation in pregnancy maintenance and termination. We use this comparative physiology to support the hypothesis that selective pressure on genomic loci involved in the timing of parturition have shaped human birth timing, and that these loci can be identified with comparative genomic strategies. Previous limitations imposed by divergence of mechanisms provide an important new opportunity to elucidate fundamental pathways of parturition control through increasing availability of sequenced genomes and associated reproductive physiology characteristics across diverse organisms. PMID:25646385

  14. CD47 target: from theory to reality

    Directory of Open Access Journals (Sweden)

    John Wu

    2014-05-01

    Full Text Available Irving Weissman at the Stanford University School of Medicine in Palo Alto, California found that leukemia cells produced higher levels of CD47. This high expression help tumor cells to escape from the immune system. To date, the CD47 receptor becomes the interesting target in cancer treatment. Some recent studies from in vitro to pre-clinical trials showed that blocking CD47 by anti-CD47 or morpholino efficiently tumor cells or tumor growth. From these results, some clinical trials were suggested to test the safety and efficacy of anti-CD47 therapy. There is at least a clinical trial using anti-CD47 therapy registered in clinicaltrial.gov. Some other clinical trials will be performed at Stanford in the mid-2014 as well as in the United Kingdom.

  15. CD147 in cardiovascular disease and thrombosis.

    Science.gov (United States)

    Pennings, Gabrielle J; Kritharides, Leonard

    2014-10-01

    Thrombotic and inflammatory pathways play a key role in coronary artery disease (CAD) development. Extracellular matrix metalloproteinase (aka CD147) is a member of the immunoglobulin superfamily that is expressed on many cell types including hematopoietic, endothelial cells, leukocytes, keratinocytes, platelets, and others. The binding partners of CD147 are numerous and diverse, and give some indication to the various roles that CD147 can play; these include homophilic interactions, integrins, cyclophilins, glycoprotein VI (GPVI), caveolin 1, and monocarboxylate transporters. Recent evidence suggests a role for CD147 in both thrombosis and inflammation, as well as involvement in CAD and cancer. In this review, we summarize the role of CD147 and its binding partners in platelets, thrombosis, and arterial disease and assess mechanistic aspects of CD147 biology.

  16. Immunization with a peptide containing MHC class I and II epitopes derived from the tumor antigen SIM2 induces an effective CD4 and CD8 T-cell response.

    Directory of Open Access Journals (Sweden)

    Haydn T Kissick

    Full Text Available Here, we sought to determine whether peptide vaccines designed harbor both class I as well as class II restricted antigenic motifs could concurrently induce CD4 and CD8 T cell activation against autologous tumor antigens. Based on our prior genome-wide interrogation of human prostate cancer tissues to identify genes over-expressed in cancer and absent in the periphery, we targeted SIM2 as a prototype autologous tumor antigen for these studies. Using humanized transgenic mice we found that the 9aa HLA-A*0201 epitope, SIM2(237-245, was effective at inducing an antigen specific response against SIM2-expressing prostate cancer cell line, PC3. Immunization with a multi-epitope peptide harboring both MHC-I and MHC-II restricted epitopes induced an IFN-γ response in CD8 T cells to the HLA-A*0201-restricted SIM2(237-245 epitope, and an IL-2 response by CD4 T cells to the SIM2(240-254 epitope. This peptide was also effective at inducing CD8+ T-cells that responded specifically to SIM2-expressing tumor cells. Collectively, the data presented in this study suggest that a single peptide containing multiple SIM2 epitopes can be used to induce both a CD4 and CD8 T cell response, providing a peptide-based vaccine formulation for potential use in immunotherapy of various cancers.

  17. Facile method to prepare CdS nanostructure based on the CdTe films

    Energy Technology Data Exchange (ETDEWEB)

    Ma, Ligang; Chen, Yuehui; Wei, Zelu; Cai, Hongling; Zhang, Fengming; Wu, Xiaoshan, E-mail: xswu@nju.edu.cn

    2015-09-15

    Graphical abstract: - Highlights: • CdS nanostructure is directly fabricated on CdTe film only by heating treatment under H{sub 2}S/N{sub 2} mixed atmosphere at a relatively low temperature (450 °C) with gold layer as the intermediate. • Nanostructure of CdS layer, varying from nanowires to nanosheets, may be controlled by the thickness of gold film. • The change of morphology adjusts its luminescence properties. - Abstract: Nanostructured cadmium sulfide (CdS) plays critical roles in electronics and optoelectronics. In this paper, we report a method to fabricate CdS nanostructure directly on CdTe film, via a thermal annealing method in H{sub 2}S/N{sub 2} mixed gas flow at a relatively low temperature (450 °C). The microstructure and optical properties of CdS nanostructure are investigated by X-ray diffraction, transmission electron microscopy, Raman, and photoluminescence. The morphology of CdS nanostructure, evolving from nanowires to nanosheets, can be controlled by the thickness of Au film deposited on the CdTe film. And CdS nanostructures are single crystalline with the hexagonal wurtzite structure. Raman spectroscopy under varying the excitation wavelengths confirm that synthesized CdS-CdTe films contain two layers, i.e., CdS nanostructure (top) and CdTe layer (bottom). The change of morphology modifies its luminescence properties. Obviously, through simply thermal annealing in H{sub 2}S/N{sub 2} mixed gas, fabricating CdS nanostructure on CdTe film can open up the new possibility for obtaining high efficient CdTe solar cell.

  18. Daily subcutaneous injections of peptide induce CD4+ CD25+ T regulatory cells.

    Science.gov (United States)

    Dahlberg, P E; Schartner, J M; Timmel, A; Seroogy, C M

    2007-08-01

    Peptide immunotherapy is being explored to modulate varied disease states; however, the mechanism of action remains poorly understood. In this study, we investigated the ability of a subcutaneous peptide immunization schedule to induce of CD4(+) CD25(+) T regulatory cells. DO11.10 T cell receptor (TCR) transgenic mice on a Rag 2(-/-) background were injected subcutaneously with varied doses of purified ovalbumin (OVA(323-339)) peptide daily for 16 days. While these mice have no CD4(+) CD25(+) T regulatory cells, following this injection schedule up to 30% of the CD4(+) cells were found to express CD25. Real-time quantitative polymerase chain reaction (QPCR) analysis of the induced CD4(+) CD25(+) T cells revealed increased expression of forkhead box P3 (FoxP3), suggesting that these cells may have a regulatory function. Proliferation and suppression assays in vitro utilizing the induced CD4(+) CD25(+) T cells revealed a profound anergic phenotype in addition to potent suppressive capability. Importantly, co-injection of the induced CD4(+) CD25(+) T cells with 5,6-carboxy-succinimidyl-fluorescence-ester (CFSE)-labelled naive CD4(+) T cells (responder cells) into BALB/c recipient mice reduced proliferation and differentiation of the responder cells in response to challenge with OVA(323-339) peptide plus adjuvant. We conclude that repeated subcutaneous exposure to low-dose peptide leads to de novo induction of CD4(+) CD25(+) FoxP3(+) T regulatory cells with potent in vitro and in vivo suppressive capability, thereby suggesting that one mechanism of peptide immunotherapy appears to be induction of CD4(+) CD25(+) Foxp3(+) T regulatory cells.

  19. Synthesis of near-infrared-emitting CdTe/CdSe/ZnSe/ZnS heterostructure.

    Science.gov (United States)

    Yang, Ping

    2014-04-01

    Near-infrared-emitting quantum dots (QDs) were fabricated via organic synthesis strategies through constructing CdTe/CdSe/ZnSe/ZnS multishell heterostructure. An effective shell-coating route was developed for multishell growth on CdTe cores. Core/shell growth was monitored by absorption and photoluminescence (PL) spectroscopy and transmission electron microscopy observation. Yellow emitting CdTe cores were coated with a CdSe shell to generate type II structure. This yields core/shell QDs with red photoluminescence. The passivation by the ZnSe shell having a substantially wide bandgap confines the excitons within the CdTe/CdSe interface and isolates them from the solution environment and consequently improves the stability of the heterostructure. An additional ZnS shell was deposited around the outer layer of CdTe/CdSe/ZnSe QDs to form a heterostructure through the reaction between zinc oleate and trioctylphosphine sulfur in the crude CdTe/CdSe/ZnSe solution. By varying CdTe core size and each shell thickness, the PL wavelength of the obtained heterostructure can span from 580 to 770 nm. The PL efficiency is quenched in CdTe QDs in diluted solution but increases substantially up to 24% for CdTe/CdSe core/shell QDs. The PL efficiency of CdTe/CdSe/ZnSe/ZnS QDs with average diameter of 5.4 nm and a PL peak wavelength of 770 nm is 20%.

  20. Surface treatment of the window layer in CdS/CdTe solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Shin Haeng; Kim, Sang Su; Park, Min Hyuk; Suh, Jong Hee; Hong, Jin Ki [Korea University, Jochiwon (Korea, Republic of)

    2014-11-15

    CdS films are used as window layers in CdS/CdTe solar cells, and an annealing process is required to promote grain growth and recrystallization in them. However, when annealing is performed in an air atmosphere, oxides such as CdO and CdSO{sub 4} form on parts of the layer's surface, which reduces the shunt resistance and the fill factor and results in poor device performance. In this study, we annealed the CdS film in a CdCl{sub 2} atmosphere instead of air. Then, CdCl{sub 2} annealing and air annealing were compared by investigating the structural and the electrical properties of the CdS window layers. Our results reveal that the CdCl{sub 2} annealing protects the CdS film from oxidation and provides good recrystallization conditions. We also found that this CdCl{sub 2} annealing enhance the device's performance. In particular, considerably higher shunt resistance and conversion efficiency were obtained for the CdCl{sub 2}-annealed device compared with the air-annealed device.

  1. Structures of CD6 and Its Ligand CD166 Give Insight into Their Interaction

    Science.gov (United States)

    Chappell, Paul E.; Garner, Lee I.; Yan, Jun; Metcalfe, Clive; Hatherley, Deborah; Johnson, Steven; Robinson, Carol V.; Lea, Susan M.; Brown, Marion H.

    2015-01-01

    Summary CD6 is a transmembrane protein with an extracellular region containing three scavenger receptor cysteine rich (SRCR) domains. The membrane proximal domain of CD6 binds the N-terminal immunoglobulin superfamily (IgSF) domain of another cell surface receptor, CD166, which also engages in homophilic interactions. CD6 expression is mainly restricted to T cells, and the interaction between CD6 and CD166 regulates T-cell activation. We have solved the X-ray crystal structures of the three SRCR domains of CD6 and two N-terminal domains of CD166. This first structure of consecutive SRCR domains reveals a nonlinear organization. We characterized the binding sites on CD6 and CD166 and showed that a SNP in CD6 causes glycosylation that hinders the CD6/CD166 interaction. Native mass spectrometry analysis showed that there is competition between the heterophilic and homophilic interactions. These data give insight into how interactions of consecutive SRCR domains are perturbed by SNPs and potential therapeutic reagents. PMID:26146185

  2. Therapeutic effect of curcumin on experimental colitis mediated by inhibiting CD8+CD11c+ cells

    Science.gov (United States)

    Zhao, Hai-Mei; Han, Fei; Xu, Rong; Huang, Xiao-Ying; Cheng, Shao-Min; Huang, Min-Fang; Yue, Hai-Yang; Wang, Xin; Zou, Yong; Xu, Han-Lin; Liu, Duan-Yong

    2017-01-01

    AIM To verify whether curcumin (Cur) can treat inflammatory bowel disease by regulating CD8+CD11c+ cells. METHODS We evaluated the suppressive effect of Cur on CD8+CD11c+ cells in spleen and Peyer’s patches (PPs) in colitis induced by trinitrobenzene sulfonic acid. Mice with colitis were treated by 200 mg/kg Cur for 7 d. On day 8, the therapeutic effect of Cur was evaluated by visual assessment and histological examination, while co-stimulatory molecules of CD8+CD11c+ cells in the spleen and PPs were measured by flow cytometry. The levels of interleukin (IL)-10, interferon (IFN)-γ and transforming growth factor (TGF)-β1 in spleen and colonic mucosa were determined by ELISA. RESULTS The disease activity index, colon weight, weight index of colon and histological score of experimental colitis were obviously decreased after Cur treatment, while the body weight and colon length recovered. After treatment with Cur, CD8+CD11c+ cells were decreased in the spleen and PPs, and the expression of major histocompatibility complex II, CD205, CD40, CD40L and intercellular adhesion molecule-1 was inhibited. IL-10, IFN-γ and TGF-β1 levels were increased compared with those in mice with untreated colitis. CONCLUSION Cur can effectively treat experimental colitis, which is realized by inhibiting CD8+CD11c+ cells. PMID:28348486

  3. 13.4% efficient thin-film CdS/CdTe solar cells

    Science.gov (United States)

    Chu, T. L.; Chu, S. S.; Ferekides, C.; Wu, C. Q.; Britt, J.; Wang, C.

    1991-12-01

    Cadmium telluride is a promising thin-film photovoltaic material as shown by the more than 10% efficient CdS/CdTe heterojunction solar cells. In this work, thin-film CdS/CdTe solar cells have been prepared using CdS films grown from an aqueous solution and p-CdTe films deposited by close-spaced sublimation (CSS). The properties of CdS films deposited from an ammonical solution of a Cd-salt, an ammonium salt, and thiourea have been controlled by optimizing the temperature and composition of the solution. The solution-grown CdS films have a high photoconductivity ratio, and its optical transmission is superior to that of vacuum evaporated CdS films. The properties of p-CdTe films deposited by CSS have been optimized by controlling the temperature and composition of the source material, and the substrate temperature. The properties of CdS/CdTe heterojunctions have been studied; junction photovoltage spectroscopy is used for the qualitative comparison of junction characteristics. Solar cells of 1-cm2 area with an AM 1.5 efficiency of 13.4% are reported.

  4. Photoluminescence studies of CdS and CdS:Cu

    Science.gov (United States)

    Price, K. J.

    2000-03-01

    Copper plays an important role in CdS/CdTe heterojunction solar cells, both as a dopant and a back contact to the CdTe. However, Cu is also thought to be responsible for the unstable performance of some types of CdS/CdTe devices under extreme conditions. Recently, Cu has been shown to diffuse from the back contact of the CdTe all the way to the CdS/CdTe interface and into the CdS. We have used photoluminescence (PL) to examine the electrically active states of CdS and CdS:Cu single crystals and polycrystalline films. In undoped films, we detect an exitonic feature at 2.54 eV related to a Cd vacancy. This feature is dramatically reduced in Cu-doped samples, indicating Cu in the Cd vacancy site. In addition, we will present results of light-soaking at 1 sun on the stability of the photoluminescence spectra.

  5. Circulating (CD3−CD19+CD20−IgD−CD27highCD38high) Plasmablasts: A Promising Cellular Biomarker for Immune Activity for Anti-PLA2R1 Related Membranous Nephropathy?

    Science.gov (United States)

    Beukinga, Ingrid; Willard-Gallo, Karen; Nortier, Joëlle; Pradier, Olivier

    2016-01-01

    Membranous nephropathy (MN) is a kidney specific autoimmune disease mainly mediated by anti-phospholipase A2 receptor 1 autoantibody (PLA2R1 Ab). The adequate assessment of chimeric anti-CD20 monoclonal antibody, rituximab (RTX), efficacy is still needed to improve clinical outcome of patient with MN. We evaluated the modification of plasmablasts (CD3−CD19+CD20−IgD−CD27highCD38high), a useful biomarker of RTX response in other autoimmune diseases, and memory (CD3−CD19+CD20+IgD−CD27+CD38−) and naive (CD3−CD19+CD20+IgD+CD27−CD38low) B cells by fluorescence-activated cell sorter analysis in PLA2R1 related MN in one patient during the 4 years of follow-up after RTX. RTX induced complete disappearance of CD19+ B cells, plasmablasts, and memory B cells as soon as day 15. Despite severe CD19+ lymphopenia, plasmablasts and memory B cells reemerged early before naive B cells (days 45, 90, and 120, resp.). During the follow-up, plasmablasts decreased more rapidly than memory B cells but still remained elevated as compared to day 0 of RTX. Concomitantly, anti-PLA2R1 Ab increased progressively. Our single case report suggests that, besides monitoring of serum anti-PLA2R1 Ab level, enumeration of circulating plasmablasts and memory B cells represents an attractive and complementary tool to assess immunological activity and efficacy of RTX induced B cells depletion in anti-PLA2R1 Ab related MN. PMID:27493452

  6. CD+4CD+25调节性T细胞与肿瘤的相关性研究%CD+4 CD+25 regulatory T cells and lung cancer

    Institute of Scientific and Technical Information of China (English)

    翟晋芳; 韩福才

    2009-01-01

    通过了解CD+4 CD+25调节性T细胞(CD+4 CD+25Treg)表面分子的特性和CD+4 CD+25Treg在外周血和组织中的表达,认识CD+4 CD+25 Treg在肿瘤免疫凋节中的作用,探索其作用的分子机制.%To know CD+4 CD+25 regulatory T cells' s function in tumor immunological regulation and to search for its functionary molecule mechanism by reviewing researches associated with the characteristics of CD+4 CD+25 regulatory T cells surface molecules and the expression of CD+4 CD+25 regulatory T cells in the peripheral blood and tissues.

  7. Nucleoprotein structure of the CD4 locus: Implications for the mechanisms underlying CD4 regulation during T cell development

    OpenAIRE

    Yu, Ming; Wan, Mimi; Zhang, Jianmin; Wu, Jie; Khatri, Rohini; Chi, Tian

    2008-01-01

    The CD4 gene is regulated in a stage-specific manner during T cell development, being repressed in CD4−CD8− double-negative (DN) and CD8 cells, but expressed in CD4+CD8+ double-positive (DP) and CD4 cells. Furthermore, the expression/repression pattern is reversible in developing (DN and DP) thymocytes, but irreversible in mature (CD4 and CD8) T cells. Here, we explored the molecular mechanisms underlying this complex mode of regulation by examining the nucleoprotein structure of the CD4 locu...

  8. Impact of HIV on CD8+ T cell CD57 expression is distinct from that of CMV and aging.

    Directory of Open Access Journals (Sweden)

    Sulggi A Lee

    Full Text Available Chronic antigenic stimulation by cytomegalovirus (CMV is thought to increase "immunosenesence" of aging, characterized by accumulation of terminally differentiated CD28- CD8+ T cells and increased CD57, a marker of proliferative history. Whether chronic HIV infection causes similar effects is currently unclear.We compared markers of CD8+ T cell differentiation (e.g., CD28, CD27, CCR7, CD45RA and CD57 expression on CD28- CD8+ T cells in healthy HIV-uninfected adults with and without CMV infection and in both untreated and antiretroviral therapy (ART-suppressed HIV-infected adults with asymptomatic CMV infection.Compared to HIV-uninfected adults without CMV (n=12, those with asymptomatic CMV infection (n=31 had a higher proportion of CD28-CD8+ T cells expressing CD57 (P=0.005. Older age was also associated with greater proportions of CD28-CD8+ T cells expressing CD57 (rho: 0.47, P=0.007. In contrast, untreated HIV-infected CMV+ participants (n=55 had much lower proportions of CD28- CD8+ cells expressing CD57 than HIV-uninfected CMV+ participants (P<0.0001 and were enriched for less well-differentiated CD28- transitional memory (TTR CD8+ T cells (P<0.0001. Chronically HIV-infected adults maintaining ART-mediated viral suppression (n=96 had higher proportions of CD28-CD8+ T cells expressing CD57 than untreated patients (P<0.0001, but continued to have significantly lower levels than HIV-uninfected controls (P=0.001. Among 45 HIV-infected individuals initiating their first ART regimen, the proportion of CD28-CD8+ T cells expressing CD57 declined (P<0.0001, which correlated with a decline in percent of transitional memory CD8+ T cells, and appeared to be largely explained by a decline in CD28-CD57- CD8+ T cell counts rather than an expansion of CD28-CD57+ CD8+ T cell counts.Unlike CMV and aging, which are associated with terminal differentiation and proliferation of effector memory CD8+ T cells, HIV inhibits this process, expanding less well

  9. Overexpression of CD97 confers an invasive phenotype in glioblastoma cells and is associated with decreased survival of glioblastoma patients.

    Directory of Open Access Journals (Sweden)

    Michael Safaee

    Full Text Available Mechanisms of invasion in glioblastoma (GBM relate to differential expression of proteins conferring increased motility and penetration of the extracellular matrix. CD97 is a member of the epidermal growth factor seven-span transmembrane family of adhesion G-protein coupled receptors. These proteins facilitate mobility of leukocytes into tissue. In this study we show that CD97 is expressed in glioma, has functional effects on invasion, and is associated with poor overall survival. Glioma cell lines and low passage primary cultures were analyzed. Functional significance was assessed by transient knockdown using siRNA targeting CD97 or a non-target control sequence. Invasion was assessed 48 hours after siRNA-mediated knockdown using a Matrigel-coated invasion chamber. Migration was quantified using a scratch assay over 12 hours. Proliferation was measured 24 and 48 hours after confirmed protein knockdown. GBM cell lines and primary cultures were found to express CD97. Knockdown of CD97 decreased invasion and migration in GBM cell lines, with no difference in proliferation. Gene-expression based Kaplan-Meier analysis was performed using The Cancer Genome Atlas, demonstrating an inverse relationship between CD97 expression and survival. GBMs expressing high levels of CD97 were associated with decreased survival compared to those with low CD97 (p = 0.007. CD97 promotes invasion and migration in GBM, but has no effect on tumor proliferation. This phenotype may explain the discrepancy in survival between high and low CD97-expressing tumors. This data provides impetus for further studies to determine its viability as a therapeutic target in the treatment of GBM.

  10. Influence of CdTe thickness on structural and electrical properties of CdTe/CdS solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Salavei, A.; Rimmaudo, I. [Laboratory for Applied Physics, Department of Computer Science, University of Verona, Strada Le Grazie 15, 37134 Verona (Italy); Piccinelli, F. [Laboratorio di Chimica dello Stato Solido, DB, Univ. Verona, and INSTM, UdR Verona, Strada Le Grazie 15, 37134 Verona (Italy); Romeo, A., E-mail: alessandro.romeo@univr.it [Laboratory for Applied Physics, Department of Computer Science, University of Verona, Strada Le Grazie 15, 37134 Verona (Italy)

    2013-05-01

    Due to its high scalability and low production cost, CdTe solar cells have shown a very strong potential for large scale energy production. Although the number of modules produced could be limited by tellurium scarcity, it has been reported that reducing CdTe thickness down to 1.5 μm would solve this issue. There are, however, issues to be considered when reducing thickness, such as formation of pinholes, lower crystallization, and different possible effects on material diffusion within the interfaces. In this work, we present the study of CdTe solar cells fabricated by vacuum evaporation with different CdTe thicknesses. Several cells with a CdTe thickness ranging from 0.7 to 6 μm have been fabricated. The deposition process has been optimized accordingly and their physical and electrical properties have been studied. Thin cells show a different electrical behavior in terms of open circuit voltage and fill factor. Efficiencies range from 7% for thin CdTe cells to 13.5% for the standard thickness. - Highlights: ► Ultra thin CdTe absorbers have been prepared and studied. ► Grain size is depending on the CdTe thickness but spread in the grains increases. ► Lattice parameter is reduced only for ultra thin CdTe. ► The band gap reveals an intermixed CdTe absorber. ► The reason for lower efficiency of ultra thin CdTe is explained.

  11. Immunohistochemical detection of SWC3, CD2, CD3, CD4 and CD8 antigens in paraformaldehyde fixed and paraffin embedded porcine lymphoid tissue

    DEFF Research Database (Denmark)

    Tingstedt, Jens Erik; Tornehave, Ditte; Lind, Peter;

    2003-01-01

    porcine tissue sections using the highly sensitive tyramide signal amplification system. Combining this method with different antigen retrieval techniques enabled us to detect CD2, CD3, CD4, CD8 and SWC3 antigen expressing cells in porcine lymphoid tissue. Thus, we describe herein methods......Identification of the different cell types of the immune system is important for in situ studies on the pathogenesis of infectious diseases in various animals, including the pig. Unfortunately, many monoclonal anti-leukocyte antibodies are only useful for staining frozen tissue sections...... for the detection of several major cell types of the porcine immune system in fixed tissue with optimal preservation of histological details....

  12. Investigation of biocompatible and protein sensitive highly luminescent quantum dots/nanocrystals of CdSe, CdSe/ZnS and CdSe/CdS.

    Science.gov (United States)

    Ratnesh, R K; Mehata, Mohan Singh

    2017-02-16

    The size and shape dependent semiconductor quantum dots (0D nanoparticles) with color tunability demonstrating significant influence in a biological system and considered as ideal probes. Here, a non-coordinated colloidal approach was used for the synthesis of CdSe, CdSe/ZnS and CdSe/CdS core-shell quantum dots (QDs) of 3-4nm. The synthesized nanocrystals show a high crystallinity, examined by X-ray diffraction (XRD) and high-resolution electron microscopy (HRTEM). The core-shell semiconductor QDs exhibit stronger photoluminescence (PL) as compared to the core QDs. The strong PL with small full-width half maximum (FWHM) indicates that the prepared QDs have a nearly uniform size distribution and well dispersibility. The quantum yield (QY) of core-shell QDs increases due to the surface passivation. Further, the PL of BSA is quenched strongly by the presence of core-shell QDs and follows the well-known Stern-Volmer (S-V) relation, whereas the PL lifetime does not follow the S-V relation, demonstrating that the observed quenching is predominantly static in nature. Among CdSe core, CdSe/ZnS and CdSe/CdS core-shell QDs, the CdSe/ZnS QDs shows the least cytotoxicity and most biocompatibility. Thus, the prepared core-shell QDs are biocompatible and exhibit strong sensing ability.

  13. CD40 signaling and Alzheimer's disease pathogenesis.

    Science.gov (United States)

    Town, T; Tan, J; Mullan, M

    2001-01-01

    The interaction between CD40 and its cognate ligand, CD40 ligand, is a primary regulator of the peripheral immune response, including modulation of T lymphocyte activation, B lymphocyte differentiation and antibody secretion, and innate immune cell activation, maturation, and survival. Recently, we and others have identified CD40 expression on a variety of CNS cells, including endothelial cells, smooth muscle cells, astroglia and microglia, and have found that, on many of these cells, CD40 expression is enhanced by pro-inflammatory stimuli. Importantly, the CD40-CD40 ligand interaction on microglia triggers a series of intracellular signaling events that are discussed, beginning with Src-family kinase activation and culminating in microglial activation as evidenced by tumor necrosis factor-alpha secretion. Based on the involvement of microglial activation and brain inflammation in Alzheimer's disease pathogenesis, we have investigated co-stimulation of microglia, smooth muscle, and endothelial cells with CD40 ligand in the presence of low doses of freshly solubilized amyloid-beta peptides. Data reviewed herein show that CD40 ligand and amyloid-beta act synergistically to promote pro-inflammatory responses by these cells, including secretion of interleukin-1 beta by endothelial cells and tumor necrosis factor-alpha by microglia. As these cytokines have been implicated in neuronal injury, a comprehensive model of pro-inflammatory CD40 ligand and amyloid-beta initiated Alzheimer's disease pathogenesis (mediated by multiple CNS cells) is proposed.

  14. Association of CD247 polymorphisms with rheumatoid arthritis: a replication study and a meta-analysis.

    Directory of Open Access Journals (Sweden)

    María Teruel

    Full Text Available Given the role of CD247 in the response of the T cells, its entailment in autoimmune diseases and in order to better clarify the role of this gene in RA susceptibility, we aimed to analyze CD247 gene variants previously associated with other autoimmune diseases (rs1052237, rs2056626 and rs864537 in a large independent European Caucasian population. However, no evidence of association was found for the analyzed CD247 single-nucleotide polymorphisms (SNPs with RA and with the presence/absence of anti-cyclic citrullinated polypeptide. We performed a meta-analysis including previously published GWAS data from the rs864537 variant, revealing an overall genome-wide significant association between this CD247 SNP and RA with anti-CCP (OR = 0.90, CI 95% = 0.87-0.93, Poverall = 2.1×10(-10. Our results show for first time a GWAS-level association between this CD247 polymorphism and RA risk.

  15. The morphology, microstructure, and luminescent properties of CdS/CdTe films

    Energy Technology Data Exchange (ETDEWEB)

    Al-Jassim, M.M.; Dhere, R.G.; Jones, K.M.; Hasoon, F.S.; Sheldon, P. [National Renewable Energy Lab., Golden, CO (United States)

    1998-09-01

    This paper is concerned with the characterization of CdS/CdTe polycrystalline thin films for solar cells. The morphology, microstructure, and luminescent properties are studied by a powerful array of characterization techniques. The presence of pinholes in 100-nm thick CdS is observed. The microstructure of CdS and CdTe films is shown to be heavily faulted polycrystalline. The effect of deposition temperature on the grain size and the microstructure is investigated. The interdiffusion of sulfur and tellurium at the CdS/CdTe interface is studied for the first time by a nanoprobe technique. Considerable amount of sulfur is detected in CdTe in the vicinity of the interface of samples deposited at 625 C. The recombination behavior of grain boundaries and intragrain defects is investigated in as-deposited and heat-treated samples.

  16. Synthesis and fluorescence properties of CdSe/CdS nanoparticles in aqueous media

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    On the basis of unique structural characteristics of α-cyclodextrin,α-cyclodextrin modified CdSe/CdS nanoparticles have been successfully synthesized in aqueous media.Techniques of AFM,TEM,EDS,FTIR,UV-vis absorbance and photoluminescence spectra were used to characterize the morphology,composition and optical characteristics of the synthesized nanoparticles.The results showed that the as-synthesized nanoparticles were elliptical and composed of several small particles.Their average length and diameter were about 20 nm and 15 nm.CdSe/CdS nanoparticles had single well-crystallized hexagonal structure.Packaged with a shell of CdS on the surface,α-CD/CdSe-CdS nanoparticles exhibited a red shift in the absorption spectrum,intensity growth in the emission spectrum and a substantial increase in Quantum yields.The size distribution could be adjusted by precursor ratios in the presence of α-cyclodextrins.

  17. Nanostructured CdS/CdSSe glass composite for photonic application

    Indian Academy of Sciences (India)

    S D Naik; S K Apte; R S Sonawane; U P Mulik; B B Kale

    2005-10-01

    The present work describes the synthesis of CdS/CdSSe glass nanocomposites and its characterization. A few glass compositions were optimized and the optimized host glass was remelted along with different semiconductors like CdS and CdSSe at high temperature. The CdS/CdSSe is present in amorphous state in the glass matrix. The thermal treatments have been carefully optimized to obtain well-defined uniform crystal growth of CdS and CdSSe. The glasses with optimized conditions were fabricated and characterized thoroughly using UV, TG/DTA and TEM. The shift in absorption edge to the longer wavelength with heat treatment implies the increase in the crystal size. The band gap has been increased with decrease in the particle size. Crystal size of semiconductors obtained by TEM was 2.5-5 nm for the glass showing absorption edge cut-off at 475 nm (CM-475).

  18. Flexible CdTe/CdS solar cells on thin glass substrates.

    Science.gov (United States)

    Seo, Won-Oh; Kim, Donghwan; Kim, Jihyun

    2015-04-06

    We demonstrate flexible CdTe/CdS thin-film solar cells in a superstrate configuration with a cell conversion efficiency as high as 10.9%. We deposit a CdS window layer and a CdTe absorber layer on a flexible glass substrate using the chemical bath deposition method and close-spaced sublimation method, respectively. The thin and flexible glass substrates were able to tolerate a high growth temperature and post-growth processes. We repeatedly apply a strain of 0.15% to the fabricated CdTe/CdS solar cells, and this was shown to have a negligible effect on their performances. Our proposed thin films-on-compliant substrate structure, which was prepared by replacing a rigid glass with a bendable one, demonstrated flexible CdTe/CdS p-n junction thin-film solar cells without compromising the cell performance.

  19. Improving pan-genome annotation using whole genome multiple alignment

    Directory of Open Access Journals (Sweden)

    Salzberg Steven L

    2011-06-01

    Full Text Available Abstract Background Rapid annotation and comparisons of genomes from multiple isolates (pan-genomes is becoming commonplace due to advances in sequencing technology. Genome annotations can contain inconsistencies and errors that hinder comparative analysis even within a single species. Tools are needed to compare and improve annotation quality across sets of closely related genomes. Results We introduce a new tool, Mugsy-Annotator, that identifies orthologs and evaluates annotation quality in prokaryotic genomes using whole genome multiple alignment. Mugsy-Annotator identifies anomalies in annotated gene structures, including inconsistently located translation initiation sites and disrupted genes due to draft genome sequencing or pseudogenes. An evaluation of species pan-genomes using the tool indicates that such anomalies are common, especially at translation initiation sites. Mugsy-Annotator reports alternate annotations that improve consistency and are candidates for further review. Conclusions Whole genome multiple alignment can be used to efficiently identify orthologs and annotation problem areas in a bacterial pan-genome. Comparisons of annotated gene structures within a species may show more variation than is actually present in the genome, indicating errors in genome annotation. Our new tool Mugsy-Annotator assists re-annotation efforts by highlighting edits that improve annotation consistency.

  20. Exploring functional elements and genomic variation in the noncoding genome

    NARCIS (Netherlands)

    van Heesch, S.A.A.C.

    2014-01-01

    Gene expression regulation is a delicate process that depends on multiple aspects including genome structure and transcription factor binding to DNA elements. The majority of our genome consists of noncoding DNA, which was shown to be crucial in providing the correct context for genome function. Alt

  1. Detection and significance of CD4+ CD25+ CD127low/-Treg cells in patients with SLE%系统性红斑狼疮患者外周血CD4+CD25+CD127low/-调节性T细胞的检测及意义

    Institute of Scientific and Technical Information of China (English)

    韦月梅; 邹洪才; 崔俊; 孔建忠; 田安国; 葛建英

    2013-01-01

    Objective To investigate the feasibility of application of CD4+ CD25+ CD127low/- as an Treg cells new marker in patients with systemic lupus erythematosus (SLE). Methods The proportions of CD4+CD25+CD127low-/and CD4+CD25+ FoxP3+Treg cells in peripheral blood of SLE patients(group A) and healthy people(group B) were determined by flow cytometry. The correlation between CD4+ CD25+ CD127low/- Treg cells and CD4+ CD25+ FoxP3+ Treg cells was analyzed. Results The proportions of CD4+CD25+CD127low/- Treg cells and CD4+ CD25+ FoxP3+Treg cells in group A were significantly lower than those in group B [(3. 31 + 0. 82)% and (2. 28 + 0. 47)% vs. (6. 07 + 1. 59)% and (5. 01 + 1. 09)%](P<0. 01). The proportion of CD4+ CD25+ CD127 low/- Treg cells was positively correlated to that of CD4+ CD25+ FoxP3+ T cells in both groups(r=0. 713 and r=0. 709, P<0. 01). Conclusion The surface marker CD4+ CD25+ CD127low/- can be used to identify Treg cells. The decreases of CD4+CD25+CD127low/- Treg cells may play an important role in the pathogenesis of SLE.%目的 探讨用膜表面标志CD4+ CD25+ CD127low/-作为检测调节性T(Treg)细胞标记的可行性,并探讨其在系统性红斑狼疮(SLE)中的临床意义.方法 用流式细胞术检测SLE组及健康对照组外周血CD4+ CD25+ CD127low/-Treg细胞及CD4+ CD25+ FoxP3+ Treg细胞的比例,并分析两组CD4+ CD25+ CD127low/-Treg细胞与CD4+ CD25+ FoxP3+ Treg细胞比例之间的相关性.结果 SLE组外周血CD4+ CD25+ CD127low/-Treg细胞比例为(3.31±0.82)%CD4+ CD25+ FoxP3+ Treg细胞比例为(2.28±0.47)%,均显著低于健康对照组的(6.07±1.59)%和(5.01±1.09)%(P<0.01).SLE组及健康对照组外周血CD4+ CD25+ CD127low/-Treg细胞比例与CD4+ CD25+FoxP3+ Treg细胞比例之间呈显著正相关(r=0.713、r=0.709,P<0.01).结论 膜表面标志CD4+ CD25+ CD127low/-可以用来鉴定Treg细胞;SLE患者外周血CD4+ CD25+ CD127low/-Treg细胞的显著减少可能与SLE的发病有关.

  2. Stability of XIST repression in relation to genomic imprinting following global genome demethylation in a human cell line

    Energy Technology Data Exchange (ETDEWEB)

    Araújo, E.S.S. de [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil); Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Vasques, L.R. [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil); Stabellini, R.; Krepischi, A.C.V. [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil); Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São Paulo, SP (Brazil); Pereira, L.V. [Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP (Brazil)

    2014-10-17

    DNA methylation is essential in X chromosome inactivation and genomic imprinting, maintaining repression of XIST in the active X chromosome and monoallelic repression of imprinted genes. Disruption of the DNA methyltransferase genes DNMT1 and DNMT3B in the HCT116 cell line (DKO cells) leads to global DNA hypomethylation and biallelic expression of the imprinted gene IGF2 but does not lead to reactivation of XIST expression, suggesting that XIST repression is due to a more stable epigenetic mark than imprinting. To test this hypothesis, we induced acute hypomethylation in HCT116 cells by 5-aza-2′-deoxycytidine (5-aza-CdR) treatment (HCT116-5-aza-CdR) and compared that to DKO cells, evaluating DNA methylation by microarray and monitoring the expression of XIST and imprinted genes IGF2, H19, and PEG10. Whereas imprinted genes showed biallelic expression in HCT116-5-aza-CdR and DKO cells, the XIST locus was hypomethylated and weakly expressed only under acute hypomethylation conditions, indicating the importance of XIST repression in the active X to cell survival. Given that DNMT3A is the only active DNMT in DKO cells, it may be responsible for ensuring the repression of XIST in those cells. Taken together, our data suggest that XIST repression is more tightly controlled than genomic imprinting and, at least in part, is due to DNMT3A.

  3. Complementary Dendritic Cell–activating Function of CD8+ and CD4+ T Cells

    Science.gov (United States)

    Mailliard, Robbie B.; Egawa, Shinichi; Cai, Quan; Kalinska, Anna; Bykovskaya, Svetlana N.; Lotze, Michael T.; Kapsenberg, Martien L.; Storkus, Walter J.; Kalinski, Pawel

    2002-01-01

    Dendritic cells (DCs) activated by CD40L-expressing CD4+ T cells act as mediators of “T helper (Th)” signals for CD8+ T lymphocytes, inducing their cytotoxic function and supporting their long-term activity. Here, we show that the optimal activation of DCs, their ability to produce high levels of bioactive interleukin (IL)-12p70 and to induce Th1-type CD4+ T cells, is supported by the complementary DC-activating signals from both CD4+ and CD8+ T cells. Cord blood– or peripheral blood–isolated naive CD8+ T cells do not express CD40L, but, in contrast to naive CD4+ T cells, they are efficient producers of IFN-γ at the earliest stages of the interaction with DCs. Naive CD8+ T cells cooperate with CD40L-expressing naive CD4+ T cells in the induction of IL-12p70 in DCs, promoting the development of primary Th1-type CD4+ T cell responses. Moreover, the recognition of major histocompatibility complex class I–presented epitopes by antigen-specific CD8+ T cells results in the TNF-α– and IFN-γ–dependent increase in the activation level of DCs and in the induction of type-1 polarized mature DCs capable of producing high levels of IL-12p70 upon a subsequent CD40 ligation. The ability of class I–restricted CD8+ T cells to coactivate and polarize DCs may support the induction of Th1-type responses against class I–presented epitopes of intracellular pathogens and contact allergens, and may have therapeutical implications in cancer and chronic infections. PMID:11854360

  4. Ex Vivo Restimulation of Human PBMC Expands a CD3+CD4-CD8-γδ+ T Cell Population That Can Confound the Evaluation of CD4 and CD8 T Cell Responses to Vaccination

    Directory of Open Access Journals (Sweden)

    B. J. Sedgmen

    2013-01-01

    Full Text Available The measurement of vaccine-induced humoral and CD4+ and CD8+ cellular immune responses represents an important correlate of vaccine efficacy. Accurate and reliable assays evaluating such responses are therefore critical during the clinical development phase of vaccines. T cells play a pivotal role both in coordinating the adaptive and innate immune responses and as effectors. During the assessment of cell-mediated immunity (CMI in subjects participating in a large-scale influenza vaccine trial, we identified the expansion of an IFN-γ-producing CD3+CD4-CD8-γδ+ T cell population in the peripheral blood of 90/610 (15% healthy subjects. The appearance of CD3+CD4-CD8-γδ+ T cells in the blood of subjects was transient and found to be independent of the study cohort, vaccine group, subject gender and ethnicity, and ex vivo restimulation conditions. Although the function of this population and relevance to vaccination are unclear, their inclusion in the total vaccine-specific T-cell response has the potential to confound data interpretation. It is thus recommended that when evaluating the induction of IFN-γ-producing CD4+ and CD8+ immune responses following vaccination, the CD3+CD4-CD8-γδ+ T cells are either excluded or separately enumerated from the overall frequency determination.

  5. Ex Vivo Restimulation of Human PBMC Expands a CD3+CD4−CD8−γδ+ T Cell Population That Can Confound the Evaluation of CD4 and CD8 T Cell Responses to Vaccination

    Science.gov (United States)

    Sedgmen, B. J.; Papalia, L.; Wang, L.; Dyson, A. R.; McCallum, H. A.; Simson, C. M.; Pearse, M. J.; Maraskovsky, E.; Hung, D.; Eomois, P. P.; Hartel, G.; Barnden, M. J.; Rockman, S. P.

    2013-01-01

    The measurement of vaccine-induced humoral and CD4+ and CD8+ cellular immune responses represents an important correlate of vaccine efficacy. Accurate and reliable assays evaluating such responses are therefore critical during the clinical development phase of vaccines. T cells play a pivotal role both in coordinating the adaptive and innate immune responses and as effectors. During the assessment of cell-mediated immunity (CMI) in subjects participating in a large-scale influenza vaccine trial, we identified the expansion of an IFN-γ-producing CD3+CD4−CD8−γδ+ T cell population in the peripheral blood of 90/610 (15%) healthy subjects. The appearance of CD3+CD4−CD8−γδ+ T cells in the blood of subjects was transient and found to be independent of the study cohort, vaccine group, subject gender and ethnicity, and ex vivo restimulation conditions. Although the function of this population and relevance to vaccination are unclear, their inclusion in the total vaccine-specific T-cell response has the potential to confound data interpretation. It is thus recommended that when evaluating the induction of IFN-γ-producing CD4+ and CD8+ immune responses following vaccination, the CD3+CD4−CD8−γδ+ T cells are either excluded or separately enumerated from the overall frequency determination. PMID:24066003

  6. On genomics, kin, and privacy.

    Science.gov (United States)

    Telenti, Amalio; Ayday, Erman; Hubaux, Jean Pierre

    2014-01-01

    The storage of greater numbers of exomes or genomes raises the question of loss of privacy for the individual and for families if genomic data are not properly protected. Access to genome data may result from a personal decision to disclose, or from gaps in protection. In either case, revealing genome data has consequences beyond the individual, as it compromises the privacy of family members. Increasing availability of genome data linked or linkable to metadata through online social networks and services adds one additional layer of complexity to the protection of genome privacy.  The field of computer science and information technology offers solutions to secure genomic data so that individuals, medical personnel or researchers can access only the subset of genomic information required for healthcare or dedicated studies.

  7. Illuminating the Druggable Genome (IDG)

    Data.gov (United States)

    Federal Laboratory Consortium — Results from the Human Genome Project revealed that the human genome contains 20,000 to 25,000 genes. A gene contains (encodes) the information that each cell uses...

  8. A study of vapor CdCl{sub 2} treatment by CSS in CdS/CdTe solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Rios-Flores, A.; Pena, J.L.; Castro-Pena, V.; Ares, O.; Castro-Rodriguez, R. [Applied Physics Department, CINVESTAV-IPN Merida, C.P. 97310 Merida, Yucatan (Mexico); Bosio, A. [University of Parma, Department of Physics, v.le G.P. Usberti 7/A, 43100 Parma (Italy)

    2010-06-15

    We report the effect of CdCl{sub 2} vapor treatment on the photovoltaic parameters of CdS/CdTe solar cells. Vapor treatment allows combining CdCl{sub 2} exposure time and annealing in one step. In this alternative treatment, the CdS/CdTe substrates were treated with CdCl{sub 2} vapor in a close spaced sublimation (CSS) configuration. The substrate temperature and CdCl{sub 2} powder source temperature were 400 C. The treatment was done by varying the treatment time (t) from 15 to 90 min. Such solar cells are examined by measuring their current density versus voltage (J-V) characteristics. The open-circuit voltage (V{sub oc}), short circuit current density (J{sub sc}) and fill factor (FF) of our best cell, fabricated and normalized to the area of 1 cm{sup 2}, were V{sub oc} = 663 mV, J{sub sc} = 18.5 mA/cm{sup 2} and FF = 40%, respectively, corresponding to a total area conversion efficiency of {eta} = 5%. In cells of minor area (0.1 cm{sup 2}) efficiencies of 8% have been obtained. (author)

  9. CdS and CdS/CdSe sensitized ZnO nanorod array solar cells prepared by a solution ions exchange process

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Ling; Gong, Haibo; Zheng, Xiaopeng; Zhu, Min; Zhang, Jun [Key Laboratory of Inorganic Functional Materials in Universities of Shandong, School of Materials Science and Engineering, University of Jinan, Jinan 250022, Shandong (China); Yang, Shikuan [Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802-6812 (United States); Cao, Bingqiang, E-mail: mse_caobq@ujn.edu.cn [Key Laboratory of Inorganic Functional Materials in Universities of Shandong, School of Materials Science and Engineering, University of Jinan, Jinan 250022, Shandong (China)

    2013-10-15

    Graphical abstract: - Highlights: • CdS and CdS/CdSe quantum dots are assembled on ZnO nanorods by ion exchange process. • The CdS/CdSe sensitization of ZnO effectively extends the absorption spectrum. • The performance of ZnO/CdS/CdSe cell is improved by extending absorption spectrum. - Abstract: In this paper, cadmium sulfide (CdS) and cadmium sulfide/cadmium selenide (CdS/CdSe) quantum dots (QDs) are assembled onto ZnO nanorod arrays by a solution ion exchange process for QD-sensitized solar cell application. The morphology, composition and absorption properties of different photoanodes were characterized with scanning electron microscope, transmission electron microscope, energy-dispersive X-ray spectrum and Raman spectrum in detail. It is shown that conformal and uniform CdS and CdS/CdSe shells can grow on ZnO nanorod cores. Quantum dot sensitized solar cells based on ZnO/CdS and ZnO/CdS/CdSe nanocable arrays were assembled with gold counter electrode and polysulfide electrolyte solution. The CdS/CdSe sensitization of ZnO can effectively extend the absorption spectrum up to 650 nm, which has a remarkable impact on the performance of a photovoltaic device by extending the absorption spectrum. Preliminary results show one fourth improvement in solar cell efficiency.

  10. Chronic Brucellosis Patients Retain Low Frequency of CD4+ T-Lymphocytes Expressing CD25 and CD28 after Escherichia coli LPS Stimulation of PHA-Cultured PBMCs

    Directory of Open Access Journals (Sweden)

    Panagiotis Skendros

    2008-01-01

    Full Text Available Chronic brucellosis patients display a defective Th1 response to PHA. We have previously shown that heat-killed B. abortus (HKBA can downregulate the PHA-induced increase of CD4+/CD25+ and CD14+/CD80+ cells of brucellosis patients. In the present study, we investigate the effect of E. coli LPS, as a potent stimulant of monocytes and autologous T-lymphocytes, on the PHA-cultured PBMCs of the same groups of patients. Thirteen acute brucellosis (AB patients, 22 chronic brucellosis (CB patients, 11 “cured” subjects, and 15 healthy volunteers were studied. The percentage of CD4+/CD25+ and CD4+/CD28+ T-lymphocytes as well as CD14+/CD80+ monocytes were analyzed by flow cytometry after PBMCs culture with PHA plus E. coli LPS. A significant decrease in the percentage of CD4+/CD25+ and CD4+/CD28+ T-lymphocytes was observed in CB compared to AB. In HKBA cultures, compared to E. coli LPS-cultures, there was a significant reduction of CD4+/CD25+ T-lymphocytes in all groups and CD14+/CD80+ in patients groups. We suggest that Brucella can modulate host immune response, leading to T-cell anergy and chronic infection.

  11. The Nostoc punctiforme Genome

    Energy Technology Data Exchange (ETDEWEB)

    John C. Meeks

    2001-12-31

    Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9 Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.

  12. The tomato genome

    Science.gov (United States)

    The tomato genome sequence was undertaken at a time when state-of-the-art sequencing methodologies were undergoing a transition to co-called next generation methodologies. The result was an international consortium undertaking a strategy merging both old and new approaches. Because biologists were...

  13. Better chocolate through genomics

    Science.gov (United States)

    Theobroma cacao, the cacao or chocolate tree, is a tropical understory tree whose seeds are used to make chocolate. And like any important crop, cacao is the subject of much research. On September 15, 2010, scientists publicly released a preliminary sequence of the cacao genome--which contains all o...

  14. RIKEN mouse genome encyclopedia.

    Science.gov (United States)

    Hayashizaki, Yoshihide

    2003-01-01

    We have been working to establish the comprehensive mouse full-length cDNA collection and sequence database to cover as many genes as we can, named Riken mouse genome encyclopedia. Recently we are constructing higher-level annotation (Functional ANnoTation Of Mouse cDNA; FANTOM) not only with homology search based annotation but also with expression data profile, mapping information and protein-protein database. More than 1,000,000 clones prepared from 163 tissues were end-sequenced to classify into 159,789 clusters and 60,770 representative clones were fully sequenced. As a conclusion, the 60,770 sequences contained 33,409 unique. The next generation of life science is clearly based on all of the genome information and resources. Based on our cDNA clones we developed the additional system to explore gene function. We developed cDNA microarray system to print all of these cDNA clones, protein-protein interaction screening system, protein-DNA interaction screening system and so on. The integrated database of all the information is very useful not only for analysis of gene transcriptional network and for the connection of gene to phenotype to facilitate positional candidate approach. In this talk, the prospect of the application of these genome resourced should be discussed. More information is available at the web page: http://genome.gsc.riken.go.jp/.

  15. Genetics, genomics and fertility

    Science.gov (United States)

    In order to enhance the sustainability of dairy businesses, new management tools are needed to increase the fertility of dairy cattle. Genomic selection has been successfully used by AI studs to screen potential sires and significantly decrease the generation interval of bulls. Buoyed by the success...

  16. Poster: the macaque genome.

    Science.gov (United States)

    2007-04-13

    The rhesus macaque (Macaca mulatta) facilitates an extraordinary range of biomedical and basic research, and the publication of the genome only makes it a more powerful model for studies of human disease; moreover, the macaque's position relative to humans and chimpanzees affords the opportunity to learn about the processes that have shaped the last 25 million years of primate evolution. To allow users to explore these themes of the macaque genome, Science has created a special interactive version of the poster published in the print edition of the 13 April 2007 issue. The interactive version includes additional text and exploration, as well as embedded video featuring seven scientists discussing the importance of the macaque and its genome sequence in studies of biomedicine and evolution. We have also created an accompanying teaching resource, including a lesson plan aimed at teachers of advanced high school life science students, for exploring what a comparison of the macaque and human genomes can tell us about human biology and evolution. These items are free to all site visitors.

  17. The Genomic Standards Consortium

    DEFF Research Database (Denmark)

    Field, Dawn; Amaral-Zettler, Linda; Cochrane, Guy;

    2011-01-01

    A vast and rich body of information has grown up as a result of the world's enthusiasm for 'omics technologies. Finding ways to describe and make available this information that maximise its usefulness has become a major effort across the 'omics world. At the heart of this effort is the Genomic S...

  18. The Genome Atlas Resource

    DEFF Research Database (Denmark)

    Azam Qureshi, Matloob; Rotenberg, Eva; Stærfeldt, Hans Henrik;

    2010-01-01

    with scripts and algorithms developed in a variety of programming languages at the Centre for Biological Sequence Analysis in order to create a three-tier software application for genome analysis. The results are made available via a web interface developed in Java, PHP and Perl CGI. User...

  19. Study of the CdS/CdTe interface and its relevance to solar cell properties

    Science.gov (United States)

    Dhere, Ramesh Gurupad

    CdTe based devices have shown significant progress over the last decade. CdS/CdTe devices fabricated by close-spaced sublimation have resulted in 15.8% efficiency. To understand the effect of CdS/CdTe interface properties on device properties, a detailed investigation of the dependence of properties of CdS, CdTe and CdS/CdTe interface on various processing parameters is reported. Analysis of CdS/CdTe devices fabricated under identical conditions, was carried out to determine any correlation between the interface properties and device characteristics. Possible mechanisms to explain the correlation are presented. The CdS layers were deposited by chemical bath deposition (CBD) on glass/SnOsb2 substrates. The CdTe layers were grown by close-spaced sublimation (CSS) on glass/SnOsb2/CdS substrates. Post-deposition CdClsb2 heat-treatment was carried out using different concentrations of CdClsb2/methanol solution. CBD CdS gives conformal coverage on rough SnOsb2 layers at a thickness as low as 30 nm. Under optimal conditions, CdS films with refractive index close to bulk index are obtained indicating that the layers are void-free. The grain-size of CBD CdS films is independent of film thickness and is established during the early part of growth. AFM analysis of CSS CdTe shows that the films are faceted for the entire temperature range (475sp°C-625sp°C) investigated, the grain-size increases with substrate temperature, and the films are free of voids. X-ray diffraction analysis reveals that CdTe films grown at substrate temperatures ≥525sp°C have preferred orientation and the orientation is not affected by the CdClsb2 heat-treatment, indicating that the films deposited at these temperatures are more compact. TEM analysis of CdS/CdTe structures suggests that the majority of structural defects in the CdTe layers are generated at the interface and are caused by lattice mismatch and growth conditions. Cathodoluminescence and photoluminescence analysis shows that CdClsb2

  20. Analysis of the association between CD40 and CD40 ligand polymorphisms and systemic sclerosis

    NARCIS (Netherlands)

    Teruel, M.; Simeon, C.P.; Broen, J.C.A.; Vonk, M.C.; Carreira, P.; Camps, M.T.; Garcia-Portales, R.; Delgado-Frias, E.; Gallego, M.; Espinosa, G.; Spanish Scleroderma, G.; Beretta, L.; Airo, P.; Lunardi, C.; Riemekasten, G.; Witte, T.; Krieg, T.; Kreuter, A.; Distler, J.H.; Hunzelmann, N.; Koeleman, B.P.; Voskuyl, A.E.; Schuerwegh, A.J.; Gonzalez-Gay, M.A.; Radstake, T.R.D.J.; Martin, J.

    2012-01-01

    INTRODUCTION: The aim of the present study was to investigate the possible role of CD40 and CD40 ligand (CD40LG) genes in the susceptibility and phenotype expression of systemic sclerosis (SSc). METHODS: In total, 2,670 SSc patients and 3,245 healthy individuals from four European populations (Spain

  1. CD4+ T cell effects on CD8+ T cell location defined using bioluminescence.

    Directory of Open Access Journals (Sweden)

    Mitra Azadniv

    Full Text Available T lymphocytes of the CD8+ class are critical in delivering cytotoxic function and in controlling viral and intracellular infections. These cells are "helped" by T lymphocytes of the CD4+ class, which facilitate their activation, clonal expansion, full differentiation and the persistence of memory. In this study we investigated the impact of CD4+ T cells on the location of CD8+ T cells, using antibody-mediated CD4+ T cell depletion and imaging the antigen-driven redistribution of bioluminescent CD8+ T cells in living mice. We documented that CD4+ T cells influence the biodistribution of CD8+ T cells, favoring their localization to abdominal lymph nodes. Flow cytometric analysis revealed that this was associated with an increase in the expression of specific integrins. The presence of CD4+ T cells at the time of initial CD8+ T cell activation also influences their biodistribution in the memory phase. Based on these results, we propose the model that one of the functions of CD4+ T cell "help" is to program the homing potential of CD8+ T cells.

  2. CD81 and CD9 work independently as extracellular components upon fusion of sperm and oocyte

    Directory of Open Access Journals (Sweden)

    Naoko Ohnami

    2012-05-01

    When a sperm and oocyte unite into one cell upon fertilization, membranous fusion between the sperm and oocyte occurs. In mice, Izumo1 and a tetraspanin molecule CD9 are required for sperm-oocyte fusion as one of the oocyte factors, and another tetraspanin molecule CD81 is also thought to involve in this process. Since these two tetraspanins often form a complex upon cell-cell interaction, it is probable that such a complex is also formed in sperm-oocyte interaction; however, this possibility is still under debate among researchers. Here we assessed this problem using mouse oocytes. Immunocytochemical analysis demonstrated that both CD9 and CD81 were widely distributed outside the oocyte cell membrane, but these molecules were separate, forming bilayers, confirmed by immunobiochemical analysis. Electron-microscopic analysis revealed the presence of CD9- or CD81-incorporated extracellular structures in those bilayers. Finally, microinjection of in vitro-synthesized RNA showed that CD9 reversed a fusion defect in CD81-deficient oocytes in addition to CD9-deficient oocytes, but CD81 failed in both oocytes. These results suggest that both CD9 and CD81 independently work upon sperm-oocyte fusion as extracellular components.

  3. CD64-directed immunotoxin inhibits arthritis in a novel CD64 transgenic rat model

    NARCIS (Netherlands)

    van Vuuren, AJ; van Roon, JAG; Walraven, [No Value; Stuij, [No Value; Harmsen, MC; McLaughlin, PMJ; de Winkel, JGJV; Thepen, T

    2006-01-01

    Macrophages are known to play a key role during inflammation in rheumatoid arthritis (RA). Inflammatory macrophages have increased expression of CD64, the high-affinity receptor for IgG. Targeting this receptor through a CD64-directed immunotoxin, composed of an Ab against CD64 and Ricin A, results

  4. Simulation of the Efficiency of CdS/CdTe Tandem Multi-Junction Solar Cells

    CERN Document Server

    Mirkamali, Ashrafalsadat S

    2016-01-01

    In this paper we study CdS/CdTe solar cells by means of AMPS-1D software. First we study the effect of thickness of semiconductor layers on the output parameters of the CdS/CdTe solar cell, such as density of short-circuit current, open circuit voltage, fill factor and efficiency. Numerical simulation shows that the highest efficiency of single-junction CdS/CdTe solar cell equal to 18.3% is achieved when the CdTe layer thickness is 1000 nm and a CdS layer is 60 nm. Then, in order to obtain the maximal value of the efficiency, new tandem multi-junction structure consisting of layers of two solar cells connected with each other back to back are designed and engineered taking into account the results obtained for the single-junction solar cells. Numerical simulations show that its highest efficiency in 31.8% can be obtained when the thickness of CdS p-layer is equal to 50 nm, and the thickness of the CdS n-layer is equal to 200 nm, while thicknesses of the CdTe n-layer and CdTe p-layer are kept fixed and equal t...

  5. A transferable force field for CdS-CdSe-PbS-PbSe solid systems

    NARCIS (Netherlands)

    Fan, Zhaochuan; Koster, Rik S.; Wang, Shuaiwei; Fang, Changming; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; van Huis, Marijn A.; Vlugt, Thijs J. H.

    2014-01-01

    A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heterona

  6. Immunoexpression of CD30 and CD30 ligand in deciduas from spontaneous abortions

    Directory of Open Access Journals (Sweden)

    M Trovato

    2009-06-01

    Full Text Available In the present study, using immunohistochemistry, we studied the expression of CD30 and CD30-L in 35 deciduas obtained from women following elective abortion during normal physiological gestation and in 60 deciduas obtained from women after spontaneous abortion with or without signs of inflammation. The main difference was noticed in the first trimester of gestation in which was found a decrease in CD30/CD30-L-positive decidual glandular and stromal cells in a greater number of cases of spontaneous abortions with respect to cases of physiological pregnancies (70% vs 50%, p<0.05. In addition, deciduas from spontaneous abortions with inflammation and without inflammation reacted similarly. The reduced expression of CD30 and CD30-L and their cellular pattern detected in the deciduas from spontaneous abortions suggest that the CD30/CD30-L system is crucial for preventing abortions in the first trimester. And furthermore, the distinctive expression of CD30/CD30- L in deciduas from physiological pregnancies may indicate that the CD30/CD30-L system exerts its main role in the first trimester.

  7. Close linkage of the mouse and human CD3. gamma. - and delta-chain genes suggests that their transcription is controlled by common regulatory elements

    Energy Technology Data Exchange (ETDEWEB)

    Saito, H.; Koyama, T.; Georgopoulos, K.; Clevers, H.; Haser, W.G.; LeBien, T.; Tonegawa, S.; Terhorst, C.

    1987-12-01

    Antigen receptors on the T-cell surface are noncovalently associated with at least four invariant polypeptide chains, CD3-..gamma.., -delta, -epsilon, and -zeta. The mouse CD3-..gamma.. gene, consisting of seven exons, was found to be highly homologous to the CD3-..gamma.. described earlier. Both the high level of sequence homology and the exon/intron organization indicate that the CD3-..gamma.. and -delta genes arose by gene duplication. Surprisingly, murine and human genomic DNA clones could be isolated that contained elements of both the CD3-..gamma.. and CD3-delta genes. In fact, the putative transcription start site of the mouse CD3-..gamma.. gene is less than 1.4 kilobases from the transcription initiation site of the mouse CD3-delta gene. Common elements that regulate the divergent transcription of the two genes are therefore proposed to be located in the intervening 1.4-kilobase DNA segment. This might contribute to the coordinate expression of the CD3-..gamma.. and -delta genes during intrathymic maturation of T lymphocytes.

  8. Membrane expression of NK receptors CD160 and CD158k contributes to delineate a unique CD4+ T-lymphocyte subset in normal and mycosis fungoides skin.

    Science.gov (United States)

    Sako, Nouhoum; Schiavon, Valérie; Bounfour, Touda; Dessirier, Valérie; Ortonne, Nicolas; Olive, Daniel; Ram-Wolff, Caroline; Michel, Laurence; Sicard, Hélène; Marie-Cardine, Anne; Bagot, Martine; Bensussan, Armand; Schmitt, Christian

    2014-10-01

    CD160 is a GPI-anchored Ig-like receptor identified by the BY55 mAb on human circulating CD56dim+ NK cells and TCRγδ lymphocytes. In addition, while most intestinal T lymphocytes express it, only a minor circulating CD4+ or CD8+ T lymphocyte subset is CD160+. Here we describe a population of CD4+ CD160+ human blood T lymphocytes of circulating cutaneous T cells. These rare T lymphocytes represent 2.1 ± 1.9% of the circulating CD3+ CD4+ T cells, coexpress CD8αα, CD244, and perforin but lack CD28 expression, a phenotype corresponding to effector memory cytotoxic T-lymphocytes. Functional studies further confirmed their cytotoxic potential. These cells lack αEβ7 integrin and CCR7 expression but do express skin-addressing molecules CLA, and CCR4. In normal human skin, CD4+ CD160+ cells represent 34.6 ± 14.7% of the CD4+ T lymphocytes extracted by collagenase treatment. These T cells coexpress CLA (81 ± 13.6%), CCR4 (62.3 ± 15.9%), and some CD8αα (19.6 ± 13%) or CCR7 (24.4 ± 11.7%) expression. Cutaneous T-cell lymphoma cells express the natural killer receptor KIR3DL2 (CD158k) used as a tumor marker. Not only we confirmed the expression of this marker in the blood and/or skin of mycosis fungoides patients but we also show for the first time CD158k expression (often associated with CD160) on cutaneous CD4+ T cells from healthy individuals (25.3 ± 15%). Therefore, CD4+ CD160+ T cells expressing CD158k might represent specialized cutaneous lymphocytes devoted to immune surveillance, from which could originate cutaneous T-cell lymphomas such as mycosis fungoides.

  9. Anti-CD22/CD20 Bispecific antibody with enhanced trogocytosis for treatment of Lupus.

    Directory of Open Access Journals (Sweden)

    Edmund A Rossi

    Full Text Available The humanized anti-CD22 antibody, epratuzumab, has demonstrated therapeutic activity in clinical trials of lymphoma, leukemia and autoimmune diseases, treating currently over 1500 cases of non-Hodgkin lymphoma, acute lymphoblastic leukemias, Waldenström's macroglobulinemia, Sjögren's syndrome, and systemic lupus erythematosus. Because epratuzumab reduces on average only 35% of circulating B cells in patients, and has minimal antibody-dependent cellular cytotoxicity and negligible complement-dependent cytotoxicity when evaluated in vitro, its therapeutic activity may not result completely from B-cell depletion. We reported recently that epratuzumab mediates Fc/FcR-dependent membrane transfer from B cells to effector cells via trogocytosis, resulting in a substantial reduction of multiple BCR modulators, including CD22, CD19, CD21, and CD79b, as well as key cell adhesion molecules, including CD44, CD62L, and β7 integrin, on the surface of B cells in peripheral blood mononuclear cells obtained from normal donors or SLE patients. Rituximab has clinical activity in lupus, but failed to achieve primary endpoints in a Phase III trial. This is the first study of trogocytosis mediated by bispecific antibodies targeting neighboring cell-surface proteins, CD22, CD20, and CD19, as demonstrated by flow cytometry and immunofluorescence microscopy. We show that, compared to epratuzumab, a bispecific hexavalent antibody comprising epratuzumab and veltuzumab (humanized anti-CD20 mAb exhibits enhanced trogocytosis resulting in major reductions in B-cell surface levels of CD19, CD20, CD21, CD22, CD79b, CD44, CD62L and β7-integrin, and with considerably less immunocompromising B-cell depletion that would result with anti-CD20 mAbs such as veltuzumab or rituximab, given either alone or in combination with epratuzumab. A CD22/CD19 bispecific hexavalent antibody, which exhibited enhanced trogocytosis of some antigens and minimal B-cell depletion, may also be

  10. Characterization of regulatory T cells identified as CD4+CD25highCD39+ in patients with active tuberculosis

    Science.gov (United States)

    Chiacchio, T; Casetti, R; Butera, O; Vanini, V; Carrara, S; Girardi, E; Di Mitri, D; Battistini, L; Martini, F; Borsellino, G; Goletti, D

    2009-01-01

    Forkhead box P3 (FoxP3) is a transcription factor whose expression characterizes regulatory T cells (Treg), but it is also present on activated T cells, thus hindering correct Treg identification. Using classical markers for Treg recognition, discordant results were found in terms of Treg expansion during active tuberculosis (TB) disease. Recently CD39 has been shown to be an accurate marker for Treg detection. The objectives of this study were: (i) to identify Treg expressing CD39 in patients with TB and to compare the results with those obtained by the standard phenotypic markers; (ii) to evaluate if Treg are expanded in vitro by exogenous interleukin (IL)-2 or by antigen-specific stimulation; and (iii) to characterize Treg function on the modulation of antigen-specific responses. We enrolled 13 patients with pulmonary TB and 12 healthy controls. Treg were evaluated by flow cytometry ex vivo and after antigen-specific in vitro stimulation using CD25, FoxP3, CD127 and CD39 markers. Results indicate that CD39+ cells within the CD4+CD25high cells have Treg properties (absence of interferon-γ production and transforming growth factor-β1 release upon stimulation). Ex vivo analysis did not show significant differences between TB patients and controls of Treg by classical or novel markers. In contrast, a significantly higher percentage of Treg was found in TB patients after antigen-specific stimulation both in the presence or absence of IL-2. Depletion of CD39+ Treg increased RD1-specific responses significantly. In conclusion, CD39 is an appropriate marker for Treg identification in TB. These results can be useful for future studies to monitor Mycobacterium tuberculosis-specific response during TB. PMID:19438599

  11. Genome stability in Caenorhabditis elegans

    NARCIS (Netherlands)

    Haaften, G.W. van

    2006-01-01

    Genome stability is closely linked to cancer. Most, if not all tumor cells show some form of genome instability, mutations can range from single point mutations to gross chromosomal rearrangements and aneuploidy. Genome instability is believed to be the driving force behind tumorigenesis. In order t

  12. The UCSC genome browser database

    DEFF Research Database (Denmark)

    Kuhn, R M; Karolchik, D; Zweig, A S

    2007-01-01

    The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up t...

  13. The UCSC Genome Browser Database

    DEFF Research Database (Denmark)

    Hinrichs, A S; Karolchik, D; Baertsch, R

    2006-01-01

    The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, ...

  14. Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway.

    Directory of Open Access Journals (Sweden)

    Gang Li

    2013-05-01

    Full Text Available Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA, there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P = 1.4×10(-9. Second, we demonstrate that subjects homozygous for the RA risk allele have ∼33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P = 10(-9, a finding corroborated by expression quantitative trait loci (eQTL analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2 and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65, a subunit of the NF-κB transcription factor. Finally, we develop a high-throughput NF-κB luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L and conduct an HTS of 1,982 chemical compounds and FDA-approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-κB signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel

  15. Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway

    Science.gov (United States)

    Li, Gang; Diogo, Dorothée; Wu, Di; Spoonamore, Jim; Dancik, Vlado; Franke, Lude; Kurreeman, Fina; Rossin, Elizabeth J.; Duclos, Grant; Hartland, Cathy; Zhou, Xuezhong; Li, Kejie; Liu, Jun; De Jager, Philip L.; Siminovitch, Katherine A.; Zhernakova, Alexandra; Raychaudhuri, Soumya; Bowes, John; Eyre, Steve; Padyukov, Leonid; Gregersen, Peter K.; Worthington, Jane; Gupta, Namrata; Clemons, Paul A.; Stahl, Eli; Tolliday, Nicola; Plenge, Robert M.

    2013-01-01

    Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS) and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P = 1.4×10−9). Second, we demonstrate that subjects homozygous for the RA risk allele have ∼33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P = 10−9), a finding corroborated by expression quantitative trait loci (eQTL) analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2) and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65), a subunit of the NF-κB transcription factor. Finally, we develop a high-throughput NF-κB luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L) and conduct an HTS of 1,982 chemical compounds and FDA–approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-κB signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel therapies in

  16. Detection of CD4+/CD8+T Lymphocyte Ratio and CD4+CD25+ Treg in Peripheral Blood of Patients with Sporadic Vitiligo%散发型白癜风患者外周血CD4+/CD8+T细胞比值及CD4+CD25+T细胞的检测

    Institute of Scientific and Technical Information of China (English)

    叶蓉; 马刚; 胡小平; 彭曦

    2012-01-01

    目的 检测散发型白癜风患者外周血CD4+/CD8+T细胞比值及CD4+CD25+调节性T细胞水平,探讨其与散发型白癜风发病的关系.方法 散发型白癜风患者29例,男13例,女16例.通过流式细胞仪对散发型白癜风患者外周血CD4+/CD8+T细胞比值及CD4+CD25+调节性T细胞水平进行检测,并与20例健康人相比较.结果 与健康对照组相比,散发型白癜风患者外周血中CD4+/CD8+T细胞比值的差异无统计学意义(P>0.05),而CD4+CD25+调节性T细胞水平明显减少,差异有统计学意义(P<0.05),但在不同病程的患者中CD4+CD25+调节性T细胞数量的差异无统计学意义(P>0.05).结论 散发型白癜风患者外周血中存在CD4+CD25+调节性T细胞水平下降,可能与散发型白癜风的发生发展有一定关系.%Objective To detect the CD4+/CD8+ T lymphocyte ratio and the CD4+CD25+ Treg level in peripheral blood of patients with sporadic vitiligo, and to investigate its role in the pathogenesis of sporadic vitiligo. Methods Peripheral blood samples were taken from 29 outpatients with sporadic vitiligo, including 13 males and 16 females. The CD4+/CD8+ T lymphocyte ratio and the CD4+CD25+ Treg level was detected in peripheral blood of patients with sporadic vitiligo by flow cytometry, as well as controlled samples from 20 healthy human. Results There was no difference on the ratio of CD4+/CD8+ T lymphocyte between the patients with sporadic vitiligo and healthy people (P>0.05). Compared to the controlled group, the proportion of CD4+CD25+ Treg was significantly lower in sporadic vitiligo patients(P0.05). Conclusion The level of CD4+CD25+ Treg is lower in peripheral blood of sporadic vitiligo patients, which might play a role in the pathogenesis and development of sporadic vitiligo.

  17. Characterization of antibodies against ferret immunoglobulins, cytokines and CD markers

    DEFF Research Database (Denmark)

    Martel, Cyril Jean-Marie; Aasted, Bent

    2009-01-01

    immunoglobulins, we identified and characterized polyclonal antibodies towards ferret IgG, IgM and IgA. We also identified 22 monoclonal antibodies (mAbs) raised mostly against human CD markers which cross-reacted with ferret leukocytes. These antibodies were originally specific against human CD8, CD9, CD14, CD18...

  18. Physical properties of Bi doped CdTe thin films grown by CSVT and their influence on the CdS/CdTe solar cells PV-properties

    Energy Technology Data Exchange (ETDEWEB)

    Vigil-Galan, O. [Escuela Superior de Fisica y Matematicas-I.P.N., Edificio de Fisica Avanzada, av. IPN y Juan de Dios Batiz s/n U.P.A.L.M. 07738 Mexico D.F. (Mexico)]. E-mail: osvaldo@esfm.ipn.mx; Sanchez-Meza, E. [Escuela Superior de Fisica y Matematicas-I.P.N., Edificio de Fisica Avanzada, av. IPN y Juan de Dios Batiz s/n U.P.A.L.M. 07738 Mexico D.F. (Mexico); Ruiz, C.M. [Departamento de Fisica de Materiales, Universidad Autonoma de Madrid, Madrid 28049 (Spain); Sastre-Hernandez, J. [Escuela Superior de Fisica y Matematicas-I.P.N., Edificio de Fisica Avanzada, av. IPN y Juan de Dios Batiz s/n U.P.A.L.M. 07738 Mexico D.F. (Mexico); Morales-Acevedo, A. [Escuela Superior de Fisica y Matematicas-I.P.N., Edificio de Fisica Avanzada, av. IPN y Juan de Dios Batiz s/n U.P.A.L.M. 07738 Mexico D.F. (Mexico); CINVESTAV-IPN, Electrical Engineering Department, Av. IPN No2508, C. P. 07360, Mexico, D. F. (Mexico); Cruz-Gandarilla, F. [Escuela Superior de Fisica y Matematicas-I.P.N., Edificio de Fisica Avanzada, av. IPN y Juan de Dios Batiz s/n U.P.A.L.M. 07738 Mexico D.F. (Mexico); Aguilar-Hernandez, J. [Escuela Superior de Fisica y Matematicas-I.P.N., Edificio de Fisica Avanzada, av. IPN y Juan de Dios Batiz s/n U.P.A.L.M. 07738 Mexico D.F. (Mexico); Saucedo, E. [Departamento de Fisica de Materiales, Universidad Autonoma de Madrid, Madrid 28049 (Spain); Contreras-Puente, G. [Escuela Superior de Fisica y Matematicas-I.P.N., Edificio de Fisica Avanzada, av. IPN y Juan de Dios Batiz s/n U.P.A.L.M. 07738 Mexico D.F. (Mexico); Bermudez, V. [Departamento de Fisica de Materiales, Universidad Autonoma de Madrid, Madrid 28049 (Spain)

    2007-05-31

    The physical properties of Bi doped CdTe films, grown on glass substrates by the Closed Space Transport Vapour (CSVT) method, from different Bi doped CdTe powders are presented. The CdTe:Bi films were characterized using Photoluminescence, Hall effect, X-Ray diffraction, SEM and Photoconductivity measurements. Moreover, CdS/CdTe:Bi solar cells were made and their characteristics like short circuit current density (J {sub sc}), open circuit voltage (V {sub OC}), fill factor (FF) and efficiency ({eta}) were determined. These devices were fabricated from Bi doped CdTe layers deposited on CdS with the same growth conditions than those used for the single CdTe:Bi layers. A correlation between the CdS/CdTe:Bi solar cell characteristics and the physical properties of the Bi doped CdTe thin films are presented and discussed.

  19. Decreased Expression of T-Cell Costimulatory Molecule CD28 on CD4 and CD8 T Cells of Mexican Patients with Pulmonary Tuberculosis

    Directory of Open Access Journals (Sweden)

    German Bernal-Fernandez

    2010-01-01

    Full Text Available Patients with tuberculosis frequently develop anergy, a state of T-cell hyporesponsiveness in which defective T-cell costimulation could be a factor. To know if the expression of T-cell costimulatory molecules was altered in tuberculosis, we analyzed the peripheral blood T-cell phenotype of 23 Mexican patients with pulmonary tuberculosis. There was severe CD4 (P<.001 and CD8 (P<.01 lymphopenia and upregulation of costimulatory molecule CD30 on CD4 and CD8 T cells (P<.05; this increase was higher in relapsing tuberculosis. The main finding was severe downregulation of the major costimulatory molecule CD28 on both CD8 and CD4 T cells (P<.001. Depletion of the CD4/CD28 subset, a hitherto undescribed finding, is relevant because CD4 T cells constitute the main arm of the cell-mediated antimycobacterial immune response.

  20. Immunity to experimental Salmonella typhimurium infections in rats. Transfer of immunity with primed CD4+CD25high and CD4+CD25low T lymphocytes

    DEFF Research Database (Denmark)

    Thygesen, P; Brandt, L; Jørgensen, T

    1994-01-01

    The protective effect of primed CD4+ T lymphocytes against a lethal dose of 10(8) viable Salmonella typhimurium was studied in Lewis rats. Primed CD4+ T lymphocytes were obtained by inoculating Lewis rats with a non-lethal dose of 10(6) viable S. typhimurium. Four weeks after the infection, splee...

  1. Lenalidomide potentiates CD4(+)CD25(+)Treg-related suppression of lymphoma B-cell proliferation.

    Science.gov (United States)

    Grygorowicz, Monika Anna; Borycka, Ilona Sara; Nowak, Eliza; Paszkiewicz-Kozik, Ewa; Rymkiewicz, Grzegorz; Błachnio, Katarzyna; Biernacka, Marzena; Bujko, Mateusz; Walewski, Jan; Markowicz, Sergiusz

    2016-03-10

    We have previously found that ex vivo expanded human CD4(+)CD25(+)Treg cells suppress proliferation of lymphoma B-cell lines. Here we demonstrate that the immunomodulatory drug lenalidomide potentiates suppression of lymphoma B-cell proliferation by freshly isolated CD4(+)CD25(+)Tregs, as well as suppression by Tregs expanded polyclonally in the presence of rapamycin from CD4(+)CD25(+)T cells or CD4(+)CD25(+)CD127(lo)T cells. The regulation of lymphoma cell proliferation by Tregs pre-expanded with "third-party" allogeneic MoDCs in the presence of rapamycin was also potentiated by lenalidomide. Lenalidomide contributed to the suppression exerted by Tregs despite concomitant downregulation of Treg proliferation. Lenalidomide did not reduce the suppression of conventional T cells by expanded Tregs. The exposure of polyclonally expanded Tregs to lenalidomide did not significantly alter their phenotype. There was no uniform pattern of lenalidomide effect on Treg-mediated regulation of lymphoma B cells freshly isolated from patients. Freshly isolated lymphoma cells activated with multimeric CD40L and IL-4 to support their survival in vitro varied in their sensitivity to lenalidomide, and the regulatory effect of Tregs on such lymphoma cells ranged from suppression to help in individual patients. Lenalidomide potentiated or attenuated Treg effects on the survival of freshly isolated lymphoma cells. A combination of lenalidomide treatment with adoptive transfer of CD4(+)CD25(+)Tregs or CD4(+)CD25(+)CD127(lo)Tregs expanded ex vivo could be used to suppress proliferation of residual lymphoma in select patients with lymphoma responsive to the regulation by Tregs and sensitive to lenalidomide.

  2. Autophagy positively regulates the CD44(+) CD24(-/low) breast cancer stem-like phenotype.

    Science.gov (United States)

    Cufí, Sílvia; Vazquez-Martin, Alejandro; Oliveras-Ferraros, Cristina; Martin-Castillo, Begoña; Vellon, Luciano; Menendez, Javier A

    2011-11-15

    The molecular mechanisms used by breast cancer stem cells (BCSCs) to survive and/or maintain their undifferentiated CD44(+) CD24(-/low ) mesenchymal-like antigenic state remains largely unexplored. Autophagy, a key homeostatic process of cytoplasmic degradation and recycling evolved to respond to stress conditions, might be causally fundamental in the biology of BCSCs. Stable & specific knockdown of autophagy-regulatory genes by lentiviral-delivered small hairpin (sh) RNA drastically decreased the number of JIMT-1 epithelial BC cells bearing CD44(+) CD24(-/low) cell-surface antigens from ~75% in parental and control (-) shRNA-transduced cells to 26% and 7% in ATG8/LC3 shRNA- and ATG12 shRNA-transduced cells, respectively. Autophagy inhibition notably enhanced transcriptional activation of CD24 gene, potentiating the epithelial-like phenotype of CD44(+) CD24(+) cells versus the mesenchymal CD44(+) CD24(-/low ) progeny. EMT-focused Real Time RT-PCR profiling revealed that genetic ablation of autophagy transcriptionally repressed the gene coding for the mesenchymal filament vimentin (VIM). shRNA-driven silencing of the ATG12 gene and disabling the final step in the autophagy pathway by the antimalarial drug chloroquine both prevented TGFb1-induced accumulation of vimentin in JIMT-1 cells. Knockdown of autophagy-specific genes was sufficient also to increase by up to 11-times the number of CD24(+) cells in MDA-MB-231 cells, a BC model of mesenchymal origin that is virtually composed of CD44(+) CD24(-/low ) cells. Chloroquine treatment augmented the number of CD24(+) cells and concomitantly reduced constitutive overexpression of vimentin in MDA-MB-231 cells. This is the first report demonstrating that autophagy is mechanistically linked to the maintenance of tumor cells expressing high levels of CD44 and low levels of CD24, which are typical of BCSCs.

  3. Functional characterization of DNAM-1 (CD226) interaction with its ligands PVR (CD155) and nectin-2 (PRR-2/CD112).

    Science.gov (United States)

    Tahara-Hanaoka, Satoko; Shibuya, Kazuko; Onoda, Yuko; Zhang, Hua; Yamazaki, Satoshi; Miyamoto, Akitomo; Honda, Shin-Ichiro; Lanier, Lewis L; Shibuya, Akira

    2004-04-01

    CD226 (DNAM-1) is an adhesion molecule involved in NK and T cell-mediated cytotoxicity against certain tumors. Here, we have identified the human poliovirus receptor-related (PRR) family members CD155 [poliovirus receptor (PVR)] and CD112 (nectin-2/PRR-2) as the ligands for human CD226. Ectopic expression of human CD155 and/or CD112 rendered mouse BW5147 T cells more susceptible to IL-2-activated T and NK cell-mediated cytotoxicity, and killing was specifically inhibited by anti-CD226 mAb, demonstrating functional interactions of CD226 with CD155 and CD112. Although the binding affinities between soluble CD226 and CD155 or CD112 were comparable, the homophilic interaction of cell-surface CD112 may adversely affect CD226 binding to CD112. We also demonstrate that ligation of CD226 and LFA-1 with their respective ligands cooperates in triggering cytotoxicity and cytokine secretion by T and NK cells.

  4. Cancer Cell Targeting Using Folic Acid/Anti-HER2 Antibody Conjugated Fluorescent CdSe/CdS/ZnS-MPA and CdTe-MSA Quantum Dots.

    Science.gov (United States)

    Singh, Gurpal; Kumar, Manoj; Soni, Udit; Arora, Vikas; Bansal, Vivek; Gupta, Dikshi; Bhat, Madhusudan; Dinda, Amit K; Sapra, Sameer; Singh, Harpal

    2015-12-01

    CdSe/CdS/ZnS and CdTe quantum dots (QDs) were synthesized by successive ion layer adsorption and reaction (SILAR) technique and direct aqueous synthesis respectively using thiol stabilizers. Synthesized CdSe/CdS/ZnS and CdTe QDs stabilized with 3-mercaptopropionic acid (MPA) and mercaptosuccinic acid (MSA) were used as fluorescent labels after conjugation with folic acid (FA) and anti-HER2 antibodies. Photoluminescence quantum yield of folated CdSe/CdS/ZnS-MPA and CdTe-MSA QDs was 59% and 77% than that of non-folated hydrophilic QDs. The folate receptor-mediated delivery of folic acid-conjugated CdTe-MSA and CdSe/CdS/ZnS-MPA QDs showed higher cellular internalization as observed by confocal laser scanning microscopic studies. Folated and non-folated CdTe-MSA QDs were highly toxic and exhibited only 10% cell viability as compared to > 80% cell viability with CdSe/CdS/ZnS-MPA QDs over the concentration ranging from 3.38 to 50 pmoles. Immunohistochemistry (IHC) results of human breast cancer tissue samples showed positive results with anti-HER2 antibody conjugated CdSe/CdS/ZnS-MPA QDs with better sensitivity and specificity as compared to conventional IHC analysis using diaminobenzedene staining.

  5. CdTe,核-壳型CdTe/CdS及CdTe/ZnS量子点的合成及表征%CdTe, Core-shell CdTe/CdS and CdTe/ZnS Quantum Dots: Their Synthesis and Characterization*

    Institute of Scientific and Technical Information of China (English)

    张纪梅; 许世超; 宋秀云; 代昭; 孙波; 姚翠翠

    2009-01-01

    Semiconductor CdTe, core-shell CdTe/CdS and CdTe/ZnS nanocrystals(quantum dots; QDs) were prepared in aqueous phase. Investigations of the prepared nanocrystals were performed via scanning tunneling microscope(STM) and fluorescence spectrum(FS), and quantum yields(Qys) was calculated based on the resulting data from FS. Particle size of well dispersed CdTe was evaluated to be ca 3 nm via STM. Some reaction conditions were investigated and discussed to enhance Qys of CdTe/CdS core-shell QDs, such as dependence of Cd2+ concentration, and effect of Cd2+∶S2- etc. Among all of those methods, Qys of core-shell CdTe/CdS is generally degressive with refluxing time elapsing. The best Qys of ca 80.0% can be achieved when pH was set at 8.5, Cd2+∶S2-=10:1(mol ratio). Moreover, CdTe/ZnS core-shell QDs was prepared, and results indicated a red-shift from 551 nm to 635 nm comparing with CdTe core, which suggested the growth of QDs size, however, Qys of CdTe/ZnS decreased to 14.4%. QDs currently discussed in this research are easily synthesized, and they will be useful in applications of biolabeling, imaging, and biosensing based on fluorescence resonance energy transfer(FRET).%在水相中制备了半导体CdTe纳米晶,核-壳型CdTe/CdS和CdTe/ZnS纳米晶(即量子点;QDs).利用扫描隧道显微镜(STM)和荧光光谱(FS)对合成的纳米晶量子点进行了研究,并且根据FS的数据进行了量子效率的计算.STM的结果表明合成的量子点直径约为3 nm并且分布良好.为了提高量子效率,对Cd2+浓度和Cd2+∶S2-比例等反应条件进行了研究,结果表明随着回流时间的增加,核-壳型量子点CdTe/CdS的量子效率总体上呈下降趋势.CdTe/CdS在pH8.5,Cd2+∶S2-=10∶1(摩尔比)时可获得80.0%的最大量子效率.同时制备了核-壳型量子点CdTe/ZnS,其最大发射波长由551 nm(CdTe)红移到635 nm(CdTe/ZnS)表明量子点的尺寸在增长,但是量子效率下降到14.4%. 当前研究的量子点可适用于生

  6. Evolution of cd59 gene in mammals

    Institute of Scientific and Technical Information of China (English)

    GONG; YuanYing; PENG; MinSheng; ZHOU; WeiPing; ZHANG; YaPing

    2007-01-01

    The CD59-coding sequences were obtained from 5 mammals by PCR and BLAST, and combined with the available sequences in GenBank, the nucleotide substitution rates of mammalian cd59 were calculated. Results of synonymous and nonsynonymous substitution rates revealed that cd59 experienced negative selection in mammals overall. Four sites experiencing positive selection were found by using "site-specific" model in PAML software. These sites were distributed on the molecular surface, of which 2 sites located in the key functional domain. Furthermore, "branch-site-specific" model detected 1 positive site in cd59a and cd59b lineages which underwent accelerated evolution caused by positive selection after gene duplication in mouse.

  7. Creating Virtual CD-ROM Collections

    Directory of Open Access Journals (Sweden)

    Kam Woods

    2009-10-01

    Full Text Available Over the past 20 years, more than 100,000 CD-ROM titles have been published including thousands of collections of government documents and data. CD-ROMs present preservation challenges at the bit level and in ensuring usability of the preserved artifact. We present techniques we have developed to archive and support user access to a collection of approximately 2,900 CD-ROMs published under the Federal Depository Library Program (FDLP by the United States Government Printing Office (GPO. The project provides web-based access to CD-ROM contents using both migration and emulation and supports remote execution of the raw CD-ROM images. Our project incorporates off-the-shelf, primarily open-source software. The raw data and (METS metadata are made available through AFS, a standard distributed file system, to encourage sharing among libraries.

  8. High temperature continuous flow synthesis of CdSe/CdS/ZnS, CdS/ZnS, and CdSeS/ZnS nanocrystals

    Science.gov (United States)

    Naughton, Matt S.; Kumar, Vivek; Bonita, Yolanda; Deshpande, Kishori; Kenis, Paul J. A.

    2015-09-01

    Continuous flow reactors show great promise for large-scale synthesis of quantum dots. Here, we discuss results for the synthesis of multi-layered Cd-based hybrid nanocrystals - CdSe/CdS/ZnS, CdS/ZnS, and CdSeS/ZnS - in a continuous flow reactor. The simple reactor design and liquid-phase chemistry obviate the need for preheating or in-line mixing, and the chosen reactor dimensions and operating conditions allow for high flow rates (~10 mL min-1). Additionally, the simple reactor design is well suited for scale-up. The CdSe/CdS/ZnS particles synthesized at elevated temperatures in the reactor exhibit quantum yields of over 60% at longer wavelengths (red region). The shell growth for these particles is conducted without the need for complex dropwise addition or SILAR shell growth procedures used in batch reactors. CdS-based particles were shown to have a higher performance when using octadecene-S instead of TOP-S, which improved the quality of shell growth. In addition, stoichiometric synthesis of the alternate CdSeS/ZnS alloy particles was conducted, removing the need for a large excess of S to offset the lower S reactivity. CdSeS/ZnS alloy nanoparticles exhibit quantum yields of about 50% in the intermediate wavelength range (500-600 nm).Continuous flow reactors show great promise for large-scale synthesis of quantum dots. Here, we discuss results for the synthesis of multi-layered Cd-based hybrid nanocrystals - CdSe/CdS/ZnS, CdS/ZnS, and CdSeS/ZnS - in a continuous flow reactor. The simple reactor design and liquid-phase chemistry obviate the need for preheating or in-line mixing, and the chosen reactor dimensions and operating conditions allow for high flow rates (~10 mL min-1). Additionally, the simple reactor design is well suited for scale-up. The CdSe/CdS/ZnS particles synthesized at elevated temperatures in the reactor exhibit quantum yields of over 60% at longer wavelengths (red region). The shell growth for these particles is conducted without the need

  9. S and Te inter-diffusion in CdTe/CdS hetero junction

    Energy Technology Data Exchange (ETDEWEB)

    Enriquez, J. Pantoja [Cuerpo Academico-Energia y Sustentabilidad, Universidad Politecnica de Chiapas, Eduardo J. Selvas S/N, Col. Magisterial, Tuxtla Gutierrez 29010, Chiapas (Mexico); Gomez Barojas, E. [CIDS-ICUAP, Apdo. Postal 1651, 72000 Puebla (Mexico); Silva Gonzalez, R.; Pal, U. [Instituto de Fisica, Benemerita Universidad Autonoma de Puebla, Puebla (Mexico)

    2007-09-22

    Effects of post formation thermal annealing of the CdTe-CdS device on the inter-diffusion of S and Te at the junction in a substrate configuration device have been studied by Auger electron spectroscopy. While the migration of S and Te atoms increases with annealing temperature, the extent of S diffusion is always higher than the diffusion of Te atoms. Inter-diffusion of S and Te causes the formation of CdTe{sub 1-x}S{sub x} ternary compound at the CdTe-CdS interface. (author)

  10. Expansion of CD8+CD57+ T Cells in an Immunocompetent Patient with Acute Toxoplasmosis

    Science.gov (United States)

    García-Muñoz, R.; Rodríguez-Otero, P.; Galar, A.; Merino, J.; Beunza, J. J.; Páramo, J. A.; Lecumberri, R.

    2009-01-01

    CD57+ T cells increase in several viral infections like cytomegalovirus, herpesvirus, parvovirus, HIV and hepatitis C virus and are associated with several clinical conditions related to immune dysfunction and ageing. We report for the first time an expansion of CD8+ CD57+ T cells in a young patient with an acute infection with Toxoplasma gondii. Our report supports the concept that CD8+ CD57+ T cells could be important in the control of chronic phase of intracellular microorganisms and that the high numbers of these cells may reflect the continuing survey of the immune system, searching for parasite proliferation in the tissues. PMID:19946421

  11. Expansion of CD8+CD57+ T Cells in an Immunocompetent Patient with Acute Toxoplasmosis

    Directory of Open Access Journals (Sweden)

    R. García-Muñoz

    2009-01-01

    Full Text Available CD57+ T cells increase in several viral infections like cytomegalovirus, herpesvirus, parvovirus, HIV and hepatitis C virus and are associated with several clinical conditions related to immune dysfunction and ageing. We report for the first time an expansion of CD8+CD57+ T cells in a young patient with an acute infection with Toxoplasma gondii. Our report supports the concept that CD8+CD57+ T cells could be important in the control of chronic phase of intracellular microorganisms and that the high numbers of these cells may reflect the continuing survey of the immune system, searching for parasite proliferation in the tissues.

  12. Analysis of the CD161-expressing cell quantities and CD161 expression levels in peripheral blood natural killer and T cells of systemic lupus erythematosus patients.

    Science.gov (United States)

    Lin, Yi-Lung; Lin, Shih-Chang

    2017-02-01

    Expressed on the cell surface of most of NK cells and some T cells, CD161 has been shown to deliver inhibitory signal in human NK cells. To determine whether the CD161-expressing cell quantities and the cell surface expression levels of CD161 in NK and T cells were altered in systemic lupus erythematosus (SLE) patients, we analyzed the CD3, CD56 and CD161 expression patterns of peripheral blood lymphocytes by flow cytometric analysis to identify different NK and T cell subpopulations. The cell surface expression levels of CD161 were estimated by the mean florescence intensities (MFIs) of CD161. It was found that SLE patients had lower frequencies of CD161+CD56+CD3- and CD161+CD56+CD3+ cells among the lymphocyte population than normal controls, whereas the frequencies of CD161-CD56+CD3- and CD161+CD56-CD3+ cells were not statistically different between two groups. In addition, SLE patients also had decreased absolute counts of all CD161-expressing NK cells and T cells and had reduced frequencies of CD161+ cells in CD56+CD3-, CD56+CD3+ and CD56-CD3+ cell populations. Moreover, SLE patients had reduced MFIs of CD161 in CD161+CD56+CD3+ and CD161+CD56-CD3+, but not CD161+CD56+CD3-, cell populations. Our results indicated that CD161-expressing cell frequency and the CD161 expression levels were reduced in some NK and T cell subpopulations of SLE patients, suggesting possible important role of CD161 and CD161-expressing immune cells in the SLE pathogenesis.

  13. Nitric oxide inhibits the accumulation of CD4+CD44hiTbet+CD69lo T cells in mycobacterial infection

    Science.gov (United States)

    Pearl, John E.; Torrado, Egidio; Tighe, Michael; Fountain, Jeffrey J.; Solache, Alejandra; Strutt, Tara; Swain, Susan; Appelberg, Rui; Cooper, Andrea M

    2013-01-01

    Summary Animals lacking the inducible nitric oxide synthase gene (nos2−/−) are less susceptible to M. avium strain 25291 and lack nitric oxide-mediated immunomodulation of CD4+ T cells. Here we show that the absence of nos2 results in increased accumulation of neutrophils and both CD4+ and CD8+ T cells within the M. avium-containing granuloma. Examination of the T-cell phenotype in M. avium-infected mice demonstrated that CD4+CD44hi effector T cells expressing the Th1 transcriptional regulator T-bet (T-bet+) were specifically reduced by the presence of nitric oxide. Importantly, the T-bet+ effector population could be separated into CD69hi and CD69lo populations, with the CD69lo population only able to accumulate during chronic infection within infected nos2−/− mice. Transcriptomic comparison between CD4+CD44hiCD69hi and CD4+CD44hiCD69lo populations revealed that CD4+CD44hiCD69lo cells had higher expression of the integrin itgb1/itga4 (VLA-4, CD49d/CD29). Inhibition of Nos2 activity allowed increased accumulation of the CD4+CD44hiT-bet+CD69lo population in WT mice as well as increased expression of VLA-4. These data support the hypothesis that effector T cells in mycobacterial granulomata are not a uniform effector population but exist in distinct subsets with differential susceptibility to the regulatory effects of nitric oxide. PMID:22890814

  14. Implementing genomics and pharmacogenomics in the clinic: The National Human Genome Research Institute's genomic medicine portfolio.

    Science.gov (United States)

    Manolio, Teri A

    2016-10-01

    Increasing knowledge about the influence of genetic variation on human health and growing availability of reliable, cost-effective genetic testing have spurred the implementation of genomic medicine in the clinic. As defined by the National Human Genome Research Institute (NHGRI), genomic medicine uses an individual's genetic information in his or her clinical care, and has begun to be applied effectively in areas such as cancer genomics, pharmacogenomics, and rare and undiagnosed diseases. In 2011 NHGRI published its strategic vision for the future of genomic research, including an ambitious research agenda to facilitate and promote the implementation of genomic medicine. To realize this agenda, NHGRI is consulting and facilitating collaborations with the external research community through a series of "Genomic Medicine Meetings," under the guidance and leadership of the National Advisory Council on Human Genome Research. These meetings have identified and begun to address significant obstacles to implementation, such as lack of evidence of efficacy, limited availability of genomics expertise and testing, lack of standards, and difficulties in integrating genomic results into electronic medical records. The six research and dissemination initiatives comprising NHGRI's genomic research portfolio are designed to speed the evaluation and incorporation, where appropriate, of genomic technologies and findings into routine clinical care. Actual adoption of successful approaches in clinical care will depend upon the willingness, interest, and energy of professional societies, practitioners, patients, and payers to promote their responsible use and share their experiences in doing so.

  15. The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

    Science.gov (United States)

    Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

    2013-02-01

    Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

  16. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAOGuo-ping

    2004-01-01

    Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  17. Microbial Genomics Research in China

    Institute of Scientific and Technical Information of China (English)

    ZHAO Guo-ping

    2004-01-01

    @@ Microorganisms, including phage/virus, were initial targets and tools for developing DNA sequencing technology. Microbial genomic study was started as a model system for the Human Genome Project (HGP) and it did successfully supported the HGP, particularly with respect to BAC contig construction and large-scale shotgun sequencing and assembly. Microbial genomics study has become the fastest developed genomics discipline along with HGP, taking the advantage of the organisms' highly diversified physiology, extremely long history of evolution, close relationship with human/environment,as well as relatively small genome sizes and simple systems for functional analysis.

  18. Nongenetic functions of the genome.

    Science.gov (United States)

    Bustin, Michael; Misteli, Tom

    2016-05-01

    The primary function of the genome is to store, propagate, and express the genetic information that gives rise to a cell's architectural and functional machinery. However, the genome is also a major structural component of the cell. Besides its genetic roles, the genome affects cellular functions by nongenetic means through its physical and structural properties, particularly by exerting mechanical forces and by serving as a scaffold for binding of cellular components. Major cellular processes affected by nongenetic functions of the genome include establishment of nuclear structure, signal transduction, mechanoresponses, cell migration, and vision in nocturnal animals. We discuss the concept, mechanisms, and implications of nongenetic functions of the genome.

  19. Genomics and the immune system.

    Science.gov (United States)

    Pipkin, Matthew E; Monticelli, Silvia

    2008-05-01

    While the hereditary information encoded in the Watson-Crick base pairing of genomes is largely static within a given individual, access to this information is controlled by dynamic mechanisms. The human genome is pervasively transcribed, but the roles played by the majority of the non-protein-coding genome sequences are still largely unknown. In this review we focus on insights to gene transcriptional regulation by placing special emphasis on genome-wide approaches, and on how non-coding RNAs, which derive from global transcription of the genome, in turn control gene expression. We review recent progress in the field with highlights on the immune system.

  20. Genomic Analysis and Surveillance of the Coronavirus Dominant in Ducks in China.

    Directory of Open Access Journals (Sweden)

    Qing-Ye Zhuang

    Full Text Available The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV, and performed a large-scale surveillance of coronaviruses in chickens and ducks using a conserved RT-PCR assay. The viral genome harbors a tandem repeat which is rare in vertebrate RNA viruses. The repeat is homologous to some proteins of various cellular organisms, but its origin remains unknown. Many substitutions, insertions, deletions, and some frameshifts and recombination events have occurred in the genome of the DdCoV, as compared with the coronavirus dominant in chickens (CdCoV. The distances between DdCoV and CdCoV are large enough to separate them into different species within the genus Gammacoronavirus. Our surveillance demonstrated that DdCoVs and CdCoVs belong to different lineages and occupy different ecological niches, further supporting that they should be classified into different species. Our surveillance also demonstrated that DdCoVs and CdCoVs are prevalent in live poultry markets in some regions of China. In conclusion, this study shed novel insight into the genetic diversity, evolution, distribution, and taxonomy of the coronaviruses circulating in chickens and ducks.

  1. Interethnic diversity of the CD209 (rs4804803 gene promoter polymorphism in African but not American sickle cell disease

    Directory of Open Access Journals (Sweden)

    Jenelle A. Noble

    2015-02-01

    Full Text Available Elucidating the genomic diversity of CD209 gene promoter polymorphism could assist in clarifying disease pathophysiology as well as contribution to co-morbidities. CD209 gene promoter polymorphism has been shown to be associated with susceptibility to infection. We hypothesize that CD209 mutant variants occur at a higher frequency among Africans and in sickle cell disease. We analyzed the frequency of the CD209 gene (rs4804803 in healthy control and sickle cell disease (SCD populations and determined association with disease. Genomic DNA was extracted from blood samples collected from 145 SCD and 231 control Africans (from Mali, 331 SCD and 379 control African Americans and 159 Caucasians. Comparative analysis among and between groups was carried out by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP. Per ethnic diversification, we found significant disparity in genotypic (23.4% versus 16.9% versus 3.2% and allelic frequencies (48.7% versus 42.1% versus 19.8% of the homozygote mutant variant of the CD209 (snp 309A/G gene promoter between Africans, African Americans and Caucasians respectively. Comparative evaluation between disease and control groups reveal a significant difference in genotypic (10.4% versus 23.4%; p = 0.002 and allelic frequencies (39.7% versus 48.7%; p = 0.02 of the homozygote mutant variant in African SCD and healthy controls respectively, an observation that is completely absent among Americans. Comparing disease groups, we found no difference in the genotypic (p = 0.19 or allelic (p = 0.72 frequencies of CD209 homozygote mutant variant between Africans and Americans with sickle cell disease. The higher frequency of CD209 homozygote mutant variants in the African control group reveals a potential impairment of the capacity to mount an immune response to infectious diseases, and possibly delineate susceptibility to or severity of infectious co-morbidities within and between groups.

  2. CD4+ and CD8+ T cells have opposing roles in breast cancer progression and outcome

    Science.gov (United States)

    Zhang, Qunyuan; Ye, Jian; Wang, Fang; Zhang, Yanping; Hunborg, Pamela; Varvares, Mark A.; Hoft, Daniel F.; Hsueh, Eddy C.; Peng, Guangyong

    2015-01-01

    The Cancer Immunoediting concept has provided critical insights suggesting dual functions of immune system during the cancer initiation and development. However, the dynamics and roles of CD4+ and CD8+ T cells in the pathogenesis of breast cancer remain unclear. Here we utilized two murine breast cancer models (4T1 and E0771) and demonstrated that both CD4+ and CD8+ T cells were increased and involved in immune responses, but with distinct dynamic trends in breast cancer development. In addition to cell number increases, CD4+ T cells changed their dominant subsets from Th1 in the early stages to Treg and Th17 cells in the late stages of the cancer progression. We also analyzed CD4+ and CD8+ T cell infiltration in primary breast cancer tissues from cancer patients. We observed that CD8+ T cells are the key effector cell population mediating effective anti-tumor immunity resulting in better clinical outcomes. In contrast, intra-tumoral CD4+ T cells have negative prognostic effects on breast cancer patient outcomes. These studies indicate that CD4+ and CD8+ T cells have opposing roles in breast cancer progression and outcomes, which provides new insights relevant for the development of effective cancer immunotherapeutic approaches. PMID:25968569

  3. CD4 and CD8 lymphocytes in diagnosis and disease progression of pediatric HIV infection.

    Science.gov (United States)

    Aldhous, M C; Raab, G M; Mok, J Y; Doherty, K V; Bird, A G; Froebel, K S

    1996-02-01

    Vertical infection with human immunodeficiency virus-1 (HIV-1) causes profound changes in the proportions of subpopulations of lymphocytes in the peripheral circulation. In this study the percentages in whole blood of CD4 and CD8 cells, and of immunologically important subpopulations, were measured in 19 HIV-infected children over periods of up to 4 years and compared to our recently published ranges for normal children of various ages. The rate of CD4 decline and of CD8 increase differed between clinically fast and slow progressors. On CD8 cells, cytotoxic, memory (CD11abright and CD45R0), and activation (HLA-DR) markers were raised soon after birth to levels outside the normal range, and compared favorably with HIV culture as a method for early diagnosis of HIV infection. Mean levels of naive (CD45RA) and memory (CD45R0, CD29) markers on CD4 cells became significantly altered after 48 months of age, suggesting that these are markers of more advanced disease. Despite different ages of enrollment into the study, in the cohort as a whole, the levels of the lymphocyte subpopulations studied changed consistently. Thus, their measurement could be useful both in the diagnosis and prognosis of HIV infection in individual children. This is the first report showing that lymphocyte subpopulation analysis can play a major role in the diagnosis of pediatric HIV infection.

  4. Device Fabrication using Crystalline CdTe and CdTe Ternary Alloys Grown by MBE

    Energy Technology Data Exchange (ETDEWEB)

    Zaunbrecher, Katherine; Burst, James; Seyedmohammadi, Shahram; Malik, Roger; Li, Jian V.; Gessert, Timothy A.; Barnes, Teresa

    2015-06-14

    We fabricated epitaxial CdTe:In/CdTe:As homojunction and CdZnTe/CdTe and CdMgTe/CdTe heterojunction devices grown on bulk CdTe substrates in order to study the fundamental device physics of CdTe solar cells. Selection of emitter-layer alloys was based on passivation studies using double heterostructures as well as band alignment. Initial results show significant device integration challenges, including low dopant activation, high resistivity substrates and the development of low-resistance contacts. To date, the highest open-circuit voltage is 715 mV in a CdZnTe/CdTe heterojunction following anneal, while the highest fill factor of 52% was attained in an annealed CdTe homojunction. In general, all currentvoltage measurements show high series resistance, capacitancevoltages measurements show variable doping, and quantum efficiency measurements show low collection. Ongoing work includes overcoming the high resistance in these devices and addressing other possible device limitations such as non-optimum junction depth, interface recombination, and reduced bulk lifetime due to structural defects.

  5. CD99 and CD106 (VCAM—1) in human testis

    Institute of Scientific and Technical Information of China (English)

    VeraE; LaatoM

    2002-01-01

    Aim:The expression of the cytokines Il-2,IL-6,IL-10,IFN-γ and TNF-α and the adhesion proteins CD99 and CD106 was studied in the human testis at the protein level.Methods:The expression of the cytokines and the adhesion proteins was assessed using immunohistochemistry and immunoblotting.Results:None of the cytokines studied was present in the human testis,but CD99 and CD106(VCAM-1) strongly were expressed in all the testes investigated.CD99 was present in the interstitial tissue of the human testis as well as in the Sertoli cells.The identity of the CD99+ interstitial cells is unclear.CD106(VCAM-1) was present in Leydig cells as well as the basal parts of the Sertoli cells in the seminiferous tubules.In immunoblotting,CD99 was demonstrated at molecular ratios of 46-57(kD).This is a novel isoform of the molecule.Conclusion:The human testis produces both CD99 and CD106 and as CD106 mediates cell binding to lymphocytes,it is possible that the human Leydig cells adhere to lymphocytes like the rodent Leydig cells.

  6. Enhancement of binding activity of soluble human CD40 to CD40 ligand through incorporation of an isoleucine zipper motif

    Institute of Scientific and Technical Information of China (English)

    Xian-hui HE; Li-hui XU; Yi LIU

    2006-01-01

    Aim:To investigate the effect of incorporation of all isoleucine zipper(IZ)motif into CD40 on binding activity of CD40 for the CD40 ligand (CD40L).Methods:Prokaryotic expression vectors for 2 soluble CD40 derivatives,shCD40His and shCD40IZ containing an IZ dowain,were constructed and expressed in Escherichia coli.The recombinant proteins were purified to homogeneity after refolding from inclusion bodies.Their molecular weights in solution of shCD40His and shCD40IZ were compared by size-exclusion chromatography,and their binding activity for CD40L on Jurkat T cells was determined by flow cytometry.Results:shCD40His and shCD40IZ were generated.Both of them possessed significant binding activity for the cognate ligand CD40L expressed on the cell surface.shCD40IZ had much higher binding activity to its ligand(CD40L)than did shCD40His.Furthermore,size-exclusion chromatography demonstrated that shCD40IZ existed in high molecular mass forms that were most likely to be trimers in solution.Conclusion:Incorporation of an IZ motif into CD40 enhances its binding activity for CD40L through trimerization of the CD40 derivative.

  7. A comparison of statistical methods for genomic selection in a mice population

    Directory of Open Access Journals (Sweden)

    Neves Haroldo HR

    2012-11-01

    Full Text Available Abstract Background The availability of high-density panels of SNP markers has opened new perspectives for marker-assisted selection strategies, such that genotypes for these markers are used to predict the genetic merit of selection candidates. Because the number of markers is often much larger than the number of phenotypes, marker effect estimation is not a trivial task. The objective of this research was to compare the predictive performance of ten different statistical methods employed in genomic selection, by analyzing data from a heterogeneous stock mice population. Results For the five traits analyzed (W6W: weight at six weeks, WGS: growth slope, BL: body length, %CD8+: percentage of CD8+ cells, CD4+/ CD8+: ratio between CD4+ and CD8+ cells, within-family predictions were more accurate than across-family predictions, although this superiority in accuracy varied markedly across traits. For within-family prediction, two kernel methods, Reproducing Kernel Hilbert Spaces Regression (RKHS and Support Vector Regression (SVR, were the most accurate for W6W, while a polygenic model also had comparable performance. A form of ridge regression assuming that all markers contribute to the additive variance (RR_GBLUP figured among the most accurate for WGS and BL, while two variable selection methods ( LASSO and Random Forest, RF had the greatest predictive abilities for %CD8+ and CD4+/ CD8+. RF, RKHS, SVR and RR_GBLUP outperformed the remainder methods in terms of bias and inflation of predictions. Conclusions Methods with large conceptual differences reached very similar predictive abilities and a clear re-ranking of methods was observed in function of the trait analyzed. Variable selection methods were more accurate than the remainder in the case of %CD8+ and CD4+/CD8+ and these traits are likely to be influenced by a smaller number of QTL than the remainder. Judged by their overall performance across traits and computational requirements, RR

  8. Investigation of electroluminescence properties of CdTe@CdS core-shell nanocrystals (NCs)

    Indian Academy of Sciences (India)

    M Molaei; S Pourjafari

    2014-02-01

    In this work, CdTe@CdS NCs were synthesized using a thermochemical approach and synthesized NCs were used as an emissive layer, a light emitting device, with ITO/MoO3/PVK/CdTe@CdS(core-shell)/Mg:Ag structure. Structural and optical properties of synthesized NCs were investigated by means of XRD, UV–Vis and photoluminescence (PL) analyses. Fabricated device was characterized by electroluminescence spectra. XRD analysis demonstrated cubic phase NCs. Photoluminescence spectra showed a narrow band emission with a peak centred at about 600 nm. Fabricated device showed an emission at 600 nm, which is related to CdTe@CdS NCs. Turn on voltage of fabricated device is about 8 V and brightness is 53.7 Cd/m2 at a working voltage of about 14.57 V.

  9. Thin film CdS/CdTe solar cells: Research perspectives

    Energy Technology Data Exchange (ETDEWEB)

    Morales-Acevedo, Arturo [CINVESTAV del IPN, Department of Electrical Engineering, Avenida IPN No. 2508, 07360 Mexico DF (Mexico)

    2006-06-15

    Polycrystalline thin film CdTe continues to be a leading material for the development of cost effective and reliable photovoltaics. The two key properties of this material are its band gap (1.5eV), close to the ideal for photovoltaic conversion efficiency (1.45eV), and its high optical absorption coefficient. Thin film CdTe solar cells are typically hetero-junctions with CdS being the n-type partner, or window layer. Efficiencies as high as 16.5% have been achieved, but still there is some potential for increasing them. We make an analysis of the typical CdS/CdTe superstrate solar cell, and from it we establish critical issues and different lines of research in order to improve the current efficiencies. We also show that present record efficiencies are very close to the practical efficiency limit for a CdS/CdTe hetero-junction cell. (author)

  10. CdS: Characterization and recent advances in CdTe solar cell performance

    Energy Technology Data Exchange (ETDEWEB)

    Ferekides, C.; Marinskiy, D.; Morel, D.L. [Univ. of South Florida, FL (United States)

    1997-12-31

    Cadmium sulfide (CdS) films deposited by chemical bath deposition (CBD) have been used for the fabrication of high efficiency CdTe and CuIn{sub 1{minus}x}Ga{sub x}Se{sub 2} thin film solar cells. An attractive alternative deposition technology with manufacturing advantages over the CBD is the close spaced sublimation (CSS). In this work CdTe/CdS solar cells prepared entirely by the CSS process exhibited 15.0% efficiencies under global AM1.5 conditions as verified at the National Renewable Energy Laboratory. This paper reports on studies carried out on as deposited and heat treated CSS CdS films and all CSS CdTe/CdS solar cells using photoluminescence, x-ray diffraction, and I-V-T measurements.

  11. Informational laws of genome structures

    Science.gov (United States)

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-06-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  12. Evolution of small prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    David José Martínez-Cano

    2015-01-01

    Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

  13. Human CD4+ T cell epitopes from vaccinia virus induced by vaccination or infection.

    Directory of Open Access Journals (Sweden)

    J Mauricio Calvo-Calle

    2007-10-01

    Full Text Available Despite the importance of vaccinia virus in basic and applied immunology, our knowledge of the human immune response directed against this virus is very limited. CD4(+ T cell responses are an important component of immunity induced by current vaccinia-based vaccines, and likely will be required for new subunit vaccine approaches, but to date vaccinia-specific CD4(+ T cell responses have been poorly characterized, and CD4(+ T cell epitopes have been reported only recently. Classical approaches used to identify T cell epitopes are not practical for large genomes like vaccinia. We developed and validated a highly efficient computational approach that combines prediction of class II MHC-peptide binding activity with prediction of antigen processing and presentation. Using this approach and screening only 36 peptides, we identified 25 epitopes recognized by T cells from vaccinia-immune individuals. Although the predictions were made for HLA-DR1, eight of the peptides were recognized by donors of multiple haplotypes. T cell responses were observed in samples of peripheral blood obtained many years after primary vaccination, and were amplified after booster immunization. Peptides recognized by multiple donors are highly conserved across the poxvirus family, including variola, the causative agent of smallpox, and may be useful in development of a new generation of smallpox vaccines and in the analysis of the immune response elicited to vaccinia virus. Moreover, the epitope identification approach developed here should find application to other large-genome pathogens.

  14. Toward genome-enabled mycology.

    Science.gov (United States)

    Hibbett, David S; Stajich, Jason E; Spatafora, Joseph W

    2013-01-01

    Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genome-enabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

  15. Unique Challenges Accompany Thick-Shell CdSe/nCdS (n > 10) Nanocrystal Synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Y; Marchuk, K; Abraham, R; Sampat, S; Abraham, R.; Fang, N; Malko, AV; Vela, J

    2011-12-23

    Thick-shell CdSe/nCdS (n {ge} 10) nanocrystals were recently reported that show remarkably suppressed fluorescence intermittency or 'blinking' at the single-particle level as well as slow rates of Auger decay. Unfortunately, whereas CdSe/nCdS nanocrystal synthesis is well-developed up to n {le} 6 CdS monolayers (MLs), reproducible syntheses for n {ge} 10 MLs are less understood. Known procedures sometimes result in homogeneous CdS nucleation instead of heterogeneous, epitaxial CdS nucleation on CdSe, leading to broad and multimodal particle size distributions. Critically, obtained core/shell sizes are often below those desired. This article describes synthetic conditions specific to thick-shell growth (n {ge} 10 and n {ge} 20 MLs) on both small (sub2 nm) and large (>4.5 nm) CdSe cores. We find added secondary amine and low concentration of CdSe cores and molecular precursors give desired core/shell sizes. Amine-induced, partial etching of CdSe cores results in apparent shell-thicknesses slightly beyond those desired, especially for very-thick shells (n {ge} 20 MLs). Thermal ripening and fast precursor injection lead to undesired homogeneous CdS nucleation and incomplete shell growth. Core/shells derived from small CdSe (1.9 nm) have longer PL lifetimes and more pronounced blinking at single-particle level compared with those derived from large CdSe (4.7 nm). We expect our new synthetic approach will lead to a larger throughput of these materials, increasing their availability for fundamental studies and applications.

  16. Radiation increases the cellular uptake of exosomes through CD29/CD81 complex formation

    Energy Technology Data Exchange (ETDEWEB)

    Hazawa, Masaharu; Tomiyama, Kenichi; Saotome-Nakamura, Ai; Obara, Chizuka; Yasuda, Takeshi; Gotoh, Takaya; Tanaka, Izumi; Yakumaru, Haruko; Ishihara, Hiroshi; Tajima, Katsushi, E-mail: tajima@nirs.go.jp

    2014-04-18

    Highlights: • Radiation increases cellular uptake of exosomes. • Radiation induces colocalization of CD29 and CD81. • Exosomes selectively bind the CD29/CD81 complex. • Radiation increases the cellular uptake of exosomes through CD29/CD81 complex formation. - Abstract: Exosomes mediate intercellular communication, and mesenchymal stem cells (MSC) or their secreted exosomes affect a number of pathophysiologic states. Clinical applications of MSC and exosomes are increasingly anticipated. Radiation therapy is the main therapeutic tool for a number of various conditions. The cellular uptake mechanisms of exosomes and the effects of radiation on exosome–cell interactions are crucial, but they are not well understood. Here we examined the basic mechanisms and effects of radiation on exosome uptake processes in MSC. Radiation increased the cellular uptake of exosomes. Radiation markedly enhanced the initial cellular attachment to exosomes and induced the colocalization of integrin CD29 and tetraspanin CD81 on the cell surface without affecting their expression levels. Exosomes dominantly bound to the CD29/CD81 complex. Knockdown of CD29 completely inhibited the radiation-induced uptake, and additional or single knockdown of CD81 inhibited basal uptake as well as the increase in radiation-induced uptake. We also examined possible exosome uptake processes affected by radiation. Radiation-induced changes did not involve dynamin2, reactive oxygen species, or their evoked p38 mitogen-activated protein kinase-dependent endocytic or pinocytic pathways. Radiation increased the cellular uptake of exosomes through CD29/CD81 complex formation. These findings provide essential basic insights for potential therapeutic applications of exosomes or MSC in combination with radiation.

  17. Dislocation reduction in HgCdTe grown on CdTe/Si

    Science.gov (United States)

    Wijewarnasuriya, Priyalal S.

    2016-05-01

    Bulk-grown CdZnTe (Zn = 3%) substrates are the natural choice for HgCdTe epitaxy since it is lattice matched to long wave LW-HgCdTe alloy. However, lack of large area CdZnTe substrates, high production costs, and more importantly, the difference in thermal expansion coefficients between CdZnTe and silicon Read out Integrated Circuits (ROIC) are some of the inherent drawbacks of CdZnTe substrates. Consequently, Hg1-xCdxTe detectors fabricated on silicon substrates are an attractive alternative. Recent developments in the molecular beam epitaxy (MBE) buffer layer growth technology on Si substrates has revolutionized the HgCdTe research and offered a new dimension to HgCdTe-based IR technology. Si substrates provide advantages in terms of relatively large area (3 to 6-inch diameter is easily obtained) compared to CZT substrate materials, durability during processing, and reliability to thermal cycling. Innovations in Si-based composite substrates made it possible to fabricate very large-format IR arrays that offer higher resolution, low-cost arrays and more dies per wafer. Between Si substrates and HgCdTe has large lattice mismatch of 19%. This leads to dislocation densities of low-107 cm-2 for optimal growth of HgCdTe on silicon-based substrates as compared to the mid-104 cm-2 dislocation density of HgCdTe grown on CdZnTe. This paper present dislocation reduction by two orders of magnitude using thermal cycle anneal under Hg environment on HgCdTe grown on Si substrates and as well as defect reduction in Cd(Se)Te buffer layers grown on Si Substrates.

  18. Precision genome editing

    DEFF Research Database (Denmark)

    Steentoft, Catharina; Bennett, Eric P;