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Sample records for glandular trichome transcriptome

  1. Plant Glandular Trichomes

    Indian Academy of Sciences (India)

    landing on the plant. Glandular trichomes in catmint (Nepeta sp.) produce nepetalactone, closely related to the aphid sex pheromone, nepetalactol. Nepetalactone can be reduced to the corresponding nepetalactol. ... Plant glandular trichomes function either as repositories or releasing sites of various chemicals. Interest in ...

  2. Comparative glandular trichome transcriptome-based gene characterization reveals reasons for differential (-)-menthol biosynthesis in Mentha species.

    Science.gov (United States)

    Akhtar, Md Qussen; Qamar, Nida; Yadav, Pallavi; Kulkarni, Pallavi; Kumar, Ajay; Shasany, Ajit Kumar

    2017-06-01

    The genes involved in menthol biosynthesis are reported earlier in Mentha × piperita. But the information on these genes is not available in Mentha arvensis. To bridge the gap in knowledge on differential biosynthesis of monoterpenes leading to compositional variation in the essential oil of these species, a comparative transcriptome analysis of the glandular trichome (GT) was carried out. In addition to the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathway genes, about 210 and 196 different terpene synthases (TPSs) transcripts were identified from annotation in M. arvensis and M. × piperita, respectively, and correlated to several monoterpenes present in the essential oil. Six isoforms of (-)-menthol dehydrogenases (MD), the last enzyme of the menthol biosynthetic pathway, were identified, cloned and characterized from the transcriptome data (three from each species). Varied expression levels and differential enzyme kinetics of these isoforms indicated the nature and composition of the product, as these isoforms generate both (-)-menthol and (+)-neomenthol from (-)-menthone and converts (-)-menthol to (-)-menthone in the reverse reaction, and hence together determine the quantity of (-)-menthol in the essential oil in these two species. Several genes for high value minor monoterpenes could also be identified from the transcriptome data. © 2017 Scandinavian Plant Physiology Society.

  3. Structure and histochemistry of the glandular trichomes on the ...

    African Journals Online (AJOL)

    The glandular trichomes were classified into two subpopulations, namely the peltate and capitate glandular trichomes. The former was characterized by a short stalk and a large four-celled secretory head, while the latter was further subdivided into two groups; one has a short unicellular stalk and two-cellular head (type I), ...

  4. Glandular Trichomes and Essential Oil of Thymus quinquecostatus

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    Ping Jia

    2013-01-01

    Full Text Available The distribution and types of glandular trichomes and essential oil chemistry of Thymus quinquecostatus were studied. The glandular trichomes are distributed on the surface of stem, leaf, rachis, calyx and corolla, except petiole, pistil and stamen. Three morphologically distinct types of glandular trichomes are described. Peltate trichomes, consisting of a basal cell, a stalk cell and a 12-celled head, are distributed on the stem, leaf, corolla and outer side of calyx. Capitate trichomes, consisting of a unicellular base, a 1–2-celled stalk and a unicellular head, are distributed more diffusely than peltate ones, existing on stem, leaf, rachis and calyx. Digitiform trichomes are just distributed on the outer side of corolla, consisting of 1 basal cell, 3 stalk cells and 1 head cell. All three types of glandular trichomes can secrete essential oil, and in small capitate trichomes of rachis, all peltate trichomes and digitiform trichomes, essential oil is stored in a large subcuticular space, released by cuticle rupture, whereas, in other capitate trichomes, essential oil crosses the thin cuticle. The essential oil of T. quinquecostatus is yellow, and its content is highest in the growth period. 68 constituents were identified in the essential oils. The main constituent is linalool.

  5. Genetic architecture of capitate glandular trichome density in florets of domesticated sunflower (Helianthus annuus L.)

    Science.gov (United States)

    Capitate glandular trichomes (CGT), one type of glandular trichomes, are most common in Asteraceae species. Capitate glandular trichomes can produce various secondary metabolites such as sesquiterpene lactones (STLs) and provide durable resistance to insect pests. In sunflower, CGT-based host resist...

  6. Morphological differentiation of non-glandular and glandular trichomes on Marrubium vulgare L.

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    Marta Dmitruk

    2014-04-01

    Full Text Available Marrubium vulgare L., commonly known as a white horehound or common horehound, belongs to the plant family Lamiaceae. It is a perennial aromatic herb which grows naturally in Europe, Asia, and America. Since ancient Egypt, this species has been known as a remedy for upper respiratory tract ailments. Nowadays, horehound is used in herbal medicine for treatment of liver diseases, biliary tract disorders, and for increasing the appetite and supporting the function of the stomach. The main biologically active substances in M. vulgare organs are: marrubiin, tannins, essential oils, and ursolic acid. The paper presents micromorphological analyses of non-glandular and glandular trichomes of M. vulgare. The research material was sampled from the plant collection in the Botanical Garden of the Maria Curie-Sklodowska University in Lublin (51°14′ N, 22°34′ E. The above-ground parts of horehound were collected during the flowering period in July 2013. Using light microscopy (LM and scanning electron microscopy (SEM, the types and sizes of trichomes from the stem, leaf, calyx, and corolla were investigated. The results of the microscopic observations show that the surfaces of M. vulgare vegetative and reproductive organs are densely clothed with glandular and non-glandular trichomes. The glandular trichomes are of two main types: peltate and capitate. Peltate trichomes consist of a short stalk cell and a large head with secretory cells arranged in a circle. The height of a mature trichome is about 31.33 μm and the diameter of the head is 31.47 μm. The substance produced by secretory cells passes through the apical walls and accumulates within a space between the cuticle and the cell wall layer. Capitate long trichomes with a basal cell, long stalk, neck cell, and a unicellular head are 36.65 μm long and the diameter of the head is about 15.6 μm. There are two types of short capitate trichomes: with a bicellular head and a unicellular stalk and with

  7. Capitate glandular trichomes in Aldama discolor (Heliantheae - Asteraceae): morphology, metabolite profile and sesquiterpene biosynthesis.

    Science.gov (United States)

    Bombo, A B; Appezzato-da-Glória, B; Aschenbrenner, A-K; Spring, O

    2016-05-01

    The capitate glandular trichome is the most common type described in Asteraceae species. It is known for its ability to produce various plant metabolites of ecological and economic importance, among which sesquiterpene lactones are predominant. In this paper, we applied microscopy, phytochemical and molecular genetics techniques to characterise the capitate glandular trichome in Aldama discolor, a native Brazilian species of Asteraceae, with pharmacological potential. It was found that formation of trichomes on leaf primordia of germinating seeds starts between 24 h and 48 h after radicle growth indicates germination. The start of metabolic activity of trichomes was indicated by separation of the cuticle from the cell wall of secretory cells at the trichome tip after 72 h. This coincided with the accumulation of budlein A, the major sesquiterpene lactone of A. discolor capitate glandular trichomes, in extracts of leaf primordia after 96 h. In the same timeframe of 72-96 h post-germination, gene expression studies showed up-regulation of the putative germacrene A synthase (pGAS2) and putative germacrene A oxidase (pGAO) of A. discolor in the transcriptome of these samples, indicating the start of sesquiterpene lactone biosynthesis. Sequencing of the two genes revealed high similarity to HaGAS and HaGAO from sunflower, which shows that key steps of this pathway are highly conserved. The processes of trichome differentiation, metabolic activity and genetic regulation in A. discolor and in sunflower appear to be typical for other species of the subtribe Helianthinae. © 2015 German Botanical Society and The Royal Botanical Society of the Netherlands.

  8. Structure and distribution of glandular and non-glandular trichomes on above-ground organs in Inula helenium L. (Asteraceae

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    Aneta Sulborska

    2014-01-01

    Full Text Available Micromorphology and distribution of glandular and non-glandular trichomes on the above-ground organs of Inula helenium L. were investigated using light and scanning electron microscopy (SEM. Two types of biseriate glandular trichomes, i.e. sessile and stalk hairs, and non-glandular trichomes were recorded. Sessile glandular trichomes were found on all examined I. helenium organs (with their highest density on the abaxial surface of leaves and disk florets, and on stems, whereas stalk glandular trichomes were found on leaves and stems. Sessile trichomes were characterised by a slightly lower height (58–103 μm and width (32–35 μm than the stalk trichomes (62–111 μm x 31–36 μm. Glandular hairs were composed of 5–7 (sessile trichomes or 6–9 (stalk trichomes cell tiers. Apical trichome cell tiers exhibited features of secretory cells. Secretion was accumulated in subcuticular space, which expanded and ruptured at the top, and released its content. Histochemical assays showed the presence of lipids and polyphenols, whereas no starch was detected. Non-glandular trichomes were seen on involucral bracts, leaves and stems (more frequently on involucral bracts. Their structure comprised 2–9 cells; basal cells (1–6 were smaller and linearly arranged, while apical cells had a prozenchymatous shape. The apical cell was the longest and sharply pointed. Applied histochemical tests revealed orange-red (presence of lipids and brow colour (presence of polyphenols in the apical cells of the trichomes. This may suggest that beside their protective role, the trichomes may participate in secretion of secondary metabolites.

  9. Morphology and histochemistry of glandular trichomes of Orobanche alba Stephan ex Willd

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    Aneta Sulborska

    2014-04-01

    Full Text Available Orobanche alba Stephan ex Willd is an achlorophyllous root parasite rare in Poland. It prefers dry and sunny slopes, xerothermic grasslands and pastures, mountain pastures, light scrubs, and rock fissures and ledges. The hosts of O. alba include Thymus polytrichus A. ern. ex Borbás, Clinopodium vulgare L. and Origanum vulgare L. The tick and fleshy 10-70 cm high stem in this species bears an inflorescence composed of zygomorphic, white or yellow “spotted” flowers covered by purple glandular trichomes. Glandular trichomes of this type are also borne on other parts of the plant, i.e. on the stem, scaly leaves, sepals, filaments, and the style. The secondary metabolites secreted by the glandular trichomes are related to defense of plants against the attack of herbivores and pathogens or act as attractants to pollinators or for fruit dispersal. The micromorphology and histochemistry of the glandular trichomes in O. alba were examined using scanning electron and light microscopes. In order to determine the type of secondary metabolites produced by the trichomes, the flowing histochemical assays were used: Sudan III and neutral red for detection of lipophilic compounds, IKI for detection of starch, and FeCl3 for detection of phenolic compounds. The peltate glandular trichomes of O. alba were characterised by a varied length (0.15‑0.48 mm and different activity phases. The trichome was composed of one larger basal epidermal cell, 1-3 hyaline stalk cells with a striated cuticle, a neck cell with a smooth cuticle on the surface, and a globose head formed of 8-18 secretory cells arranged in a circle. Many stalk cells of the trichomes, particularly those located on the corolla, contained anthocyanins, which give the trichomes dark carmine colour. In turn, the colour of the heads was dependent on trichome age: the heads were brown in older trichomes and yellow in younger hairs. Secretion was produced by both young and older trichomes. It penetrated

  10. Higher glandular trichome density in tomato leaflets and repellence to spider mites

    International Nuclear Information System (INIS)

    Maluf, Wilson Roberto; Inoue, Irene Fumi; Ferreira, Raphael de Paula Duarte; Gomes, Luiz Antonio Augusto; Castro, Evaristo Mauro de; Cardoso, Maria das Gracas

    2007-01-01

    The objective of this work was to evaluate the feasibility of selection for higher glandular trichome densities, as an indirect criterion of selection for increasing repellence to spider mites Tetranychus urticae, in tomato populations derived from an interspecific cross between Lycopersicon esculentum x L. hirsutum var. glabratum PI 134417. Trichome densities were evaluated in 19 genotypes, including 12 from advanced backcross populations, derived from the original cross L. esculentum x L. hirsutum var. glabratum PI 134417. Counts were made both on the adaxial and abaxial leaf surfaces, and trichomes were classified into glandular types IV and VI, other glandular types (types I+VII), and nonglandular types. Mite repellence was measured by distances walked by mites onto the tomato leaf surface after 20, 40 and 60 min. Spider mite repellence biotests indicated that higher densities of glandular trichomes (especially type VI) decreased the distances walked by the mites onto the tomato leaf surface. Selection of plants with higher densities of glandular trichomes can be an efficient criterion to obtain tomato genotypes with higher resistance (repellence) to spider mites. (author)

  11. Cadmium induced changes in subcellular glutathione contents within glandular trichomes of Cucurbita pepo L.

    Science.gov (United States)

    Kolb, Dagmar; Müller, Maria; Zellnig, Günther; Zechmann, Bernd

    2010-07-01

    Plants cope with cadmium (Cd) stress by complexation with phytochelatins (Pc), metallothioneins and glutathione and sequestration within vacuoles. Especially glutathione was found to play a major role in Cd detoxification as Cd shows a high binding affinity towards thiols and as glutathione is a precursor for Pc synthesis. In the present study, we have used an immunohistochemical approach combined with computer-supported transmission electron microscopy in order to measure changes in the subcellular distribution of glutathione during Cd-stress in mesophyll cells and cells of different glandular trichomes (long and short stalked) of Cucurbita pepo L. subsp. pepo var. styriaca GREB: . Even though no ultrastructural alterations were observed in leaf and glandular trichome cells after the treatment of plants with 50 microM cadmium chloride (CdCl(2)) for 48 h, all cells showed a large decrease in glutathione contents. The strongest decrease was found in nuclei and the cytosol (up to 76%) in glandular trichomes which are considered as a major side of Cd accumulation in leaves. The ratio of glutathione between the cytosol and nuclei and the other cell compartments was strongly decreased only in glandular trichomes (more than 50%) indicating that glutathione in these two cell compartments is especially important for the detoxification of Cd in glandular trichomes. Additionally, these data indicate that large amounts of Cd are withdrawn from nuclei during Cd exposure. The present study gives a detailed insight into the compartment-specific importance of glutathione during Cd exposure in mesophyll cells and glandular trichomes of C. pepo L. plants.

  12. Phenylpropanoid biosynthesis in leaves and glandular trichomes of basil (Ocimum basilicum L.).

    Science.gov (United States)

    Deschamps, Cícero; Simon, James E

    2010-01-01

    Basil (Ocimum basilicum L.) essential oil phenylpropenes are synthesized and accumulate in peltate glandular trichomes and their content and composition depend on plant developmental stage. Studies on gene expression and enzymatic activity indicate that the phenylpropene biosynthetic genes are developmentally regulated. In this study, the methylchavicol accumulation in basil leaves and the enzyme activities and gene expression of both chavicol O-methyltransferase (CVOMT) and eugenol O-methyltransferase (EOMT) were investigated in all leaves at four plant developmental stages. Methylchavicol accumulation decreased over time as leaves matured. There was a significant correlation between methylchavicol accumulation and CVOMT (r(2) = 0.88) enzyme activity, suggesting that the levels of biosynthetic enzymes control the essential oil content. CVOMT and EOMT transcript expression levels, which decreased with leaf age, followed the same pattern in both whole leaves and isolated glandular trichomes, providing evidence that CVOMT transcript levels are developmentally regulated in basil glandular trichomes themselves and that differences in CVOMT expression observed in whole leaves are not solely the result of differences in glandular trichome density.

  13. Brassica villosa, a system for studying non-glandular trichomes and genes in the Brassicas.

    Science.gov (United States)

    Nayidu, Naghabushana K; Tan, Yifang; Taheri, Ali; Li, Xiang; Bjorndahl, Trent C; Nowak, Jacek; Wishart, David S; Hegedus, Dwayne; Gruber, Margaret Y

    2014-07-01

    Brassica villosa is a wild Brassica C genome species with very dense trichome coverage and strong resistance to many insect pests of Brassica oilseeds and vegetables. Transcriptome analysis of hairy B. villosa leaves indicated higher expression of several important trichome initiation genes compared with glabrous B. napus leaves and consistent with the Arabidopsis model of trichome development. However, transcripts of the TRY inhibitory gene in hairy B. villosa were surprisingly high relative to B. napus and relative transcript levels of SAD2, EGL3, and several XIX genes were low, suggesting potential ancillary or less important trichome-related roles for these genes in Brassica species compared with Arabidopsis. Several antioxidant, calcium, non-calcium metal and secondary metabolite genes also showed differential expression between these two species. These coincided with accumulation of two alkaloid-like compounds, high levels of calcium, and other metals in B. villosa trichomes that are correlated with the known tolerance of B. villosa to high salt and the calcium-rich natural habitat of this wild species. This first time report on the isolation of large amounts of pure B. villosa trichomes, on trichome content, and on relative gene expression differences in an exceptionally hairy Brassica species compared with a glabrous species opens doors for the scientific community to understand trichome gene function in the Brassicas and highlights the potential of B. villosa as a trichome research platform.

  14. Localization of a defensive volatile 4-hydroxy-4-methylpentan-2-one in the capitate glandular trichomes of Oenothera glazioviana

    Institute of Scientific and Technical Information of China (English)

    Yanyun Tan; Desen Li; Juan Hua; Shihong Luo; Yan Liu; Shenghong Li

    2017-01-01

    Glandular trichomes of plants produce a wide variety of secondary metabolites which are considered as major defensive chemicals. The capitate glandular trichomes of Oenothera glazioviana (Onagraceae) were collected with laser microdissection and analyzed by gas chromatography-mass spectrometry. The volatile compound 4-hydroxy-4-methylpentan-2-one (1) was identified. We found that compound 1 displays antimicrobial, insecticidal, and phytotoxic activities. These results suggest that compound 1 might function as a defensive compound in the capitate glandular trichomes of O. glazioviana against pathogens, insect herbivores, and presumably competitive plants as well.

  15. Localization of a defensive volatile 4-hydroxy-4-methylpentan-2-one in the capitate glandular trichomes of Oenothera glazioviana

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    Yanyun Tan

    2017-06-01

    Full Text Available Glandular trichomes of plants produce a wide variety of secondary metabolites which are considered as major defensive chemicals. The capitate glandular trichomes of Oenothera glazioviana (Onagraceae were collected with laser microdissection and analyzed by gas chromatography–mass spectrometry. The volatile compound 4-hydroxy-4-methylpentan-2-one (1 was identified. We found that compound 1 displays antimicrobial, insecticidal, and phytotoxic activities. These results suggest that compound 1 might function as a defensive compound in the capitate glandular trichomes of O. glazioviana against pathogens, insect herbivores, and presumably competitive plants as well.

  16. Genetic Architecture of Capitate Glandular Trichome Density in Florets of Domesticated Sunflower (Helianthus annuus L.).

    Science.gov (United States)

    Gao, Qing-Ming; Kane, Nolan C; Hulke, Brent S; Reinert, Stephan; Pogoda, Cloe S; Tittes, Silas; Prasifka, Jarrad R

    2017-01-01

    Capitate glandular trichomes (CGT), one type of glandular trichomes, are most common in Asteraceae species. CGT can produce various secondary metabolites such as sesquiterpene lactones (STLs) and provide durable resistance to insect pests. In sunflower, CGT-based host resistance is effective to combat the specialist pest, sunflower moth. However, the genetic basis of CGT density is not well understood in sunflower. In this study, we identified two major QTL controlling CGT density in sunflower florets by using a F 4 mapping population derived from the cross HA 300 × RHA 464 with a genetic linkage map constructed from genotyping-by-sequencing data and composed of 2121 SNP markers. One major QTL is located on chromosome 5, which explained 11.61% of the observed phenotypic variation, and the second QTL is located on chromosome 6, which explained 14.06% of the observed phenotypic variation. The QTL effects and the association between CGT density and QTL support interval were confirmed in a validation population which included 39 sunflower inbred lines with diverse genetic backgrounds. We also identified two strong candidate genes in the QTL support intervals, and the functions of their orthologs in other plant species suggested their potential roles in regulating capitate glandular trichome density in sunflower. Our results provide valuable information to sunflower breeding community for developing host resistance to sunflower insect pests.

  17. Identification, functional characterization and developmental regulation of sesquiterpene synthases from sunflower capitate glandular trichomes

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    Ro Dae-Kyun

    2009-07-01

    Full Text Available Abstract Background Sesquiterpene lactones are characteristic metabolites of Asteraceae (or Compositae which often display potent bioactivities and are sequestered in specialized organs such as laticifers, resin ducts, and trichomes. For characterization of sunflower sesquiterpene synthases we employed a simple method to isolate pure trichomes from anther appendages which facilitated the identification of these genes and investigation of their enzymatic functions and expression patterns during trichome development. Results Glandular trichomes of sunflower (Helianthus annuus L. were isolated, and their RNA was extracted to investigate the initial steps of sesquiterpene lactone biosynthesis. Reverse transcription-PCR experiments led to the identification of three sesquiterpene synthases. By combination of in vitro and in vivo characterization of sesquiterpene synthase gene products in Escherichia coli and Saccharomyces cerevisiae, respectively, two enzymes were identified as germacrene A synthases, the key enzymes of sesquiterpene lactone biosynthesis. Due to the very low in vitro activity, the third enzyme was expressed in vivo in yeast as a thioredoxin-fusion protein for functional characterization. In in vivo assays, it was identified as a multiproduct enzyme with the volatile sesquiterpene hydrocarbon δ-cadinene as one of the two main products with α-muuorlene, β-caryophyllene, α-humulene and α-copaene as minor products. The second main compound remained unidentified. For expression studies, glandular trichomes from the anther appendages of sunflower florets were isolated in particular developmental stages from the pre- to the post-secretory phase. All three sesquiterpene synthases were solely upregulated during the biosynthetically active stages of the trichomes. Expression in different aerial plant parts coincided with occurrence and maturity of trichomes. Young roots with root hairs showed expression of the sesquiterpene synthase genes

  18. The key role of peltate glandular trichomes in symbiota comprising clavicipitaceous fungi of the genus periglandula and their host plants.

    Science.gov (United States)

    Steiner, Ulrike; Kucht, Sabine Hellwig neé; Ahimsa-Müller, Mahalia A; Grundmann, Nicola; Li, Shu-Ming; Drewke, Christel; Leistner, Eckhard

    2015-04-16

    Clavicipitaceous fungi producing ergot alkaloids were recently discovered to be epibiotically associated with peltate glandular trichomes of Ipomoea asarifolia and Turbina corymbosa, dicotyledonous plants of the family Convolvulaceae. Mediators of the close association between fungi and trichomes may be sesquiterpenes, main components in the volatile oil of different convolvulaceous plants. Molecular biological studies and microscopic investigations led to the observation that the trichomes do not only secrete sesquiterpenes and palmitic acid but also seem to absorb ergot alkaloids from the epibiotic fungal species of the genus Periglandula. Thus, the trichomes are likely to have a dual and key function in a metabolic dialogue between fungus and host plant.

  19. Differential microRNA Analysis of Glandular Trichomes and Young Leaves in Xanthium strumarium L. Reveals Their Putative Roles in Regulating Terpenoid Biosynthesis.

    Science.gov (United States)

    Fan, Rongyan; Li, Yuanjun; Li, Changfu; Zhang, Yansheng

    2015-01-01

    The medicinal plant Xanthium strumarium L. (X. strumarium) is covered with glandular trichomes, which are the sites for synthesizing pharmacologically active terpenoids such as xanthatin. MicroRNAs (miRNAs) are a class of 21-24 nucleotide (nt) non-coding RNAs, most of which are identified as regulators of plant growth development. Identification of miRNAs involved in the biosynthesis of plant secondary metabolites remains limited. In this study, high-throughput Illumina sequencing, combined with target gene prediction, was performed to discover novel and conserved miRNAs with potential roles in regulating terpenoid biosynthesis in X. strumarium glandular trichomes. Two small RNA libraries from leaves and glandular trichomes of X. strumarium were established. In total, 1,185 conserved miRNAs and 37 novel miRNAs were identified, with 494 conserved miRNAs and 18 novel miRNAs being differentially expressed between the two tissue sources. Based on the X. strumarium transcriptome data that we recently constructed, 3,307 annotated mRNA transcripts were identified as putative targets of the differentially expressed miRNAs. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis suggested that some of the differentially expressed miRNAs, including miR6435, miR5021 and miR1134, might be involved in terpenoid biosynthesis in the X. strumarium glandular trichomes. This study provides the first comprehensive analysis of miRNAs in X. strumarium, which forms the basis for further understanding of miRNA-based regulation on terpenoid biosynthesis.

  20. Differential microRNA Analysis of Glandular Trichomes and Young Leaves in Xanthium strumarium L. Reveals Their Putative Roles in Regulating Terpenoid Biosynthesis.

    Directory of Open Access Journals (Sweden)

    Rongyan Fan

    Full Text Available The medicinal plant Xanthium strumarium L. (X. strumarium is covered with glandular trichomes, which are the sites for synthesizing pharmacologically active terpenoids such as xanthatin. MicroRNAs (miRNAs are a class of 21-24 nucleotide (nt non-coding RNAs, most of which are identified as regulators of plant growth development. Identification of miRNAs involved in the biosynthesis of plant secondary metabolites remains limited. In this study, high-throughput Illumina sequencing, combined with target gene prediction, was performed to discover novel and conserved miRNAs with potential roles in regulating terpenoid biosynthesis in X. strumarium glandular trichomes. Two small RNA libraries from leaves and glandular trichomes of X. strumarium were established. In total, 1,185 conserved miRNAs and 37 novel miRNAs were identified, with 494 conserved miRNAs and 18 novel miRNAs being differentially expressed between the two tissue sources. Based on the X. strumarium transcriptome data that we recently constructed, 3,307 annotated mRNA transcripts were identified as putative targets of the differentially expressed miRNAs. KEGG (Kyoto Encyclopedia of Genes and Genomes pathway analysis suggested that some of the differentially expressed miRNAs, including miR6435, miR5021 and miR1134, might be involved in terpenoid biosynthesis in the X. strumarium glandular trichomes. This study provides the first comprehensive analysis of miRNAs in X. strumarium, which forms the basis for further understanding of miRNA-based regulation on terpenoid biosynthesis.

  1. Development and Structure of Internal Glands and External Glandular Trichomes in Pogostemon cablin

    Science.gov (United States)

    Guo, Jiansheng; Yuan, Yongming; Liu, Zhixue; Zhu, Jian

    2013-01-01

    Pogostemon cablin possesses two morphologically and ontogenetically different types of glandular trichomes, one type of bristle hair on the surfaces of leaves and stems and one type of internal gland inside the leaves and stems. The internal gland originates from elementary meristem and is associated with the biosynthesis of oils present inside the leaves and stems. However, there is little information on mechanism for the oil biosynthesis and secretion inside the leaves and stems. In this study, we identified three kinds of glandular trichome types and two kinds of internal gland in the Pogostemon cablin. The oil secretions from internal glands of stems and leaves contained lipids, flavones and terpenes. Our results indicated that endoplasmic reticulum and plastids and vacuoles are likely involved in the biosynthesis of oils in the internal glands and the synthesized oils are transported from endoplasmic reticulum to the cell wall via connecting endoplasmic reticulum membranes to the plasma membrane. And the comparative analysis of the development, distribution, histochemistry and ultrastructures of the internal and external glands in Pogostemon cablin leads us to propose that the internal gland may be a novel secretory structure which is different from external glands. PMID:24205002

  2. Cloning of a sesquiterpene synthase from Lavandula x intermedia glandular trichomes.

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    Sarker, Lukman S; Demissie, Zerihun A; Mahmoud, Soheil S

    2013-11-01

    The essential oil (EO) of Lavandula is dominated by monoterpenes, but can also contain small amounts of sesquiterpenes, depending on species and environmental conditions. For example, the sesquiterpene 9-epi-caryophyllene can make up to 8 % of the EO in a few species, including those commercially propagated for EO production. Here, we report the cloning and functional characterization of 9-epi-caryophyllene synthase (LiCPS) from the glandular trichomes of Lavandula x intermedia, cv. Grosso. The 1,617 bp open reading frame of LiCPS, which did not encode a transit peptide, was expressed in Escherichia coli and the recombinant protein purified by Ni-NTA agarose affinity chromatography. The ca. 60 kDa recombinant protein specifically converted farnesyl diphosphate to 9-epi-caryophyllene. LiCPS also produced a few monoterpenes when assayed with the monoterpene precursor geranyl diphosphate (GPP), but--unlike most monoterpene synthases--was not able to derive detectable amounts of any products from the cis isomer of GPP, neryl diphosphate. The LiCPS transcripts accumulated in developing L. x intermedia flowers and were highly enriched in glandular trichomes, but were not detected in leaves suggesting that the transcriptional expression of this gene is spatially and developmentally regulated.

  3. Molecular cloning and functional characterization of borneol dehydrogenase from the glandular trichomes of Lavandula x intermedia.

    Science.gov (United States)

    Sarker, Lukman S; Galata, Mariana; Demissie, Zerihun A; Mahmoud, Soheil S

    2012-12-15

    Several varieties of Lavandula x intermedia (lavandins) are cultivated for their essential oils (EOs) for use in cosmetic, hygiene and personal care products. These EOs are mainly constituted of monoterpenes including camphor, which contributes an off odor reducing the olfactory appeal of the oil. We have recently constructed a cDNA library from the glandular trichomes (the sites of EO synthesis) of L. x intermedia plants. Here, we describe the cloning of a borneol dehydrogenase cDNA (LiBDH) from this library. The 780 bp open reading frame of the cDNA encoded a 259 amino acid short chain alcohol dehydrogenase with a predicted molecular mass of ca. 27.5 kDa. The recombinant LiBDH was expressed in Escherichia coli, purified by Ni-NTA agarose affinity chromatography, and functionally characterized in vitro. The bacterially produced enzyme specifically converted borneol to camphor as the only product with K(m) and k(cat) values of 53 μM and 4.0 × 10(-4) s(-1), respectively. The LiBDH transcripts were specifically expressed in glandular trichomes of mature flowers indicating that like other Lavandula monoterpene synthases the expression of this gene is regulated in a tissue-specific manner. The cloning of LiBDH has far reaching implications in improving the quality of Lavandula EOs through metabolic engineering. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Identifying three ecological chemotypes of Xanthium strumarium glandular trichomes using a combined NMR and LC-MS method.

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    Chen, Fangfang; Hao, Fuhua; Li, Changfu; Gou, Junbo; Lu, Dayan; Gong, Fujun; Tang, Huiru; Zhang, Yansheng

    2013-01-01

    Xanthanolides, as the sesquiterpene lactones, are reportedly the major components for the pharmacological properties of X. strumarium L. species. Phytochemical studies indicated that the glandular structures on the surface of plant tissues would form the primary sites for the accumulation of this class of the compounds. As the interface between plants and their natural enemies, glandular trichomes may vary with respect to which of their chemicals are sequestered against different herbivores in different ecologies. However, to date, no data are available on the chemical characterisation of X. strumarium glandular cells. In this study, the trichome secretions of the X. strumarium species originating from nineteen unique areas across eleven provinces in China, were analysed by HPLC, LC-ESI-MS and NMR. For the first time three distinct chemotypes of X. strumarium glandular trichomes were discovered along with the qualitative and quantitative evaluations of their presence of xanthanolides; these were designated glandular cell Types I, II, and III, respectively. The main xanthanolides in Type I cells were 8-epi-xanthatin and xanthumin while no xanthatin was detected. Xanthatin, 8-epi-xanthatin, and xanthumin dominated in Type II cells with comparable levels of each being present. For Type III cells, significantly higher concentrations of 8-epi-xanthatin or xanthinosin (relative to xanthatin) were detected with xanthinosin only being observed in this type. Further research will focus on understanding the ecological and molecular mechanism causing these chemotype differences in X. strumarium glandular structures.

  5. Identifying three ecological chemotypes of Xanthium strumarium glandular trichomes using a combined NMR and LC-MS method.

    Directory of Open Access Journals (Sweden)

    Fangfang Chen

    Full Text Available Xanthanolides, as the sesquiterpene lactones, are reportedly the major components for the pharmacological properties of X. strumarium L. species. Phytochemical studies indicated that the glandular structures on the surface of plant tissues would form the primary sites for the accumulation of this class of the compounds. As the interface between plants and their natural enemies, glandular trichomes may vary with respect to which of their chemicals are sequestered against different herbivores in different ecologies. However, to date, no data are available on the chemical characterisation of X. strumarium glandular cells. In this study, the trichome secretions of the X. strumarium species originating from nineteen unique areas across eleven provinces in China, were analysed by HPLC, LC-ESI-MS and NMR. For the first time three distinct chemotypes of X. strumarium glandular trichomes were discovered along with the qualitative and quantitative evaluations of their presence of xanthanolides; these were designated glandular cell Types I, II, and III, respectively. The main xanthanolides in Type I cells were 8-epi-xanthatin and xanthumin while no xanthatin was detected. Xanthatin, 8-epi-xanthatin, and xanthumin dominated in Type II cells with comparable levels of each being present. For Type III cells, significantly higher concentrations of 8-epi-xanthatin or xanthinosin (relative to xanthatin were detected with xanthinosin only being observed in this type. Further research will focus on understanding the ecological and molecular mechanism causing these chemotype differences in X. strumarium glandular structures.

  6. Glandular trichomes in Connarus suberosus (Connaraceae: distribution, structural organization and probable functions

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    João Donizete Denardi

    2012-03-01

    Full Text Available Connarus suberosus is a typical species of the Brazilian Cerrado biome, and its inflorescences and young vegetative branches are densely covered by dendritic trichomes. The objective of this study was to report the occurrence of a previously undescribed glandular trichome of this species. The localization, origin and structure of these trichomes were investigated under light, transmission and scanning electron microscopy. Collections were made throughout the year, from five adult specimens of Connarus suberosus near Botucatu, São Paulo, Brazil, including vegetative and reproductive apices, leaves and fruits in different developmental stages, as well as floral buds and flowers at anthesis. Glandular trichomes (GTs occurred on vegetative and reproductive organs during their juvenile stages. The GTs consisted of a uniseriate, multicellular peduncle, whose cells contain phenolic compounds, as well as a multicellular glandular portion that accumulates lipids. The glandular cell has thin wall, dense cytoplasm (with many mitochondria, plastids and dictyosomes, and a large nucleus with a visible nucleolus. The starch present in the plastids was hydrolyzed during the synthesis phase, reducing the density of the plastid stroma. Some plastids were fused to vacuoles, and some evidence suggested the conversion of plastids into vacuoles. During the final activity stages of the GTs, a darkening of the protoplasm was observed in some of the glandular cells, as a programmed cell death; afterwards, became caducous. The GTs in C. suberosus had a temporal restriction, being limited to the juvenile phase of the organs. Their presence on the exposed surfaces of developing organs and the chemical nature of the reserve products, suggest that these structures are food bodies. Field observations and detailed studies of plant-environment interactions, as well as chemical analysis of the reserve compounds, are still necessary to confirm the role of these GTs as feeding

  7. Caracterização e ontogenia dos tricomas glandulares de Ocimum selloi Benth. - Lamiaceae Characterization and ontogeny of the glandular trichomes of Ocimum selloi Benth. (Lamiaceae

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    Letícia de Almeida Gonçalves

    2010-12-01

    Full Text Available Ocimum selloi Benth. (Lamiaceae é uma espécie nativa da América do Sul e na medicina popular tem sido usada devido suas propriedades analgésica, anti-inflamatória e antiespasmódica. O objetivo do presente trabalho foi identificar os tipos de tricomas glandulares que ocorrem nos órgãos vegetativos e reprodutivos de O. selloi e determinar a ontogenia desses tricomas. Ramos laterais em início de formação, folhas totalmente expandidas, flores em diferentes estádios de diferenciação, amostras de caule e do eixo das inflorescências foram analisados em microscopias de luz e eletrônica de varredura. Tricomas glandulares do tipo peltado e capitado subséssil foram observados no caule, nas folhas, no eixo da inflorescência e na superfície adaxial das sépalas. Nas sépalas foi encontrado, além dos tricomas secretores peltados e capitados subsésseis, o tricoma glandular capitado pedunculado. A ontogenia inicia-se com a expansão de uma célula protodérmica que, de acordo com a seqüência de divisões periclinais e anticlinais (ora simétricas, ora assimétricas, dá origem aos tricomas. A diferenciação dos tricomas glandulares peltados e capitados não é sincrônica e ocorre muito cedo no desenvolvimento da folha, do caule e do eixo floral.Ocimum selloi Benth. (Lamiaceae is native to South America and in traditional medicine has been used due to its analgesic, anti-inflammatory, and antispasmodic properties. The aim of this study was to identify the types of glandular trichomes that occur on the vegetative and reproductive organs of O. selloi and to determine trichome ontogeny. Lateral branches at the initial formation phase, fully opened leaves, flowers at different differentiation stages, and stem and inflorescence axes were analyzed under light and scanning electron microscopy. Glandular trichomes of the peltate and subsessile capitate types were observed on the stem, leaves, inflorescence axis and the adaxial surface of the

  8. Negative ion 'chip-based' nanospray tandem mass spectrometry for the analysis of flavonoids in glandular trichomes of Lychnophora ericoides Mart. (Asteraceae).

    Science.gov (United States)

    Gobbo-Neto, Leonardo; Gates, Paul J; Lopes, Norberto P

    2008-12-01

    This paper reports a method for the analysis of secondary metabolites stored in glandular trichomes, employing negative ion 'chip-based' nanospray tandem mass spectrometry. The analyses of glandular trichomes from Lychnophora ericoides, a plant endemic to the Brazilian 'cerrado' and used in traditional medicine as an anti-inflammatory and analgesic agent, led to the identification of five flavonoids (chrysin, pinocembrin, pinostrobin, pinobanksin and 3-O-acetylpinobanksin) by direct infusion of the extracts of glandular trichomes into the nanospray ionisation source. All the flavonoids have no oxidation at ring B, which resulted in a modification of the fragmentation pathways compared with that of the oxidised 3,4-dihydroflavonoids already described in the literature. The absence of the anti-inflammatory and antioxidant di-C-glucosylflavone vicenin-2, or any other flavonoid glycosides, in the glandular trichomes was also demonstrated. The use of the 'chip-based' nanospray QqTOF apparatus is a new fast and useful tool for the identification of secondary metabolites stored in the glandular trichomes, which can be useful for chemotaxonomic studies based on metabolites from glandular trichomes.

  9. Papel dos tricomas glandulares da folha do tomateiro na oviposição de Tuta absoluta Role of tomato leaf glandular trichomes on oviposition of Tuta absoluta

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    Elsa Gilardón

    2001-03-01

    Full Text Available Os tricomas glandulares presentes nas folhas e ramos das plantas do gênero Lycopersicon são responsáveis pela secreção de metabólitos de diferentes naturezas. A presença de alguns desses compostos tem sido associada à resistência do tomate a diferentes insetos. A traça-do-tomateiro, Tuta absoluta (Meyrick, é uma das pragas mais nocivas da América do Sul. O adulto oviposita sobre as folhas do tomate e suas larvas abrem galerias no mesófilo das folhas, ramos, flores e frutos. As espécies silvestres do tomate conservam a capacidade de biossintetizar compostos químicos que lhes conferem resistência a esta praga. No presente trabalho, foi avaliada a preferência para oviposição desse inseto sobre folhas com e sem tricomas glandulares de L. esculentum (Mill. cv. Uco Plata, suscetível, e de L. hirsutum f. glabratum (Mull. PI 134417, espécie silvestre afim ao tomate, e resistente à traça. Os resultados sugerem que as fêmeas ovipositam indistintamente sobre as folhas de ambas espécies, independentemente da presença, ou não, dos tricomas glandulares. E a presença destes e de seus exsudatos não têm efeito inibidor na oviposição do inseto.In the genus Lycopersicon, different metabolites are secreted by the glandular trichomes of leaves and stems. These compounds have been associated to different tomato pests resistance. The South American tomato pinworm, Tuta absoluta (Meyrick, is one of the most harmful pests in South America. The females oviposit on tomato leaves and the larvae mine the leaf mesophyl, stems, flowers and fruits. Some wild accessions of Lycopersicon keep their capacity to synthesize allelochemicals that protect them from the pest. In this paper a comparison was made between the tomato pinworm oviposition on leaves with and without trichomes of L. esculentum (Mill. cv. Uco Plata, a susceptible cultivar, and L. hirsutum f. glabratum (Mull. PI 134417, a resistant wild accession. Results suggest that the female

  10. Volatiles and Nonvolatiles in Flourensia campestris Griseb. (Asteraceae), How Much Do Capitate Glandular Trichomes Matter?

    Science.gov (United States)

    Piazza, Leonardo A; López, Daniela; Silva, Mariana P; López Rivilli, Marisa J; Tourn, Mónica G; Cantero, Juan J; Scopel, Ana L

    2018-03-01

    The distribution and ultrastructure of capitate glandular trichomes (GTs) in Flourensia species (Asteraceae) have been recently elucidated, but their metabolic activity and potential biological function remain unexplored. Selective nonvolatile metabolites from isolated GTs were strikingly similar to those found on leaf surfaces. The phytotoxic allelochemical sesquiterpene (-)-hamanasic acid A ((-)-HAA) was the major constituent (ca. 40%) in GTs. Although GTs are quaternary ammonium compounds (QACs)-accumulating species, glycine betaine was not found in GTs; it was only present in the leaf mesophyll. Two (-)-HAA accompanying surface secreted products: compounds 4-hydroxyacetophenone (piceol; 1) and 2-hydroxy-5-methoxyacetophenone (2), which were isolated and fully characterized (GC/MS, NMR), were present in the volatiles found in GTs. The essential oils of fresh leaves revealed ca. 33% monoterpenes, 26% hydrocarbon- and 30% oxygenated sesquiterpenes, most of them related to cadinene and bisabolene derivatives. Present results suggest a main role of GTs in determining the volatile and nonvolatile composition of F. campestris leaves. Based on the known activities of the compounds identified, it can be suggested that GTs in F. campestris would play key ecological functions in plant-pathogen and plant-plant interactions. In addition, the strikingly high contribution of compounds derived from cadinene and bisabolene pathways, highlights the potential of this species as a source of high-valued bioproducts. © 2018 Wiley-VHCA AG, Zurich, Switzerland.

  11. Identification and characterization of two bisabolene synthases from linear glandular trichomes of sunflower (Helianthus annuus L., Asteraceae).

    Science.gov (United States)

    Aschenbrenner, Anna-Katharina; Kwon, Moonhyuk; Conrad, Jürgen; Ro, Dae-Kyun; Spring, Otmar

    2016-04-01

    Sunflower is known to produce a variety of bisabolene-type sesquiterpenes and accumulates these substances in trichomes of leaves, stems and flowering parts. A bioinformatics approach was used to identify the enzyme responsible for the initial step in the biosynthesis of these compounds from its precursor farnesyl pyrophosphate. Based on sequence similarity with a known bisabolene synthases from Arabidopsis thaliana AtTPS12, candidate genes of Helianthus were searched in EST-database and used to design specific primers. PCR experiments identified two candidates in the RNA pool of linear glandular trichomes of sunflower. Their sequences contained the typical motifs of sesquiterpene synthases and their expression in yeast functionally characterized them as bisabolene synthases. Spectroscopic analysis identified the stereochemistry of the product of both enzymes as (Z)-γ-bisabolene. The origin of the two sunflower bisabolene synthase genes from the transcripts of linear trichomes indicates that they may be involved in the synthesis of sesquiterpenes produced in these trichomes. Comparison of the amino acid sequences of the sunflower bisabolene synthases showed high similarity with sesquiterpene synthases from other Asteracean species and indicated putative evolutionary origin from a β-farnesene synthase. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Glandular trichome density and essential oil composition in leaves and inflorescences of Lippia origanoides Kunth (Verbenaceae in the Brazilian Cerrado

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    Luiz R.S. Tozin

    2015-06-01

    Full Text Available The essential oils from leaves and inflorescences of Lippia origanoides Kunth present aromatic and medicinal potential and have been used to treat several diseases, including melanoma. In Brazil, L. origanoides is commonly found in campo cerrado and cerrado stricto sensu, physiognomies featured mainly by the differential light conditions to which short and medium-sized plants are subjected. Our aim was to investigate the glandular trichome density and the yield and chemical composition of the essential oils in leaves and inflorescences of L. origanoides from campo cerrado and cerrado stricto sensu. For glandular density analysis, leaves and inflorescences were processed according to conventional techniques for scanning electron microscopy. The essential oils of leaves and inflorescences were obtained by hydrodistillation and identified with gas chromatography. Bracts and sepals showed the highest glandular density, followed by petals and leaves. The glandular density in the abaxial leaf surface was higher in individuals from the campo cerrado. In both populations the essential oil yield was higher in inflorescences than in leaves. The chemical composition of the essential oils varied among individuals from different areas and inside a same population. Our results demonstrated the chemical plasticity of L. origanoides suggesting the importance of monitoring its popular use.

  13. Glandular trichome density and essential oil composition in leaves and inflorescences of Lippia origanoides Kunth (Verbenaceae) in the Brazilian Cerrado.

    Science.gov (United States)

    Tozin, Luiz R S; Marques, Marcia O M; Rodrigues, Tatiane M

    2015-01-01

    The essential oils from leaves and inflorescences of Lippia origanoides Kunth present aromatic and medicinal potential and have been used to treat several diseases, including melanoma. In Brazil, L. origanoides is commonly found in campo cerrado and cerrado stricto sensu, physiognomies featured mainly by the differential light conditions to which short and medium-sized plants are subjected. Our aim was to investigate the glandular trichome density and the yield and chemical composition of the essential oils in leaves and inflorescences of L. origanoides from campo cerrado and cerrado stricto sensu. For glandular density analysis, leaves and inflorescences were processed according to conventional techniques for scanning electron microscopy. The essential oils of leaves and inflorescences were obtained by hydrodistillation and identified with gas chromatography. Bracts and sepals showed the highest glandular density, followed by petals and leaves. The glandular density in the abaxial leaf surface was higher in individuals from the campo cerrado. In both populations the essential oil yield was higher in inflorescences than in leaves. The chemical composition of the essential oils varied among individuals from different areas and inside a same population. Our results demonstrated the chemical plasticity of L. origanoides suggesting the importance of monitoring its popular use.

  14. Higher glandular trichome density in tomato leaflets and repellence to spider mites Alta densidade de tricomas glandulares em tomateiro e aumento da repelência a ácaros rajados

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    Wilson Roberto Maluf

    2007-09-01

    Full Text Available The objective of this work was to evaluate the feasibility of selection for higher glandular trichome densities, as an indirect criterion of selection for increasing repellence to spider mites Tetranychus urticae, in tomato populations derived from an interspecific cross between Lycopersicon esculentum x L. hirsutum var. glabratum PI 134417. Trichome densities were evaluated in 19 genotypes, including 12 from advanced backcross populations, derived from the original cross L. esculentum x L. hirsutum var. glabratum PI 134417. Counts were made both on the adaxial and abaxial leaf surfaces, and trichomes were classified into glandular types IV and VI, other glandular types (types I+VII, and nonglandular types. Mite repellence was measured by distances walked by mites onto the tomato leaf surface after 20, 40 and 60 min. Spider mite repellence biotests indicated that higher densities of glandular trichomes (especially type VI decreased the distances walked by the mites onto the tomato leaf surface. Selection of plants with higher densities of glandular trichomes can be an efficient criterion to obtain tomato genotypes with higher resistance (repellence to spider mites.O objetivo deste trabalho foi avaliar a eficiência da seleção para maior densidade de tricomas glandulares na resistência (repelência ao ácaro Tetranychus urticae, em populações de tomate derivadas do cruzamento interespecífico Lycopersicon esculentum x L. hirsutum var. glabratum PI 134417. Foram avaliados 19 genótipos quanto à densidade de tricomas, que incluíram 12 derivados de populações avançadas de retrocruzamentos, obtidos a partir do cruzamento original L. esculentum x L. hirsutum var. glabratum PI 134417. Nas faces abaxial e adaxial dos folíolos, realizaram-se as contagens e os tricomas foram classificados em glandulares tipo IV e VI, outros glandulares (tipo I e VII e não glandulares. A repelência aos ácaros foi medida pela distância média, percorrida pelo

  15. Effect of heat shock on ultrastructure and calcium distribution in Lavandula pinnata L. glandular trichomes.

    Science.gov (United States)

    Huang, S S; Kirchoff, B K; Liao, J P

    2013-02-01

    The effects of heat shock (HS) on the ultrastructure and calcium distribution of Lavandula pinnata secretory trichomes are examined using transmission electron microscopy and potassium antimonate precipitation. After 48-h HS at 40°C, plastids become distorted and lack stroma and osmiophilic deposits, the cristae of the mitochondria become indistinct, the endoplasmic reticulum acquires a chain-like appearance with ribosomes prominently attached to the lamellae, and the plasma and organelle membranes become distorted. Heat shock is associated with a decrease in calcium precipitates in the trichomes, while the number of precipitates increases in the mesophyll cells. Prolonged exposure to elevated calcium levels may be toxic to the mesophyll cells, while the lack of calcium in the glands cell may deprive them of the normal protective advantages of elevated calcium levels. The inequality in calcium distribution may result not only from uptake from the transpiration stream, but also from redistribution of calcium from the trichomes to the mesophyll cells.

  16. Differential microRNA Analysis of Glandular Trichomes and Young Leaves in Xanthium strumarium L. Reveals Their Putative Roles in Regulating Terpenoid Biosynthesis

    OpenAIRE

    Fan, Rongyan; Li, Yuanjun; Li, Changfu; Zhang, Yansheng

    2015-01-01

    The medicinal plant Xanthium strumarium L. (X. strumarium) is covered with glandular trichomes, which are the sites for synthesizing pharmacologically active terpenoids such as xanthatin. MicroRNAs (miRNAs) are a class of 21-24 nucleotide (nt) non-coding RNAs, most of which are identified as regulators of plant growth development. Identification of miRNAs involved in the biosynthesis of plant secondary metabolites remains limited. In this study, high-throughput Illumina sequencing, combined w...

  17. Monoterpenes in the glandular trichomes of tomato are synthesized from a neryl diphosphate precursor rather than geranyl diphosphate.

    Science.gov (United States)

    Schilmiller, Anthony L; Schauvinhold, Ines; Larson, Matthew; Xu, Richard; Charbonneau, Amanda L; Schmidt, Adam; Wilkerson, Curtis; Last, Robert L; Pichersky, Eran

    2009-06-30

    We identified a cis-prenyltransferase gene, neryl diphosphate synthase 1 (NDPS1), that is expressed in cultivated tomato (Solanum lycopersicum) cultivar M82 type VI glandular trichomes and encodes an enzyme that catalyzes the formation of neryl diphosphate from isopentenyl diphosphate and dimethylallyl diphosphate. mRNA for a terpene synthase gene, phellandrene synthase 1 (PHS1), was also identified in these glands. It encodes an enzyme that uses neryl diphosphate to produce beta-phellandrene as the major product as well as a variety of other monoterpenes. The profile of monoterpenes produced by PHS1 is identical with the monoterpenes found in type VI glands. PHS1 and NDPS1 map to chromosome 8, and the presence of a segment of chromosome 8 derived from Solanum pennellii LA0716 causes conversion from the M82 gland monoterpene pattern to that characteristic of LA0716 plants. The data indicate that, contrary to the textbook view of geranyl diphosphate as the "universal" substrate of monoterpene synthases, in tomato glands neryl diphosphate serves as a precursor for the synthesis of monoterpenes.

  18. Papel da 2-tridecanona e dos tricomas glandulares tipo VI na resistência do tomateiro a Tuta absoluta Role of 2-tridecanone and type VI glandular trichome on tomato resistance to Tuta absoluta

    Directory of Open Access Journals (Sweden)

    Elsa Gilardón

    2001-07-01

    Full Text Available O metabólito secundário 2-tridecanona, secretado pelos tricomas glandulares tipo VI das folhas de tomateiro silvestre, Lycopersicon hirsutum L., confere-lhe resistência a uma grande variedade de insetos, inclusive a traça-do-tomateiro, Tuta absoluta (Meyrick. O objetivo do trabalho foi avaliar a concentração de 2- tridecanona, a densidade de tricomas glandulares tipo VI e o grau de infestação da traça-do-tomateiro na cultivar suscetível 'Uco Plata' (Lycopersicon esculentum Mill., na linhagem resistente PI 134417 (L. hirsutum f. glabratum e em suas progênies F1 e F2. Foram avaliadas ainda as possíveis associações entre a concentração de 2-tridecanona, a densidade de tricomas glandulares tipo VI e o grau de infestação da traça-do-tomateiro. O grau médio de infestação da traça-do-tomateiro em 'Uco Plata' foi significativamente superior ao obtido em PI 134417. Ainda que a concentração de 2-tridecanona tenha sido significativamente superior no parental resistente, a presença deste metabólito somente explicaria parcialmente a resistência (R² = 8,17%. Não se detectaram diferenças significativas na densidade de tricomas tipo VI entre o parental suscetível e o resistente. Este comportamento ocorreu independentemente do conteúdo de 2-tridecanona e do grau de infestação da traça-do-tomateiro.The secondary metabolite 2-tridecanone, secreted by the type VI glandular trichomes present in the leaves of Lycopersicon hirsutum L., make it resistant to a great variety of insects, including the tomato pinworm, Tuta absoluta (Meyrick. The 2-tridecanone concentration, the type VI glandular trichome densities and the pinworm infestation degree were evaluated on the Lycopersicon esculentum Mill. susceptible cultivar 'Uco Plata', on the Lycopersicon hirsutum f. glabratum resistant accession PI 134417 and on their F1 and F2. The mean infestation degree with pinworm larvae was significantly higher in 'Uco Plata' than in PI 134417. The 2

  19. Leaf Trichomes Morphology of Hyptis suaveolens (L.) Poit. (LAMIACEAE)

    Science.gov (United States)

    Chatri, M.; Baktiar, A.; Mansyurdin, M.; Periadnadi, P.

    2018-04-01

    Hyptis suaveolens L. Poit is one of the plants from family Lamiaceae and is an aromatic plant. The aroma contained in plants is usually secreted by certain structures in plants, such as glandular trichomes. At this plant has been carried out observations about the type and distribution of trichomes by using light microscopy and SEM (Scanning Electron Microscopy). The results showed that the leaves of this plant are non-glandular trichomes types and glandular, either on the surface abaxial and adaxial and on the veins. Non-glandular trichomes consist of the monoselular and multicellular trichomes. While the glandular trichomes consist of peltate type, capitate type I and type II.

  20. Morphology, structure and ontogeny of trichomes of the grape genus (Vitis, Vitaceae

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    Zhi-Yao eMa

    2016-05-01

    Full Text Available Trichomes are widely distributed on surfaces of different organs in the grape genus Vitis and are of taxonomic utility. To explore the morphology, structure and ontogeny of Vitis trichomes, we investigated the diversity and distribution of trichomes in 34 species of Vitis. Two main types of trichomes in Vitis are documented: non-glandular and glandular. Within non-glandular trichomes, ribbon and simple trichomes are found on different vegetative plant organs. The morphology and ontogeny of these types of trichomes are further examined with light microscopy and scanning electron microscopy. The ultrastructure of the glandular trichomes is explored with transmission electron microscopy. The ribbon trichomes are twisted, greatly elongated and unicellular, and this trichome type may be a morphological synapomorphy of Vitis and its closest tropical relative Ampelocissus and Pterisanthes in Vitaceae. The simple trichomes are documented in most species sampled in the genus. The glandular trichomes are multicellular, non-vascularized and composed of both epidermis and subjacent layers. We show that prickles occurring along the stems and petioles of Vitis davidii are modified glandular trichomes. In our observation, the glandular trichomes of V. romanetii can secret mucilage and send out volatile substance so that many insects are often glued to glands. Transmission electron microscopy indicates that metabolic products accumulate in vacuoles, the cytoplasm and intercellular spaces. We infer that glandular trichomes and young prickles are involved in the secretion of these metabolic products and the intercellular spaces may be the places of temporary storage of these secretions.

  1. Trichomes morphology as a taxonomic marker in the subfamily heliotropioideae (boraginaceae from Pakistan and Kashmir)

    International Nuclear Information System (INIS)

    Parveen, A.

    2009-01-01

    Trichomes morphology of the subfamily heliotropioideae (Boraginaceae representing by 18 spectes has been examined by light and scanning microscope. Within the subfamily Heliotropoideae trichomes are generally eglandular rarely glandular as in Heliotropium ohioglossum Boiss. Within the subfamily Heliotropoideae 1-celled unicellular and two celled uniseriate trichomes are observed. Shape of the trichomes usually comical with pointed tims and distinct trichomes base. However few species have indistinct trichome base. The data is significantly useful at specific and generic level within the subfamily Heliotropioideae. (author)

  2. Comparative Transcriptome Analysis Identifies Putative Genes Involved in the Biosynthesis of Xanthanolides in Xanthium strumarium L.

    OpenAIRE

    Li, Yuanjun; Gou, Junbo; Chen, Fangfang; Li, Changfu; Zhang, Yansheng

    2016-01-01

    Xanthium strumarium L. is a traditional Chinese herb belonging to the Asteraceae family. The major bioactive components of this plant are sesquiterpene lactones, which include the xanthanolides. To date, the biogenesis of xanthanolides, especiallytheir downstream pathway, remains largely unknown. In X. strumarium, xanthanolides primarily accumulate in its glandular trichomes. To identify putative gene candidates involved in the biosynthesis of xanthanolides, three X. strumarium transcriptomes...

  3. The foliar trichomes of Hypoestes aristata (Vahl) Sol. ex Roem. & Schult var aristata (Acanthaceae) a widespread medicinal plant species in tropical sub-Saharan Africa: with comments on its possible phylogenetic significance.

    Science.gov (United States)

    Bhatt, A; Naidoo, Y; Nicholas, A

    2010-01-01

    The micromorphology of foliar trichomes of Hypoestes aristata var. aristata was studied using stereo, light and scanning microscopy (SEM). This genus belongs to the advanced angiosperm family Acanthaceae, for which few micromorphological leaf studies exist. Results revealed both glandular and non-glandular trichomes, the latter being more abundant on leaf veins, particularly on the abaxial surface of very young leaves. With leaf maturity, the density of non-glandular trichomes decreased. Glandular trichomes were rare and of two types: long-stalked capitate and globose-like peltate trichomes. Capitate trichomes were observed only on the abaxial leaf surface, while peltate trichomes were distributed on both adaxial and abaxial leaf surfaces.

  4. Trichomes morphology in petals of some Acanthaceae species.

    Directory of Open Access Journals (Sweden)

    Muhammad Amirul Aiman Ahmad Juhari

    2014-12-01

    Full Text Available A preliminary taxonomic study was carried out on seven Acanthaceae species namely as Andrographis paniculata, Pseuderanthemum graciliflorum, P. carruthersii,  Asystasia gangetica ssp. micrantha, Ruellia repens, Justicia comata and J. betonica. The study was undertaken to    investigate the morphology of trichomes present on the surfaces of flower petal. The variations found in this study are in their types and density. Based on observation, two forms of trichomes are present in all species studies which are glandular and non-glandular trichomes. There are seven types of trichomes found in this study. Trichomes types are shown to have systematic significance that can be used to differentiate and identify certain Acanthaceae species studied. 

  5. Comparative Transcriptome Analysis Identifies Putative Genes Involved in the Biosynthesis of Xanthanolides in Xanthium strumarium L.

    Science.gov (United States)

    Li, Yuanjun; Gou, Junbo; Chen, Fangfang; Li, Changfu; Zhang, Yansheng

    2016-01-01

    Xanthium strumarium L. is a traditional Chinese herb belonging to the Asteraceae family. The major bioactive components of this plant are sesquiterpene lactones (STLs), which include the xanthanolides. To date, the biogenesis of xanthanolides, especially their downstream pathway, remains largely unknown. In X. strumarium, xanthanolides primarily accumulate in its glandular trichomes. To identify putative gene candidates involved in the biosynthesis of xanthanolides, three X. strumarium transcriptomes, which were derived from the young leaves of two different cultivars and the purified glandular trichomes from one of the cultivars, were constructed in this study. In total, 157 million clean reads were generated and assembled into 91,861 unigenes, of which 59,858 unigenes were successfully annotated. All the genes coding for known enzymes in the upstream pathway to the biosynthesis of xanthanolides were present in the X. strumarium transcriptomes. From a comparative analysis of the X. strumarium transcriptomes, this study identified a number of gene candidates that are putatively involved in the downstream pathway to the synthesis of xanthanolides, such as four unigenes encoding CYP71 P450s, 50 unigenes for dehydrogenases, and 27 genes for acetyltransferases. The possible functions of these four CYP71 candidates are extensively discussed. In addition, 116 transcription factors that are highly expressed in X. strumarium glandular trichomes were also identified. Their possible regulatory roles in the biosynthesis of STLs are discussed. The global transcriptomic data for X. strumarium should provide a valuable resource for further research into the biosynthesis of xanthanolides.

  6. Comparative Transcriptome Analysis Identifies Putative Genes Involved in the Biosynthesis of Xanthanolides in Xanthium strumarium L.

    Directory of Open Access Journals (Sweden)

    Yuanjun Li

    2016-08-01

    Full Text Available Xanthium strumarium L. is a traditional Chinese herb belonging to the Asteraceae family. The major bioactive components of this plant are sesquiterpene lactones, which include the xanthanolides. To date, the biogenesis of xanthanolides, especiallytheir downstream pathway, remains largely unknown. In X. strumarium, xanthanolides primarily accumulate in its glandular trichomes. To identify putative gene candidates involved in the biosynthesis of xanthanolides, three X. strumarium transcriptomes, which were derived from the young leaves of two different cultivars and the purified glandular trichomes from one of the cultivars, were constructed in this study. In total, 157 million clean reads were generated and assembled into 91,861 unigenes, of which 59,858 unigenes were successfully annotated. All the genes coding for known enzymes in the upstream pathway to the biosynthesis of xanthanolides were present in the X. strumarium transcriptomes. From a comparative analysis of the X. strumarium transcriptomes, this study identified a number of gene candidates that are putatively involved in the downstream pathway to the synthesis of xanthanolides, such as four unigenes encoding CYP71 P450s, 50 unigenes for dehydrogenases, and 27 genes for acetyltransferases. The possible functions of these four CYP71 candidates are extensively discussed. In addition, 116 transcription factors that were highly expressed in X. strumarium glandular trichomes were also identified. Their possible regulatory roles in the biosynthesis of sesquiterpene lactones are discussed. The global transcriptomic data for X. strumarium should provide a valuable resource for further research into the biosynthesis of xanthanolides.

  7. The hexanoyl-CoA precursor for cannabinoid biosynthesis is formed by an acyl-activating enzyme in Cannabis sativa trichomes.

    Science.gov (United States)

    Stout, Jake M; Boubakir, Zakia; Ambrose, Stephen J; Purves, Randy W; Page, Jonathan E

    2012-08-01

    The psychoactive and analgesic cannabinoids (e.g. Δ(9) -tetrahydrocannabinol (THC)) in Cannabis sativa are formed from the short-chain fatty acyl-coenzyme A (CoA) precursor hexanoyl-CoA. Cannabinoids are synthesized in glandular trichomes present mainly on female flowers. We quantified hexanoyl-CoA using LC-MS/MS and found levels of 15.5 pmol g(-1) fresh weight in female hemp flowers with lower amounts in leaves, stems and roots. This pattern parallels the accumulation of the end-product cannabinoid, cannabidiolic acid (CBDA). To search for the acyl-activating enzyme (AAE) that synthesizes hexanoyl-CoA from hexanoate, we analyzed the transcriptome of isolated glandular trichomes. We identified 11 unigenes that encoded putative AAEs including CsAAE1, which shows high transcript abundance in glandular trichomes. In vitro assays showed that recombinant CsAAE1 activates hexanoate and other short- and medium-chained fatty acids. This activity and the trichome-specific expression of CsAAE1 suggest that it is the hexanoyl-CoA synthetase that supplies the cannabinoid pathway. CsAAE3 encodes a peroxisomal enzyme that activates a variety of fatty acid substrates including hexanoate. Although phylogenetic analysis showed that CsAAE1 groups with peroxisomal AAEs, it lacked a peroxisome targeting sequence 1 (PTS1) and localized to the cytoplasm. We suggest that CsAAE1 may have been recruited to the cannabinoid pathway through the loss of its PTS1, thereby redirecting it to the cytoplasm. To probe the origin of hexanoate, we analyzed the trichome expressed sequence tag (EST) dataset for enzymes of fatty acid metabolism. The high abundance of transcripts that encode desaturases and a lipoxygenase suggests that hexanoate may be formed through a pathway that involves the oxygenation and breakdown of unsaturated fatty acids. © 2012 National Research Council of Canada. The Plant Journal © 2012 Blackwell Publishing Ltd.

  8. RNA sequencing on Solanum lycopersicum trichomes identifies transcription factors that activate terpene synthase promoters

    NARCIS (Netherlands)

    Spyropoulou, E.A.; Haring, M.A.; Schuurink, R.C.

    2014-01-01

    BACKGROUND: Glandular trichomes are production and storage organs of specialized metabolites such as terpenes, which play a role in the plant's defense system. The present study aimed to shed light on the regulation of terpene biosynthesis in Solanum lycopersicum trichomes by identification of

  9. The foliar trichomes of Hypoestes aristata (Vahl Sol. ex Roem. & Schult var aristata (Acanthaceae a widespread medicinal plant species in tropical sub-Saharan Africa: with comments on its possible phylogenetic significance

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    A Bhatt

    2010-01-01

    Full Text Available The micromorphology of foliar trichomes of Hypoestes aristata var. aristata was studied using stereo, light and scanning microscopy (SEM. This genus belongs to the advanced angiosperm family Acanthaceae, for which few micromorphological leaf studies exist. Results revealed both glandular and non-glandular trichomes, the latter being more abundant on leaf veins, particularly on the abaxial surface of very young leaves. With leaf maturity, the density of non-glandular trichomes decreased. Glandular trichomes were rare and of two types: long-stalked capitate and globose-like peltate trichomes. Capitate trichomes were observed only on the abaxial leaf surface, while peltate trichomes were distributed on both adaxial and abaxial leaf surfaces.

  10. Trichomes of Cannabis sativa as viewed with scanning electron microscope

    Energy Technology Data Exchange (ETDEWEB)

    Ledbetter, M C; Krikorian, A D

    1975-06-01

    Direct examination of fresh, unfixed and uncoated specimens from vegetative and floral parts of Cannabis sativa with the scanning electron microscope enables one to obtain a faithful representation of their surface morphology. The presence of two major types of trichomes has been confirmed: a glandular type comprising or terminating in a globoid structure, and a conically-shaped nonglandular type. Moreover, three or possibly four distinct glandular types can be distinguished: sessile globoid, small-stalked and large-stalked globoid, and a peltate type. The nonglandular trichomes can be distinguished by the nature of their surfaces: those with a warty surface, and those which are relatively smooth. The range of size and distribution, and the special features of all these types of trichomes are also provided.

  11. Analysis of cannabinoids in laser-microdissected trichomes of medicinal Cannabis sativa using LCMS and cryogenic NMR

    NARCIS (Netherlands)

    Happyana, Nizar; Agnolet, Sara; Muntendam, Remco; Van Dam, Annie; Schneider, Bernd; Kayser, Oliver

    Trichomes, especially the capitate-stalked glandular hairs, are well known as the main sites of cannabinoid and essential oil production of Cannabis sativa. In this study the distribution and density of various types of Cannabis sativa L trichomes, have been investigated by scanning electron

  12. Structural features of flower trichomes in drug eyebright (Euphrasia stricta D. Wolff EX J. F. Lehm.

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    Weronika Haratym

    2014-01-01

    Full Text Available Euphrasia stricta D. Wolff ex J. F. Lehm. (Orobanchaceae is a representative of plants that are widely used in folk medicine, phytomedicine, and homeopathy. The medicinal raw material derived from the drug eyebright is applied primarily in treatment of ophthalmic diseases. The investigations of trichomes in drug eyebright (Euphrasia stricta D. Wolff ex J. F. Lehm were conducted in 2010–2011. Using light microscopy and scanning electron microscopy, their location and morphological and anatomical features were identified. Three types of non-glandular trichomes were found: short unicellular, long 1–2 celled, and long 2-celled with wall ornamentation. Additionally, 7 types of glandular trichomes were found; these included: unicellular clavate, 2–3-celled clavate, capitate with a unicellular head and a 3-cel- led stalk, capitate with a unicellular head and a 2-celled stalk, capitate with a 2-celled head, conical papillae, and ribbon-like trichomes with wall thickening.

  13. Direct Analyses of Secondary Metabolites by Mass Spectrometry Imaging (MSI) from Sunflower (Helianthus annuus L.) Trichomes.

    Science.gov (United States)

    Brentan Silva, Denise; Aschenbrenner, Anna-Katharina; Lopes, Norberto Peporine; Spring, Otmar

    2017-05-10

    Helianthus annuus (sunflower) displays non-glandular trichomes (NGT), capitate glandular trichomes (CGT), and linear glandular trichomes (LGT), which reveal different chemical compositions and locations in different plant tissues. With matrix-assisted laser desorption/ionization (MALDI) and laser desorption/ionization (LDI) mass spectrometry imaging (MSI) techniques, efficient methods were developed to analyze the tissue distribution of secondary metabolites (flavonoids and sesquiterpenes) and proteins inside of trichomes. Herein, we analyzed sesquiterpene lactones, present in CGT, from leaf transversal sections using the matrix 2,5-dihydroxybenzoic acid (DHB) and α-cyano-4-hydroxycinnamic acid (CHCA) (mixture 1:1) with sodium ions added to increase the ionization in positive ion mode. The results observed for sesquiterpenes and polymethoxylated flavones from LGT were similar. However, upon desiccation, LGT changed their shape in the ionization source, complicating analyses by MSI mainly after matrix application. An alternative method could be applied to LGT regions by employing LDI (without matrix) in negative ion mode. The polymethoxylated flavones were easily ionized by LDI, producing images with higher resolution, but the sesquiterpenes were not observed in spectra. Thus, the application and viability of MALDI imaging for the analyses of protein and secondary metabolites inside trichomes were confirmed, highlighting the importance of optimization parameters.

  14. Micromorphology of glandular structures in Echium vulgare L. flowers

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    Elżbieta Weryszko-Chmielewska

    2012-12-01

    Full Text Available The micromorphology of selected elements of Echium vulgare L. flowers was investigated, with special attention to the structure of the nectaries and the stigma of the pistil as well as types of trichomes occurring on the surface of the calyx. The nectary had the shape of an uneven disc located around the lower region of the four-parted ovary of the pistil. The glandular cells formed a tier with a height of 330 μm and a radial width of 144 μm. Nectar was secreted onto the nectary surface through anomocytic stomata located at the level of other epidermal cells. Most of the stomata were open, with a different dimension of the pore. Their largest number was observed at the base of the nectary, and 462 stomata were noted on the whole surface of the nectary. The cuticle on the surface of the guard cells formed fine, circular striae. The subsidiary cells formed striated cuticular ornamentation, with the striae arranged radially in the direction of the stoma, whereas on the surface of other epidermal cells the striae formed an arrangement with different directions. The epidermis on the surface of the stigma formed regularly arranged papillae with a fan-shaped, expanded upper part which had corrugated outer walls, whereas the base of the cell formed a widened small column. The epidermis of the abaxial part of the calyx was covered by numerous non-glandular trichomes of different length which were made up of one or several cells. The glandular trichomes in the epidermis of the calyx grew with smaller density compared to the protective trichomes, and they were composed of a 1-2-celled stalk and a glandular head.

  15. Trichomes and chemical composition of the volatile oil of Trichogonia cinerea (Gardner) R. M. King & H. Rob. (Eupatorieae, Asteraceae).

    Science.gov (United States)

    Fernandes, Yanne S; Trindade, Luma M P; Rezende, Maria Helena; Paula, José R; Gonçalves, Letícia A

    2016-03-01

    Trichogonia cinerea is endemic to Brazil and occurs in areas of cerrado and campo rupestre. In this study, we characterized the glandular and non-glandular trichomes on the aerial parts of this species, determined the principal events in the development of the former, and identified the main constituents of the volatile oil produced in its aerial organs. Fully expanded leaves, internodes, florets, involucral bracts, and stem apices were used for the characterization of trichomes. Leaves, internodes, florets, and involucral bracts were examined by light microscopy and scanning electron microscopy, whereas stem apices were examined only by light microscopy. Branches in the reproductive phase were used for the extraction and determination of the composition of the volatile oil. The species has three types of glandular trichomes, biseriate vesicular, biseriate pedunculate, and multicellular uniseriate, which secrete volatile oils and phenolic compounds. The major components identified in the volatile oil were 3,5-muuroladiene (39.56%) and butylated hydroxytoluene (13.07%).

  16. Transcriptome

    Science.gov (United States)

    ... Also: Talking Glossary of Genetic Terms Definitions for genetic terms used on this page En Español: Transcriptoma Transcriptome What is a transcriptome? What can a transcriptome tell us? How can transcriptome data be used to explore gene function? What is ...

  17. Analysis of cannabinoids in laser-microdissected trichomes of medicinal Cannabis sativa using LCMS and cryogenic NMR.

    Science.gov (United States)

    Happyana, Nizar; Agnolet, Sara; Muntendam, Remco; Van Dam, Annie; Schneider, Bernd; Kayser, Oliver

    2013-03-01

    Trichomes, especially the capitate-stalked glandular hairs, are well known as the main sites of cannabinoid and essential oil production of Cannabis sativa. In this study the distribution and density of various types of Cannabis sativa L. trichomes, have been investigated by scanning electron microscopy (SEM). Furthermore, glandular trichomes were isolated over the flowering period (8 weeks) by laser microdissection (LMD) and the cannabinoid profile analyzed by LCMS. Cannabinoids were detected in extracts of 25-143 collected cells of capitate-sessile and capitate stalked trichomes and separately in the gland (head) and the stem of the latter. Δ(9)-Tetrahydrocannabinolic acid [THCA (1)], cannabidiolic acid [CBDA (2)], and cannabigerolic acid [CBGA (3)] were identified as most-abundant compounds in all analyzed samples while their decarboxylated derivatives, Δ(9)-tetrahydrocannabinol [THC (4)], cannabidiol [CBD (5)], and cannabigerol [CBG (6)], co-detected in all samples, were present at significantly lower levels. Cannabichromene [CBC (8)] along with cannabinol (CBN (9)) were identified as minor compounds only in the samples of intact capitate-stalked trichomes and their heads harvested from 8-week old plants. Cryogenic nuclear magnetic resonance spectroscopy (NMR) was used to confirm the occurrence of major cannabinoids, THCA (1) and CBDA (2), in capitate-stalked and capitate-sessile trichomes. Cryogenic NMR enabled the additional identification of cannabichromenic acid [CBCA (7)] in the dissected trichomes, which was not possible by LCMS as standard was not available. The hereby documented detection of metabolites in the stems of capitate-stalked trichomes indicates a complex biosynthesis and localization over the trichome cells forming the glandular secretion unit. Copyright © 2012 Elsevier Ltd. All rights reserved.

  18. Within and between generation phenotypic plasticity in trichome density of Mimulus guttatus.

    Science.gov (United States)

    Holeski, L M

    2007-11-01

    Mimulus guttatus (yellow monkeyflower) frequently produce glandular trichomes, a trait that may resist herbivory. Constitutive production of trichomes is variable both within and among populations of M. guttatus and most of this variation is genetic. This study demonstrates that damage on early leaves can induce increased trichome production on later leaves, a plastic response that is likely adaptive. Moreover, this study shows that this induction can be maternally transmitted, increasing trichome density in progeny before they experience herbivory. This transgenerational response must involve a yet undescribed epigenetic mechanism. These experiments also show genetic variation among plants in the capacity for both within and between plant generation induction. Despite the clear evolutionary importance of variation in constitutive and induced herbivory-resistance traits, few other studies have noted genetic variation in both within a plant species.

  19. Are trichomes involved in the biomechanical systems of Cucurbita leaf petioles?

    Science.gov (United States)

    Zajączkowska, Urszula; Kucharski, Stanisław; Guzek, Dominika

    2015-12-01

    Trichomes are involved in petiole movement and likely function as a part of the plant biomechanical system serving as an additional reservoir of hydrostatic pressure. The large, non-glandular trichomes on Cucurbita petioles occur across collenchyma strands. Time-lapse imaging was used to study the leaf reorientation of Cucurbita maxima 'Bambino' plants placed in horizontal position. The experiment comprised four variants of the large non-glandular petiole trichomes: (1) intact, (2) mechanically removed, (3) dehydrated, and (4) intact but with longitudinally injured petioles. Isolated strands of collenchyma with intact epidermis or epidermis mechanically removed from the abaxial and adaxial sides of the petiole were subjected to breaking test. The stiffness of the non-isolated tissue with intact epidermis was measured using the micro-indentation method. Petioles without trichomes did not exhibit tropic response, and the dehydration of trichomes slowed and prevented complete leaf reorientation. Isolated strands of collenchyma showed no correlation between strength values and position on the petiole. However, strands of collenchyma with epidermis exhibited a significantly greater strength regardless of their position on the petiole. The indentation test showed that non-isolated collenchyma is stiffer on the abaxial side of the petiole. Trichomes from the abaxial side of the petiole were larger at their base. The application of the 'tensile triangles method' revealed that these trichomes had a biomechanically optimized shape in comparison to the adaxial side. We conclude that trichomes can be involved in plant biomechanical system and serve as an additional reservoir of hydrostatic pressure that is necessary for maintaining petioles in the prestressed state.

  20. Petunia hybrida PDR2 is involved in herbivore defense by controlling steroidal contents in trichomes.

    Science.gov (United States)

    Sasse, Joëlle; Schlegel, Markus; Borghi, Lorenzo; Ullrich, Friederike; Lee, Miyoung; Liu, Guo-Wei; Giner, José-Luis; Kayser, Oliver; Bigler, Laurent; Martinoia, Enrico; Kretzschmar, Tobias

    2016-12-01

    As a first line of defense against insect herbivores many plants store high concentrations of toxic and deterrent secondary metabolites in glandular trichomes. Plant Pleiotropic Drug Resistance (PDR)-type ABC transporters are known secondary metabolite transporters, and several have been implicated in pathogen or herbivore defense. Here, we report on Petunia hybrida PhPDR2 as a major contributor to trichome-related chemical defense. PhPDR2 was found to localize to the plasma membrane and be predominantly expressed in multicellular glandular trichomes of leaves and stems. Down-regulation of PhPDR2 via RNA interference (pdr2) resulted in a markedly higher susceptibility of the transgenic plants to the generalist foliage feeder Spodoptera littoralis. Untargeted screening of pdr2 trichome metabolite contents showed a significant decrease in petuniasterone and petuniolide content, compounds, which had previously been shown to act as potent toxins against various insects. Our findings suggest that PhPDR2 plays a leading role in controlling petuniasterone levels in leaves and trichomes of petunia, thus contributing to herbivory resistance. © 2016 John Wiley & Sons Ltd.

  1. Characterization of Trichome-Expressed BAHD Acyltransferases in Petunia axillaris Reveals Distinct Acylsugar Assembly Mechanisms within the Solanaceae1[OPEN

    Science.gov (United States)

    Uebler, Joseph B.; Liu, Xiaoxiao

    2017-01-01

    Acylsugars are synthesized in the glandular trichomes of the Solanaceae family and are implicated in protection against abiotic and biotic stress. Acylsugars are composed of either sucrose or glucose esterified with varying numbers of acyl chains of differing length. In tomato (Solanum lycopersicum), acylsugar assembly requires four acylsugar acyltransferases (ASATs) of the BAHD superfamily. Tomato ASATs catalyze the sequential esterification of acyl-coenzyme A thioesters to the R4, R3, R3ʹ, and R2 positions of sucrose, yielding a tetra-acylsucrose. Petunia spp. synthesize acylsugars that are structurally distinct from those of tomato. To explore the mechanisms underlying this chemical diversity, a Petunia axillaris transcriptome was mined for trichome preferentially expressed BAHDs. A combination of phylogenetic analyses, gene silencing, and biochemical analyses coupled with structural elucidation of metabolites revealed that acylsugar assembly is not conserved between tomato and petunia. In P. axillaris, tetra-acylsucrose assembly occurs through the action of four ASATs, which catalyze sequential addition of acyl groups to the R2, R4, R3, and R6 positions. Notably, in P. axillaris, PaxASAT1 and PaxASAT4 catalyze the acylation of the R2 and R6 positions of sucrose, respectively, and no clear orthologs exist in tomato. Similarly, petunia acylsugars lack an acyl group at the R3ʹ position, and congruently, an ortholog of SlASAT3, which catalyzes acylation at the R3ʹ position in tomato, is absent in P. axillaris. Furthermore, where putative orthologous relationships of ASATs are predicted between tomato and petunia, these are not supported by biochemical assays. Overall, these data demonstrate the considerable evolutionary plasticity of acylsugar biosynthesis. PMID:28701351

  2. Characterization of Trichome-Expressed BAHD Acyltransferases in Petunia axillaris Reveals Distinct Acylsugar Assembly Mechanisms within the Solanaceae.

    Science.gov (United States)

    Nadakuduti, Satya Swathi; Uebler, Joseph B; Liu, Xiaoxiao; Jones, A Daniel; Barry, Cornelius S

    2017-09-01

    Acylsugars are synthesized in the glandular trichomes of the Solanaceae family and are implicated in protection against abiotic and biotic stress. Acylsugars are composed of either sucrose or glucose esterified with varying numbers of acyl chains of differing length. In tomato ( Solanum lycopersicum ), acylsugar assembly requires four acylsugar acyltransferases (ASATs) of the BAHD superfamily. Tomato ASATs catalyze the sequential esterification of acyl-coenzyme A thioesters to the R4, R3, R3', and R2 positions of sucrose, yielding a tetra-acylsucrose. Petunia spp. synthesize acylsugars that are structurally distinct from those of tomato. To explore the mechanisms underlying this chemical diversity, a Petunia axillaris transcriptome was mined for trichome preferentially expressed BAHDs. A combination of phylogenetic analyses, gene silencing, and biochemical analyses coupled with structural elucidation of metabolites revealed that acylsugar assembly is not conserved between tomato and petunia. In P. axillaris , tetra-acylsucrose assembly occurs through the action of four ASATs, which catalyze sequential addition of acyl groups to the R2, R4, R3, and R6 positions. Notably, in P. axillaris , PaxASAT1 and PaxASAT4 catalyze the acylation of the R2 and R6 positions of sucrose, respectively, and no clear orthologs exist in tomato. Similarly, petunia acylsugars lack an acyl group at the R3' position, and congruently, an ortholog of SlASAT3, which catalyzes acylation at the R3' position in tomato, is absent in P. axillaris Furthermore, where putative orthologous relationships of ASATs are predicted between tomato and petunia, these are not supported by biochemical assays. Overall, these data demonstrate the considerable evolutionary plasticity of acylsugar biosynthesis. © 2017 American Society of Plant Biologists. All Rights Reserved.

  3. Influence of growth regulators on distribution of trichomes and the production of volatiles in micropropagated plants of Plectranthus ornatus

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    Helna C. Passinho-Soares

    Full Text Available ABSTRACT The profile of volatile organic compounds, the glandular and non-glandular trichomes of Plectranthus ornatus, obtained by in vitro cultivation, was evaluated in plants grown in Murashide and Skoog medium supplemented with benylaminopurine at 4.5, 9.0, and 18.0 µM + naphthaleneacetic acid at 5.37 µM, kinetin at 4.7, 9.3 and 18.5 µM + naphthaleneacetic acid (5.37 µM or Murashide and Skoog 0 medium (as a control. Scanning Electron Microscopy was performed on samples of the third leaf node of the 90 days old plants obtained from treatment with 4.5 or 9.0 µM benylaminopurine, and 4.7 or 9.3 µM kinetin. Headspace Solid Phase Micro-Extraction of the 30, 60 and 90 days old in vitro plants permitted to determinate by GC/MS the composition comprised of 62 compounds. The data were analyzed using Principal Component Analysis and Hierarchical Clustering Analysis and, the major constituents of these oils after treatment and aging were monoterpenes and sesquiterpenes. Morphoanatomical analysis of trichomes, by Scanning Electron Microscopy, enabled the identification of non-glandular trichomes and four types of glandular trichomes, which comprised capitate and peltate glandular trichomes that were distributed on both sides of the leaf. We observed that the regulators influenced qualitative and quantitative profiles of the volatile organic compounds and the number and distribution of hairs on the leaf surface.

  4. Estimating average glandular dose by measuring glandular rate in mammograms

    International Nuclear Information System (INIS)

    Goto, Sachiko; Azuma, Yoshiharu; Sumimoto, Tetsuhiro; Eiho, Shigeru

    2003-01-01

    The glandular rate of the breast was objectively measured in order to calculate individual patient exposure dose (average glandular dose) in mammography. By employing image processing techniques and breast-equivalent phantoms with various glandular rate values, a conversion curve for pixel value to glandular rate can be determined by a neural network. Accordingly, the pixel values in clinical mammograms can be converted to the glandular rate value for each pixel. The individual average glandular dose can therefore be calculated using the individual glandular rates on the basis of the dosimetry method employed for quality control in mammography. In the present study, a data set of 100 craniocaudal mammograms from 50 patients was used to evaluate our method. The average glandular rate and average glandular dose of the data set were 41.2% and 1.79 mGy, respectively. The error in calculating the individual glandular rate can be estimated to be less than ±3%. When the calculation error of the glandular rate is taken into consideration, the error in the individual average glandular dose can be estimated to be 13% or less. We feel that our method for determining the glandular rate from mammograms is useful for minimizing subjectivity in the evaluation of patient breast composition. (author)

  5. Evolution of oil-producing trichomes in Sisyrinchium (Iridaceae): insights from the first comprehensive phylogenetic analysis of the genus

    Science.gov (United States)

    Chauveau, Olivier; Eggers, Lilian; Raquin, Christian; Silvério, Adriano; Brown, Spencer; Couloux, Arnaud; Cruaud, Corine; Kaltchuk-Santos, Eliane; Yockteng, Roxana; Souza-Chies, Tatiana T.; Nadot, Sophie

    2011-01-01

    Background and Aims Sisyrinchium (Iridaceae: Iridoideae: Sisyrinchieae) is one of the largest, most widespread and most taxonomically complex genera in Iridaceae, with all species except one native to the American continent. Phylogenetic relationships within the genus were investigated and the evolution of oil-producing structures related to specialized oil-bee pollination examined. Methods Phylogenetic analyses based on eight molecular markers obtained from 101 Sisyrinchium accessions representing 85 species were conducted in the first extensive phylogenetic analysis of the genus. Total evidence analyses confirmed the monophyly of the genus and retrieved nine major clades weakly connected to the subdivisions previously recognized. The resulting phylogenetic hypothesis was used to reconstruct biogeographical patterns, and to trace the evolutionary origin of glandular trichomes present in the flowers of several species. Key Results and Conclusions Glandular trichomes evolved three times independently in the genus. In two cases, these glandular trichomes are oil-secreting, suggesting that the corresponding flowers might be pollinated by oil-bees. Biogeographical patterns indicate expansions from Central America and the northern Andes to the subandean ranges between Chile and Argentina and to the extended area of the Paraná river basin. The distribution of oil-flower species across the phylogenetic trees suggests that oil-producing trichomes may have played a key role in the diversification of the genus, a hypothesis that requires future testing. PMID:21527419

  6. Analyzing trichomes and spatio-temporal expression of a cysteine protease gene Mucunain in Mucuna pruriens L. (DC).

    Science.gov (United States)

    Singh, Susheel Kumar; Dhawan, Sunita Singh

    2018-03-01

    Mucuna pruriens is a well-known legume for the itching attributes of the trichome and a valuable medicinal herb that is used for the treatment of Parkinson's disease, sexual debilities, etc. Its cultivation was deprived due to its itching behavior. The wild genotype of M. pruriens have the largest trichome length (2015 ± 29 μm) compared to other genotype and mutants. The white-seeded variety of M. pruriens was found to be the most suitable for large-scale cultivation due to the small trichome size and less trichome density on the pod. The external surface trichomes have protuberance with unknown function. The unicellular trichomes of Mucuna show the flowing fluid or cytoplasm inside the trichome. The unigenes regulating the differentiation and development of the trichome such as GLABRA-1, GLABRA-2, and cpr-5 have been identified in M. pruriens transcriptome of the leaf. The Mucunain shows a higher transcript abundance in the flower and pod cover compared to the seeds. The Mucunain was found in every stage of plant growth, but it was highly expressed during maturity (about 170 days) with a high fragment per kilobase per million value.

  7. Trichome morphology in Teucrium L. (Labiatae. A taxonomic review

    Directory of Open Access Journals (Sweden)

    Navarro, Teresa

    1999-12-01

    Full Text Available The micromorphology of trichomes of 56 Teucrium L. species belonging to the 9 sections of the genus in the Mediterranean área was surveyed by scanning electrón microscopy (SEM of leaves, calyx, corolla and nutlets. 25 trichome types are described, 12 of them are new. Thin walled hairs are the exclusive type found in the corolla and are the most widespread type on the abaxial side of the leaves. Subsessile glandular hairs, 2-4-celled, are found on the nutlet and leaves of the semi-shrubby and paleoendemic species. The presence of short or elongated, generally adpressed simple thick-walled slighüy conical hairs provides an additional character to clarify the boundaries between sect. Chamedrys (Mill. Schreb, and sect. Polium (Mill. Schreb. Branched non-glandular hairs are confined to sect. Polium subsect Polium, except for the rare branched hair conical and thick-walled type found in Teucrium barbarum Jahand. & Maire (sect. Chamaedrys and T. heterophyllum L`Hér. from sect. Teucrium. This last section is well defined by the absence of simple slighüy conical thick-walled hairs and the glandular hairs in the corolla. Sect. Teucriopsis Benth, is of particular interest for the exclusive presence of branched and peltate glandular hairs on the nutlets surface. Sect. Chamedrys is a homogeneous group, distinguished from the other sections by an indumentum formed only by trichomes types evolved from the simple slighüy conical thick-walled hairs. This section overlaps, in the presence of glandular sub-sessile hair on the nutlets surface, with sects. Isotriodon Boiss, and sect. Polium subsect. Rotundifolia Cohén ex Valdés Berm. & Sánchez Crespo. The trichomes type of the calyx teeth, abaxial side of the leaf and latero-posterior corolla lobes can be used as a distinctive taxonomic character at specific and infra-specific level. This study supports Bentham's delimitaüon of sections with the addiüons subequently made by Boissier.La micromorfología de

  8. Trichomes and chemical composition of the volatile oil of Trichogonia cinerea (Gardner R. M. King & H. Rob. (Eupatorieae, Asteraceae

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    YANNE S. FERNANDES

    2016-03-01

    Full Text Available Trichogonia cinerea is endemic to Brazil and occurs in areas of cerrado and campo rupestre. In this study, we characterized the glandular and non-glandular trichomes on the aerial parts of this species, determined the principal events in the development of the former, and identified the main constituents of the volatile oil produced in its aerial organs. Fully expanded leaves, internodes, florets, involucral bracts, and stem apices were used for the characterization of trichomes. Leaves, internodes, florets, and involucral bracts were examined by light microscopy and scanning electron microscopy, whereas stem apices were examined only by light microscopy. Branches in the reproductive phase were used for the extraction and determination of the composition of the volatile oil. The species has three types of glandular trichomes, biseriate vesicular, biseriate pedunculate, and multicellular uniseriate, which secrete volatile oils and phenolic compounds. The major components identified in the volatile oil were 3,5-muuroladiene (39.56% and butylated hydroxytoluene (13.07%.

  9. Light affects Varronia curassavica essential oil yield by increasing trichomes frequency

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    Emily V.R. da S. Feijó

    Full Text Available Light can act on essential oil yield directly on synthesis of secondary metabolites, or indirectly on plant growth. Varronia curassavica Jacq., Boraginaceae, is a native medicinal species from Brazil known as “erva-baleeira”, with anti-inflammatory activity related to its essential oil. Despite pharmacological evidences of this species and its economic importance for herbal medicine production, little is known about the effect of light on growth and essential oil production. This study aimed to analyze the influence of different irradiances on growth, frequency of trichomes, essential oil yield and composition of V. curassavica. The irradiance affected plant growth, but no significant alteration on leaf biomass was detected. The increase in essential oil content under higher irradiance reflected on essential oil yield, and is associated with higher frequency of glandular, globular trichomes. The essential oil composition, rich in caryophyllene derivatives was affected by irradiance, but α-humulene, the constituent of pharmaceutical interest, remained unchanged.

  10. Seed trichome variation in Hibiscus section Furcaria in East Africa ...

    African Journals Online (AJOL)

    The micromorphology of the seed trichomes in Hibiscus section Furcaria in Tropical East Africa was surveyed. The structure of the trichomes was found to be unique for each species examined, where such trichomes are present. Seed trichomes of specimens of H. altissimus Horny from the Kenya and Tanzania coasts were ...

  11. Are leaf glandular trichomes of oregano hospitable habitats for bacterial growth?

    Science.gov (United States)

    Karamanoli, K; Thalassinos, G; Karpouzas, D; Bosabalidis, A M; Vokou, D; Constantinidou, H-I

    2012-05-01

    Phyllospheric bacteria were isolated from microsites around essential-oil-containing glands of two oregano (Origanum vulgare subsp. hirtum) lines. These bacteria, 20 isolates in total, were subjected to bioassays to examine their growth potential in the presence of essential oils at different concentrations. Although there were qualitative and quantitative differences in the essential oil composition between the two oregano lines, no differences were recorded in their antibacterial activity. In disk diffusion bioassays, four of the isolated strains could grow almost unrestrained in the presence of oregano oil, another five proved very sensitive, and the remaining 11 showed intermediate sensitivity. The strain least inhibited by oregano essential oil was further identified by complete16s rRNA gene sequencing as Pseudomonas putida. It was capable of forming biofilms even in the presence of oregano oil at high concentrations. Resistance of P. putida to oregano oil was further elaborated by microwell dilution bioassays, and its topology on oregano leaves was studied by electron microscopy. When inoculated on intact oregano plants, P. putida was able not only to colonize sites adjacent to essential oil-containing glands, but even to grow intracellularly. This is the first time that such prolific bacterial growth inside the glands has been visually observed. Results of this study further revealed that several bacteria can be established on oregano leaves, suggesting that these bacteria have attributes that allow them to tolerate or benefit from oregano secondary metabolites.

  12. Monitoring Metabolite Profiles of Cannabis sativa L. Trichomes during Flowering Period Using 1H NMR-Based Metabolomics and Real-Time PCR.

    Science.gov (United States)

    Happyana, Nizar; Kayser, Oliver

    2016-08-01

    Cannabis sativa trichomes are glandular structures predominantly responsible for the biosynthesis of cannabinoids, the biologically active compounds unique to this plant. To the best of our knowledge, most metabolomic works on C. sativa that have been reported previously focused their investigations on the flowers and leaves of this plant. In this study, (1)H NMR-based metabolomics and real-time PCR analysis were applied for monitoring the metabolite profiles of C. sativa trichomes, variety Bediol, during the last 4 weeks of the flowering period. Partial least squares discriminant analysis models successfully classified metabolites of the trichomes based on the harvest time. Δ (9)-Tetrahydrocannabinolic acid (1) and cannabidiolic acid (2) constituted the vital differential components of the organic preparations, while asparagine, glutamine, fructose, and glucose proved to be their water-extracted counterparts. According to RT-PCR analysis, gene expression levels of olivetol synthase and olivetolic acid cyclase influenced the accumulation of cannabinoids in the Cannabis trichomes during the monitoring time. Moreover, quantitative (1)H NMR and RT-PCR analysis of the Cannabis trichomes suggested that the gene regulation of cannabinoid biosynthesis in the C. sativa variety Bediol is unique when compared with other C. sativa varieties. Georg Thieme Verlag KG Stuttgart · New York.

  13. Quantification of variability in trichome patterns

    Directory of Open Access Journals (Sweden)

    Bettina eGreese

    2014-11-01

    Full Text Available While pattern formation is studied in various areas of biology, little is known about the intrinsic noise leading to variations between individual realizations of the pattern. One prominent example for de novo pattern formation in plants is the patterning of trichomes on Arabidopsis leaves, which involves genetic regulation and cell-to-cell communication. These processes are potentially variable due to , e.g., the abundance of cell components or environmental conditions. To elevate the understanding of the regulatory processes underlying the pattern formation it is crucial to quantitatively analyze the variability in naturally occurring patterns. Here, we review recent approaches towards characterization of noise on trichome initiation. We present methods for the quantification of spatial patterns, which are the basis for data-driven mathematical modeling and enable the analysis of noise from different sources. Besides the insight gained on trichome formation, the examination of observed trichome patterns also shows that highly regulated biological processes can be substantially affected by variability.

  14. Regulation of trichome development in tobacco by JcZFP8, a C2H2 zinc finger protein gene from Jatropha curcas L.

    Science.gov (United States)

    Shi, Xiaodong; Gu, Yuxi; Dai, Tingwei; Wu, Yang; Wu, Peng; Xu, Ying; Chen, Fang

    2018-06-05

    Trichomes are epidermal outgrowths of plant tissues that can secrete or store large quantities of secondary metabolites, which contribute to plant defense responses against stress. The use of bioengineering methods for regulating the development of trichomes and metabolism is a widely researched topic. In the present study, we demonstrate that JcZFP8, a C2H2 zinc finger protein gene from Jatropha curcas L., can regulate trichome development in transgenic tobacco. To understand the underlying mechanisms, we performed transcriptome profiling of overexpression JcZFP8 transgenic plants and wild-type tobacco. Based on the analysis of differentially expressed genes, we determined that genes of the plant hormone signal transduction pathway was significantly enriched, suggesting that these pathways were modulated in the transgenic plants. In addition, the transcript levels of the known trichome-related genes in Arabidopsis were not significantly changed, whereas CycB2 and MYB genes were differentially expressed in the transgenic plants. Despite tobacco and Arabidopsis have different types of trichomes, all the pathways were associated with C2H2 zinc finger protein genes. Our findings help us to understand the regulation of multicellular trichome formation and suggest a new metabolic engineering method for the improvement of plants. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Evolution of a flipped pathway creates metabolic innovation in tomato trichomes through BAHD enzyme promiscuity.

    Science.gov (United States)

    Fan, Pengxiang; Miller, Abigail M; Liu, Xiaoxiao; Jones, A Daniel; Last, Robert L

    2017-12-12

    Plants produce hundreds of thousands of structurally diverse specialized metabolites via multistep biosynthetic networks, including compounds of ecological and therapeutic importance. These pathways are restricted to specific plant groups, and are excellent systems for understanding metabolic evolution. Tomato and other plants in the nightshade family synthesize protective acylated sugars in the tip cells of glandular trichomes on stems and leaves. We describe a metabolic innovation in wild tomato species that contributes to acylsucrose structural diversity. A small number of amino acid changes in two acylsucrose acyltransferases alter their acyl acceptor preferences, resulting in reversal of their order of reaction and increased product diversity. This study demonstrates how small numbers of amino acid changes in multiple pathway enzymes can lead to diversification of specialized metabolites in plants. It also highlights the power of a combined genetic, genomic and in vitro biochemical approach to identify the evolutionary mechanisms leading to metabolic novelty.

  16. Trichomes: different regulatory networks lead to convergent structures.

    Science.gov (United States)

    Serna, Laura; Martin, Cathie

    2006-06-01

    Sometimes, proteins, biological structures or even organisms have similar functions and appearances but have evolved through widely divergent pathways. There is experimental evidence to suggest that different developmental pathways have converged to produce similar outgrowths of the aerial plant epidermis, referred to as trichomes. The emerging picture suggests that trichomes in Arabidopsis thaliana and, perhaps, in cotton develop through a transcriptional regulatory network that differs from those regulating trichome formation in Antirrhinum and Solanaceous species. Several lines of evidence suggest that the duplication of a gene controlling anthocyanin production and subsequent divergence might be the major force driving trichome formation in Arabidopsis, whereas the multicellular trichomes of Antirrhinum and Solanaceous species appear to have a different regulatory origin.

  17. Immunohistochemical characterization of glandular elements in glandular cardiac myxoma: Study of six cases

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    Devajit Nath

    2017-01-01

    Full Text Available Back ground: Glandular cardiac myxoma has varying clinical presentation with uncertain histogenesis and debatable immunohistochemical profile. Glandular epithelial differentiations are rare phenomenon known to be present as an intrinsic component of the tumor. The origin of the glands has been attributed to epithelial differentiation of a totipotent cardiomyogenic precursor cells or the entrapped foregut rests in the tumor. Materials and Methods: Retrospective study includes six cases of glandular cardiac myxoma collected over a perior of 4 years. Sections were examined to define the histogenesis, histological and immunohistochemical profile of the glandular elements. Results: Incidence of glandular cardiac myxoma was 6.6% with a male to female ratio of 1:2.Mean age was 49.9 years. Left atrium was the commonest site. Five were sporadic and one was familial. Chest pain and dyspnea were the commonest clinical symptoms. Histologically all myxoma showed well formed glandular structures with typical myxomatous area. No atypia, mitosis or necrosis was identified in the glandular elements. Markers in six cases of glandular cardiac myxoma were immunopositive for CK7, CK 19, EMA, CEA, focally for E-cadherin while immunonegative for CK20, Chromogranin, Synaptophysin, calretenin, vimentin, B-catenin, TTF-1 and GCDFP-15 favoring enteric differentiation. Conclusion: Glandular cardiac myxoma is a rare entity which shows characteristics similar to those of classical cardiac myxoma with benign glandular elements showing enteric differentiation. Complete surgical excision is the treatment of choice with good prognosis. It is important to recognize this entity to avoid an erroneous diagnosis of metastatic adenocarcinoma.

  18. Characterization of two genes for the biosynthesis of abietane-type diterpenes in rosemary (Rosmarinus officinalis) glandular trichomes

    NARCIS (Netherlands)

    Brückner, K.; Bozic, D.; Manzano, D.; Papaefthimiou, D.; Pateraki, I.; Scheler, U.; Ferrer, A.; Vos, de R.C.H.; Kanellis, A.K.; Tissier, A.

    2014-01-01

    Rosemary (Rosmarinus officinalis) produces the phenolic diterpenes carnosic acid and carnosol, which, in addition to their general antioxidant activities, have recently been suggested as potential ingredients for the prevention and treatment of neurodegenerative diseases. Little is known about the

  19. Foliar trichomes, boundary layers, and gas exchange in 12 species of epiphytic Tillandsia (Bromeliaceae).

    Science.gov (United States)

    Benz, Brett W; Martin, Craig E

    2006-04-01

    We examined the relationships between H2O and CO2 gas exchange parameters and leaf trichome cover in 12 species of Tillandsia that exhibit a wide range in trichome size and trichome cover. Previous investigations have hypothesized that trichomes function to enhance boundary layers around Tillandsioid leaves thereby buffering the evaporative demand of the atmosphere and retarding transpirational water loss. Data presented herein suggest that trichome-enhanced boundary layers have negligible effects on Tillandsia gas exchange, as indicated by the lack of statistically significant relationships in regression analyses of gas exchange parameters and trichome cover. We calculated trichome and leaf boundary layer components, and their associated effects on H2O and CO2 gas exchange. The results further indicate trichome-enhanced boundary layers do not significantly reduce transpirational water loss. We conclude that although the trichomes undoubtedly increase the thickness of the boundary layer, the increase due to Tillandsioid trichomes is inconsequential in terms of whole leaf boundary layers, and any associated reduction in transpirational water loss is also negligible within the whole plant gas exchange pathway.

  20. Elimination of salmonella from animal glandular products.

    Science.gov (United States)

    De Fiebre, C W; Burck, K T; Feldman, D

    1969-03-01

    Methods for the elimination of salmonellae from selected powdered pharmaceuticals of animal glandular origin were studied. Terminal heat treatment under carefully controlled conditions was effective for pancreatin-a powder containing proteolytic, amylolytic, and lipolytic enzymes prepared from hog pancreas glands. Use of this method resulted in a significant reduction in the number of salmonella-positive batches and also reduced the testing procedures required to confirm the absence of viable salmonellae among the majority of samples tested. Powders such as stomach substance and thyroid, in which the biological activity is not enzyme in nature, were treated successfully with acidified organic solvents. Other methods were investigated but were not suitable because of a deleterious effect on the biological activity or physical properties of the product or an inability to effect salmonella elimination.

  1. Elimination of Salmonellae from Animal Glandular Products

    Science.gov (United States)

    De Fiebre, Conrad W.; Burck, Kenneth T.; Feldman, David

    1969-01-01

    Methods for the elimination of salmonellae from selected powdered pharmaceuticals of animal glandular origin were studied. Terminal heat treatment under carefully controlled conditions was effective for pancreatin—a powder containing proteolytic, amylolytic, and lipolytic enzymes prepared from hog pancreas glands. Use of this method resulted in a significant reduction in the number of salmonella-positive batches and also reduced the testing procedures required to confirm the absence of viable salmonellae among the majority of samples tested. Powders such as stomach substance and thyroid, in which the biological activity is not enzyme in nature, were treated successfully with acidified organic solvents. Other methods were investigated but were not suitable because of a deleterious effect on the biological activity or physical properties of the product or an inability to effect salmonella elimination. PMID:5780395

  2. Glandular odontogenic cyst: A case report

    International Nuclear Information System (INIS)

    Tambawaia, Shahnaz S.; Karjodkar, Freny R.; Yadav, Archana; Sansare, Kaustubh; Sontakke, Subodh

    2014-01-01

    Glandular odontogenic cysts (GOCs) are rare intrabony solitary or multiloculated cysts of odontogenic origin. The importance of GOCs lies in the fact that they exhibit a propensity for recurrence similar to keratocystic odontogenic tumors and that they may be confused microscopically with central mucoepidermoid carcinoma. Thus, the oral and maxillofacial radiologists play an important role in definitive diagnosis of GOC based on distinctive cases; though they are rare. In large part, this is due to the GOC's complex and frequently non-specific histopathology. This report describes a case of GOC occurrence in the posterior mandibular ramus region in a 17-year-old female, which is a rare combination of site, age, and gender for occurrence.

  3. Glandular odontogenic cyst: A case report

    Energy Technology Data Exchange (ETDEWEB)

    Tambawaia, Shahnaz S.; Karjodkar, Freny R.; Yadav, Archana; Sansare, Kaustubh; Sontakke, Subodh [Nair Hospital Dental College, Mumbai (India)

    2014-03-15

    Glandular odontogenic cysts (GOCs) are rare intrabony solitary or multiloculated cysts of odontogenic origin. The importance of GOCs lies in the fact that they exhibit a propensity for recurrence similar to keratocystic odontogenic tumors and that they may be confused microscopically with central mucoepidermoid carcinoma. Thus, the oral and maxillofacial radiologists play an important role in definitive diagnosis of GOC based on distinctive cases; though they are rare. In large part, this is due to the GOC's complex and frequently non-specific histopathology. This report describes a case of GOC occurrence in the posterior mandibular ramus region in a 17-year-old female, which is a rare combination of site, age, and gender for occurrence.

  4. Control of trichome branching by Chromatin Assembly Factor-1

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    Hennig Lars

    2008-05-01

    Full Text Available Abstract Background Chromatin dynamics and stability are both required to control normal development of multicellular organisms. Chromatin assembly factor CAF-1 is a histone chaperone that facilitates chromatin formation and the maintenance of specific chromatin states. In plants and animals CAF-1 is essential for normal development, but it is poorly understood which developmental pathways require CAF-1 function. Results Mutations in all three CAF-1 subunits affect Arabidopsis trichome morphology and lack of CAF-1 function results in formation of trichomes with supernumerary branches. This phenotype can be partially alleviated by external sucrose. In contrast, other aspects of the CAF-1 mutant phenotype, such as defective meristem function and organ formation, are aggravated by external sucrose. Double mutant analyses revealed epistatic interactions between CAF-1 mutants and stichel, but non-epistatic interactions between CAF-1 mutants and glabra3 and kaktus. In addition, mutations in CAF-1 could partly suppress the strong overbranching and polyploidization phenotype of kaktus mutants. Conclusion CAF-1 is required for cell differentiation and regulates trichome development together with STICHEL in an endoreduplication-independent pathway. This function of CAF-1 can be partially substituted by application of exogenous sucrose. Finally, CAF-1 is also needed for the high degree of endoreduplication in kaktus mutants and thus for the realization of kaktus' extreme overbranching phenotype.

  5. Variation in vegetative growth and trichomes in Cannabis sativa L. (Marihuana) in response to enviromental pollution

    Energy Technology Data Exchange (ETDEWEB)

    Sharma, G.K.; Mann, S.K.

    1984-07-01

    Four populations of Cannabis sativa L. (marihuana) growing in their native habitat and exposed to different levels of environmental pollution were studied for several leaf morphology and leaf trichome features. Leaf length, petiole length, length and width of central leaflet, and the number of teeth on leaf margin decreased with increase in pollution. Trichome length and trichome density values were found to be higher in populations exposed to higher levels of environmental pollution.

  6. An overview of the gene regulatory network controlling trichome development in the model plant, Arabidopsis

    Directory of Open Access Journals (Sweden)

    Sitakanta ePattanaik

    2014-06-01

    Full Text Available Trichomes are specialized epidermal cells located on aerial parts of plants and are associated with a wide array of biological processes. Trichomes protect plants from adverse conditions including UV light and herbivore attack and are also an important source of a number of phytochemicals. The simple unicellular trichomes of Arabidopsis serve as an excellent model to study molecular mechanism of cell differentiation and pattern formation in plants. The emerging picture suggests that the developmental process is controlled by a transcriptional network involving three major groups of transcription factors: the R2R3 MYB, basic helix-loop-helix (bHLH and WD40 repeat (WDR protein. These regulatory proteins form a trimeric activator complex that positively regulates trichome development. The single repeat R3 MYBs act as negative regulators of trichome development. They compete with the R2R3 MYBs to bind the bHLH factor and form a repressor complex. In addition to activator-repressor mechanism, a depletion mechanism may operate in parallel during trichome development. In this mechanism, the bHLH factor traps the WDR protein which results in depletion of WDR protein in neighboring cells. Consequently, the cells with high levels of bHLH and WDR proteins are developed into trichomes. A group of C2H2 zinc finger TFs has also been implicated in trichome development. Phytohormones, including gibberellins and jasmonic acid, play significant roles in this developmental process. Recently, microRNAs have been shown to be involved in trichome development. Furthermore, it has been demonstrated that the activities of the key regulatory proteins involved in trichome development are controlled by the 26S/ubiquitin proteasome system (UPS, highlighting the complexity of the regulatory network controlling this developmental process. To complement several excellent recent relevant reviews, this review focuses on the transcriptional network and hormonal interplay

  7. Genetic evidence suggests that GIS functions downstream of TCL1 to regulate trichome formation in Arabidopsis.

    Science.gov (United States)

    Zhang, Na; Yang, Li; Luo, Sha; Wang, Xutong; Wang, Wei; Cheng, Yuxin; Tian, Hainan; Zheng, Kaijie; Cai, Ling; Wang, Shucai

    2018-04-13

    Trichome formation in Arabidopsis is regulated by a MBW complex formed by MYB, bHLH and WD40 transcriptional factors, which can activate GLABRA2 (GL2) and the R3 MYB transcription factor genes. GL2 promotes trichome formation, whereas R3 MYBs are able to block the formation of the MBW complex. It has been reported that the C2H2 transcription factor GIS (GLABROUS INFLORESCENCE STEMS) functions upstream of the MBW activator complex to regulate trichome formation, and that the expression of TCL1 is not regulated by the MBW complex. However, gis and the R3 MYB gene mutant tcl1 (trichomeless 1) have opposite inflorescence trichome phenotypes, but their relationship in regulating trichome formation remained unknown. By generating and characterization of the gis tcl1 double mutant, we found that trichome formation in the gis tcl1double and the tcl1 single mutants were largely indistinguishable, but the trichome formation in the 35S:TCL1/gis transgenic plant was similar to that in the gis mutant. By using quantitative RT-PCR analysis, we showed that expression level of GIS was increased in the triple mutant tcl1 try cpc, but the expression level of TCL1 was not affected in the gis mutant. On the other hand, trichome morphology in both gis tcl1 and 35S:TCL1/gis plants was similar to that in the gis mutant. In summary, our results indicate that GIS may work downstream of TCL1 to regulate trichome formation, and GIS has a dominant role in controlling trichome morphology.

  8. Evaluation of exposure in mammography: limitations of average glandular dose and proposal of a new quantity

    International Nuclear Information System (INIS)

    Geeraert, N.; Bosmans, H.; Klausz, R.; Muller, S.; Bloch, I.

    2015-01-01

    The radiation risk in mammography is traditionally evaluated using the average glandular dose. This quantity for the average breast has proven to be useful for population statistics and to compare exposure techniques and systems. However it is not indicating the individual radiation risk based on the individual glandular amount and distribution. Simulations of exposures were performed for six appropriate virtual phantoms with varying glandular amount and distribution. The individualised average glandular dose (iAGD), i.e. the individual glandular absorbed energy divided by the mass of the gland, and the glandular imparted energy (GIE), i.e. the glandular absorbed energy, were computed. Both quantities were evaluated for their capability to take into account the glandular amount and distribution. As expected, the results have demonstrated that iAGD reflects only the distribution, while GIE reflects both the glandular amount and distribution. Therefore GIE is a good candidate for individual radiation risk assessment. (authors)

  9. GLABROUS INFLORESCENCE STEMS (GIS) is required for trichome branching through gibberellic acid signaling in Arabidopsis.

    Science.gov (United States)

    An, Lijun; Zhou, Zhongjing; Su, Sha; Yan, An; Gan, Yinbo

    2012-02-01

    Cell differentiation generally corresponds to the cell cycle, typically forming a non-dividing cell with a unique differentiated morphology, and Arabidopsis trichome is an excellent model system to study all aspects of cell differentiation. Although gibberellic acid is reported to be involved in trichome branching in Arabidopsis, the mechanism for such signaling is unclear. Here, we demonstrated that GLABROUS INFLORESCENCE STEMS (GIS) is required for the control of trichome branching through gibberellic acid signaling. The phenotypes of a loss-of-function gis mutant and an overexpressor showed that GIS acted as a repressor to control trichome branching. Our results also show that GIS is not required for cell endoreduplication, and our molecular and genetic study results have shown that GIS functions downstream of the key regulator of trichome branching, STICHEL (STI), to control trichome branching through the endoreduplication-independent pathway. Furthermore, our results also suggest that GIS controls trichome branching in Arabidopsis through two different pathways and acts either upstream or downstream of the negative regulator of gibbellic acid signaling SPINDLY (SPY).

  10. Interactive Effects of Jasmonic Acid, Salicylic Acid, and Gibberellin on Induction of Trichomes in Arabidopsis1

    Science.gov (United States)

    Traw, M. Brian; Bergelson, Joy

    2003-01-01

    Leaf trichomes protect plants from attack by insect herbivores and are often induced following damage. Hormonal regulation of this plant induction response has not been previously studied. In a series of experiments, we addressed the effects of artificial damage, jasmonic acid, salicylic acid, and gibberellin on induction of trichomes in Arabidopsis. Artificial damage and jasmonic acid caused significant increases in trichome production of leaves. The jar1-1 mutant exhibited normal trichome induction following treatment with jasmonic acid, suggesting that adenylation of jasmonic acid is not necessary. Salicylic acid had a negative effect on trichome production and consistently reduced the effect of jasmonic acid, suggesting negative cross-talk between the jasmonate and salicylate-dependent defense pathways. Interestingly, the effect of salicylic acid persisted in the nim1-1 mutant, suggesting that the Npr1/Nim1 gene is not downstream of salicylic acid in the negative regulation of trichome production. Last, we found that gibberellin and jasmonic acid had a synergistic effect on the induction of trichomes, suggesting important interactions between these two compounds. PMID:14551332

  11. Papillae formation on trichome cell walls requires the function of the mediator complex subunit Med25.

    Science.gov (United States)

    Fornero, Christy; Suo, Bangxia; Zahde, Mais; Juveland, Katelyn; Kirik, Viktor

    2017-11-01

    Glassy Hair 1 (GLH1) gene that promotes papillae formation on trichome cell walls was identified as a subunit of the transcriptional mediator complex MED25. The MED25 gene is shown to be expressed in trichomes. The expression of the trichome development marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) is not affected in the glh1 mutant. Presented data suggest that Arabidopsis MED25 mediator component is likely involved in the transcription of genes promoting papillae deposition in trichomes. The plant cell wall plays an important role in communication, defense, organization and support. The importance of each of these functions varies by cell type. Specialized cells, such as Arabidopsis trichomes, exhibit distinct cell wall characteristics including papillae. To better understand the molecular processes important for papillae deposition on the cell wall surface, we identified the GLASSY HAIR 1 (GLH1) gene, which is necessary for papillae formation. We found that a splice-site mutation in the component of the transcriptional mediator complex MED25 gene is responsible for the near papillae-less phenotype of the glh1 mutant. The MED25 gene is expressed in trichomes. Reporters for trichome developmental marker genes GLABRA2 (GL2) and Ethylene Receptor2 (ETR2) were not affected in the glh1 mutant. Collectively, the presented results show that MED25 is necessary for papillae formation on the cell wall surface of leaf trichomes and suggest that the Arabidopsis MED25 mediator component is likely involved in the transcription of a subset of genes that promote papillae deposition in trichomes.

  12. Average glandular dose in patients submitted to mammographic examinations

    International Nuclear Information System (INIS)

    Nogueira, M.S.; Silva, T.A. da; Oliveira, M. de; Joana, G.S.; Oliveira, A.L.K.

    2008-01-01

    Doses in mammography should be maintained as low as possible without reducing the high image quality needed to the early detection of the breast cancer. As the breast is composed of tissues with very soft composition and densities, it increases the difficulty to detect small changes in the normal anatomical structures that may be associated with breast cancer. To achieve the standards of resolution and contrast for mammography, the quality and intensity of the X-ray beam, the breast positioning and compression, the film screen system, and the film processing must be in optimal operational conditions. This study intended to evaluate the mean glandular dose of patients undergoing routine exams in one mammography unit. Patient image analyses were done by a radiologist doctor who took into account 10 evaluation criteria for each CC and MLO incidences. For estimating each patient glandular dose the radiographic technique parameters (kV and mAs) and the thickness of the compressed breast were recorded. European image quality criteria were adopted by the radiologist doctor to accept the image for diagnostic purpose. For breast densities of 50% adipose and 50% glandular tissues the incident air-kerma was measured and the glandular dose calculated considering the x-ray output during the exam. In the study of 50 patients the mean glandular dose varied from 0.90 to 3.27 mGy with a mean value of 1.98 mGy for CC incidences. For MLO incidences the mean glandular doses ranged from 0.97 to 3.98 mGy and a mean value of 2.60 mGy. (author)

  13. Evaluation of glandular dose in conventional and digital mammography systems

    International Nuclear Information System (INIS)

    Coutinho, Celia Maria Campos

    2009-01-01

    A survey was conducted to estimate the average glandular dose (D g ) for patients undergoing mammography and to report the distribution of incident air kerma (K i ), patient age, compressed breast thickness and glandular tissue content. From 1183 cranio caudal mammograms clinical data were collected and doses were measured. The survey data included mammograms from six mammography equipment: two screen/film units (SFM), two computed radiography units (CR) and two full-field digital (DR). Mean value for patient age and compressed breast thickness were 57 +-12 y and 5.4 +-1.4 cm, respectively. To investigate the importance of technical characteristics of three different mammography systems and breast glandularity, K i and D g were measured for individual breast of 392 patients from the original sample with compressed breast thickness in the range of 5.5 cm to 6.5 cm using tissue-equivalent phantoms of different glandularities manufactured in this study to mimic both the attenuation and the density of breast tissues. Mean K i value was 10.0 +-3.6 mGy for SFM systems, 12.0 +-3.6 mGy for CR systems and 4.9 +-1.3 mGy for DR systems. Mean D g value was 1.4 +-0.5 mGy for S/F systems, 1.7 +-0.5 mGy for CR systems and 0.9 +-0.2 mGy for D R systems. Statistical analysis for differences in mean values of K i and D g between mammography systems showed significant effect of their technical characteristics (p i and D g , it was observed statistically significant differences between the group of patients with 0 to 50% glandularity and the group of patients with 50 to 100% glandularity. (author)

  14. Boomeranging in structural defense: phytophagous insect uses cycad trichomes to defend against entomophagy.

    Science.gov (United States)

    Marler, Thomas E

    2012-11-01

    Plant defensive behaviors that resist arthropod herbivory include trichome-mediated defenses, and variation in plant trichome morphology and abundance provides examples of the mechanistic complexities of insect-plant interactions. Trichomes were removed from Cycas revoluta cataphylls on the island of Guam to reveal Aulacaspis yasumatsui scale infestation, and predation of the newly exposed insects by pre-existing Rhyzobius lophanthae beetles commenced within one day. The quotient of predated/total scale insects was 0.5 by day 4 and stabilized at that found on adjacent glabrous leaves in about one week. The trichome phenotype covering the C. revoluta cataphyll complex offers the invasive A. yasumatsui armored scale effectual enemy-free space in this system. This pest and predator share no known evolutionary history with C. revoluta, therefore, the adaptive significance of this plant behavior in natural habitat is not yet known.

  15. Biosynthesis of a new tobacco alkaloid, hydroxy-N-acylnornicotine in the trichomes of Nicotiana stocktonii

    International Nuclear Information System (INIS)

    Zador, E.; Jones, D.

    1986-01-01

    A new tobacco alkaloid from section Repandae is highly toxic to an insect (Manduca sexta) unsusceptible to previously described nicotine alkaloids (1). They have localized the alkaloid, HO-N-acylnornicotine (HO-NAN) nearly entirely to the exudate secreted by the epidermal trichomes of N. stocktonii. Only the nicotine and nornicotine were found in abundance inside the trichomes, while primarily nicotine was present inside the aerial vegetative parts and root. These results suggest that the HO-NAN is synthesized by the trichomes. When unlabelled nicotine was fed to isolated leaves there was an increase in internal nicotine, nornicotine and secretion of HO-NAN. Feeding leaves with 2'-C 14 nicotine resulted in labelling of both nornicotine and HO-NAN. These data strongly suggest synthesis of HO-NAN from nicotine via nornicotine in the trichomes, followed by rapid secretion. The possible evolutionary significance of this pathway of synthesis and secretion is discussed

  16. Trichomes that secrete substances of a mixed nature in the vegetative and reproductive organs of some species of Moraceae

    Directory of Open Access Journals (Sweden)

    Bruna Noce Schnetzler

    Full Text Available ABSTRACT This study aimed to obtain new information about the distribution, morphology and content of secretory trichomes present in the vegetative and reproductive organs of four species of Moraceae: Artocarpus heterophyllus, Dorstenia cayapia, Maclura tinctoria and Sorocea bonplandii. Stem, leaf, flower and inflorescence samples were processed for scanning electron and light microscopy. The species have secretory trichomes on the leaf blade, petiole and stem and also on the inflorescence and flowers of D. cayapia and S. bonplandii and on the peduncle of the inflorescence in A. heterophyllus. These trichomes are of the capitate type in all species, but A. heterophyllus also possess peltate secretory trichomes. Both trichome types exhibit a multicellular head and a unicellular peduncle. Peduncle size and head cell number varies according to species. Peltate trichomes located in depressions were found only in species of Artocarpus, and so should be of diagnostic value for the genus. In all species the trichomes secrete polysaccharides, alkaloids and lipids; phenolic compounds occur in A. heterophyllus and M. tinctoria trichomes. These trichomes probably act in the protection against herbivores, pathogens, desiccation and/ or UV radiation. Moreover, the trichomes found in the inflorescence of D. cayapia may exert a function in pollen grain adhesion.

  17. Herbivore handling of a plant's trichome: the case of Heliconius charithonia (L.) (Lepidoptera: Nymphalidae) and Passiflora lobata (Killip) Hutch. (Passifloraceae)

    International Nuclear Information System (INIS)

    Cardoso, Marcio Z.

    2008-01-01

    Trichomes reduce herbivore attack on plants by physically and/or chemically inhibiting movement or other activities. Despite evidence that herbivores are negatively affected by trichomes there also reports of insect counter-adaptations that circumvent the plant's defense. This paper reports on a study that investigated the likely mechanisms employed by larvae of the nymphalid butterfly, Heliconius charithonia (L.), that allow it to feed on a host that is presumably protected by hooked trichomes (Passiflora lobata (Killip) Hutch). Evidence were gathered using data from direct observations of larval movement and behavior, faeces analysis, scanning electron microscopy of plant surface and experimental analysis of larval movement on plants with and without trichomes (manually removed). The latter involved a comparison with a non specialist congener, Heliconius pachinus Salvin. Observations showed that H. charithonia larvae are capable of freeing themselves from entrapment on trichome tips by physical force. Moreover, wandering larvae lay silk mats on the trichomes and remove their tips by biting. In fact, trichome tips were found in the faeces. Experimental removal of trichomes aided in the movement of the non specialist but had no noticeable effect on the specialist larvae. These results support the suggestion that trichomes are capable of deterring a non specialist herbivore (H. pachinus). The precise mechanisms that allow the success of H. charithonia are not known, but I suggest that a blend of behavioral as well as physical resistance mechanisms is involved. Future studies should ascertain whether larval integument provides physical resistance to trichomes. (author)

  18. Comparative Transcriptomics Unravel Biochemical Specialization of Leaf Tissues of Stevia for Diterpenoid Production1

    Science.gov (United States)

    Kim, Mi Jung; Jin, Jingjing; Zheng, Junshi

    2015-01-01

    Stevia (Stevia rebaudiana) produces not only a group of diterpenoid glycosides known as steviol glycosides (SGs), but also other labdane-type diterpenoids that may be spatially separated from SGs. However, their biosynthetic routes and spatial distribution in leaf tissues have not yet been elucidated. Here, we integrate metabolome and transcriptome analyses of Stevia to explore the biosynthetic capacity of leaf tissues for diterpenoid metabolism. Tissue-specific chemical analyses confirmed that SGs were accumulated in leaf cells but not in trichomes. On the other hand, Stevia leaf trichomes stored other labdane-type diterpenoids such as oxomanoyl oxide and agatholic acid. RNA sequencing analyses from two different tissues of Stevia provided a comprehensive overview of dynamic metabolic activities in trichomes and leaf without trichomes. These metabolite-guided transcriptomics and phylogenetic and gene expression analyses clearly identified specific gene members encoding enzymes involved in the 2-C-methyl-d-erythritol 4-phosphate pathway and the biosynthesis of steviol or other labdane-type diterpenoids. Additionally, our RNA sequencing analysis uncovered copalyl diphosphate synthase (SrCPS) and kaurene synthase1 (SrKS1) homologs, SrCPS2 and KS-like (SrKSL), which were specifically expressed in trichomes. In vitro and in planta assays showed that unlike SrCPS and SrKS1, SrCPS2 synthesized labda-13-en-8-ol diphosphate and successively catalyzed the formation of manoyl oxide and epi-manoyl oxide in combination with SrKSL. Our findings suggest that Stevia may have evolved to use distinct metabolic pathways to avoid metabolic interferences in leaf tissues for efficient production of diverse secondary metabolites. PMID:26438788

  19. Comparative Transcriptomics Unravel Biochemical Specialization of Leaf Tissues of Stevia for Diterpenoid Production.

    Science.gov (United States)

    Kim, Mi Jung; Jin, Jingjing; Zheng, Junshi; Wong, Limsoon; Chua, Nam-Hai; Jang, In-Cheol

    2015-12-01

    Stevia (Stevia rebaudiana) produces not only a group of diterpenoid glycosides known as steviol glycosides (SGs), but also other labdane-type diterpenoids that may be spatially separated from SGs. However, their biosynthetic routes and spatial distribution in leaf tissues have not yet been elucidated. Here, we integrate metabolome and transcriptome analyses of Stevia to explore the biosynthetic capacity of leaf tissues for diterpenoid metabolism. Tissue-specific chemical analyses confirmed that SGs were accumulated in leaf cells but not in trichomes. On the other hand, Stevia leaf trichomes stored other labdane-type diterpenoids such as oxomanoyl oxide and agatholic acid. RNA sequencing analyses from two different tissues of Stevia provided a comprehensive overview of dynamic metabolic activities in trichomes and leaf without trichomes. These metabolite-guided transcriptomics and phylogenetic and gene expression analyses clearly identified specific gene members encoding enzymes involved in the 2-C-methyl-d-erythritol 4-phosphate pathway and the biosynthesis of steviol or other labdane-type diterpenoids. Additionally, our RNA sequencing analysis uncovered copalyl diphosphate synthase (SrCPS) and kaurene synthase1 (SrKS1) homologs, SrCPS2 and KS-like (SrKSL), which were specifically expressed in trichomes. In vitro and in planta assays showed that unlike SrCPS and SrKS1, SrCPS2 synthesized labda-13-en-8-ol diphosphate and successively catalyzed the formation of manoyl oxide and epi-manoyl oxide in combination with SrKSL. Our findings suggest that Stevia may have evolved to use distinct metabolic pathways to avoid metabolic interferences in leaf tissues for efficient production of diverse secondary metabolites. © 2015 American Society of Plant Biologists. All Rights Reserved.

  20. Characterization of two genes for the biosynthesis of abietane-type diterpenes in rosemary (Rosmarinus officinalis) glandular trichomes

    DEFF Research Database (Denmark)

    Brückner, Kathleen; Božić, Dragana; Manzano, David

    2014-01-01

    normal CDP to produce an abietane diterpene. Comparison to the already characterized diterpene synthase from Salvia miltiorrhiza (SmKSL) demonstrates that the product of RoKSL1 and RoKSL2 is miltiradiene. Expression analysis supports a major contributing role for RoKSL2. Like SmKSL and the sclareol...... synthase from Salvia sclarea, RoKSL1/2 are diterpene synthases of the TPS-e group which have lost the internal gamma-domain. Furthermore, phylogenetic analysis indicates that RoKSL1 and RoKSL2 belong to a distinct group of KSL enzymes involved in specialized metabolism which most likely emerged before...

  1. Maxilary glandular odontogenic cyst: case report = Cisto odontogênico glandular em maxila: relato de caso

    Directory of Open Access Journals (Sweden)

    Cardoso, Juliana Andrade

    2015-01-01

    Full Text Available Objetivo: O presente trabalho objetiva relatar um caso clínico de cisto odontogênico glandular (COG em maxila, cisto de desenvolvimento raro que pode apresentar comportamento agressivo e recidivante, dando ênfase no tratamento e proservação desta doença. Relato de Caso: Paciente faioderma, gênero feminino, 36 anos, foi encaminhada pelo Ortodontista por apresentar aumento de volume em maxila com abaulamento e crepitação. Foram realizadas radiografias e punção aspirativa. Uma vez observado o conteúdo da lesão, foi realizada a biópsia incisional e iniciada a descompressão com colocação de dreno rígido. Tendo a confirmação do diagnóstico para COG, a paciente foi submetida à cirurgia para remoção do cisto maxilar, através da enucleação cirúrgica, curetagem e osteotomia periférica. Conclusões: O COG é uma patologia incomum, recentemente reconhecida, cujo comportamento biológico pouco ainda se sabe. Sugere-se, portanto, a realização de investigações futuras sobre critérios para classificação de variáveis comumente utilizadas em estudos epidemiológicos, na tentativa de padronizar e possibilitar comparação entre estudos, todavia, para auxiliar em um diagnóstico bem sucedido

  2. Development of an excel spreadsheet formean glandular dose in mammography

    International Nuclear Information System (INIS)

    Nagoshi, Kazuyo; Fujisaki, Tatsuya

    2008-01-01

    The purpose of this study was to develop an Excel spreadsheet to calculate mean glandular dose (D g ) in mammography using clinical exposure data. D g can be calculated as the product of incident air kerma (K a ) and D gN (i.e., D g =K a x D gN ). According to the method of Klein et al (Phys Med Biol 1997; 42: 651-671), K a was measured at the entrance surface with an ionization dosimeter. Normalized glandular dose (D gN ) coefficients, taking into account breast glandularity, were computed using Boone's method (Med Phys 2002; 29: 869-875). D gN coefficients can be calculated for any arbitrary X-ray spectrum. These calculation procedures were input into a Microsoft Excel spreadsheet. The resulting Excel spreadsheet is easy to use and is always applicable in the field of mammography. The exposure conditions concerning D g in clinical practice were also investigated in 22 women. Four exposure conditions (target/filter combination and tube voltage) were automatically selected in this study. This investigation found that average D g for each exposure was 1.9 mGy. Because it is recommended that quality control of radiation dose management in mammography is done using an American College of Radiology (ACR) phantom, information about patient dose is not obtained in many facilities. The present Excel spreadsheet was accordingly considered useful for optimization of exposure conditions and explanation of mammography to patients. (author)

  3. The study of mean glandular dose in mammography in Yazd and the factors affecting it

    International Nuclear Information System (INIS)

    Bouzarjomehri, F.; Mostaar, A.; Ghasemi, A.; Ehramposh, M. H.; Khosravi, H.

    2006-01-01

    The objective of this study was to determine the mean glandular dose resulting from mammography examinations in Yazd, southeastern Iran and to identify the factors affecting it. Patients and Methods: This survey was conducted during May to December 2005 to estimate the mean glandular dose for women undergoing mammography and to report the distribution of dose. compressed breast thickness, glandular tissue content, and mammography technique used. The clinical data were collected from 946 mammograms taken from 246 women who were referred to four mammography centers. The mammography instruments in these centers were four modern units with a molybdenum anode and either molybdenum or rhodium filter. The exposure conditions of each mammogram were recorded. The breast glandular content of each mammogram was estimated by a radiologist. The mean glandular dose was calculated based on measuring the normalized entrance skin dose in air. half value layer, kVp, mAs, breast thickness and glandular content. Half value layer, kVp and entrance skin dose were measured by a solid-state detector. The analytical method of Sobol et al. was used for calculation of mean glandular dose . Results: The mean±SD mean glandular dose per film was.2±0.6 mGy for cranio caudal and 1.63±O.9 mGy for mediolateral oblique views. The mean±SD mean glandular dose per woman was 5.5 3.1.mGy. A positive correlation was found between the beam Half value layer with mean glandular dose (r=O.38) and the breast thickness with mean glandular dose (r=O.5). Conclusion: The mean±SD mean glandular dose per film of 1.42±0.8 mGy in present study was lower than most of similar reports. However, the mean mean glandular dose per woman was higher than that in other studies

  4. A new quantitative classification of ecological types in the bromeliad genus Tillandsia (Bromeliaceae) based on trichomes.

    Science.gov (United States)

    Stefano, Mosti; Papini, Alessio; Brighigna, Luigi

    2008-03-01

    Using collection specimens, we measured the density and wing area of trichomes in 37 species of the bromeliad genus Tillandsia, specifically the abaxial proximal, abaxial distal, adaxial proximal and adaxial distal parts of the leaf. The product of the trichome "wing" area by the number of trichomes (means) produced a pure number (T) that was correlated to ecological features. The correlation was positive with respect to arid environments (xeric Tillands) and negative with respect to humid environments (mesic Tillands). Bulbous, and particularly myrmecophytic species and species with tanks, represented particular categories. Other intermediate types were identified based on the T number, totalling five ecological types. In comparison with other systems of ecological typification for Tillands and other Bromeliaceae, the present system offers measurable data whose analysis is reproducible.

  5. Comparison of Five Major Trichome Regulatory Genes in Brassica villosa with Orthologues within the Brassicaceae

    Science.gov (United States)

    Nayidu, Naghabushana K.; Kagale, Sateesh; Taheri, Ali; Withana-Gamage, Thushan S.; Parkin, Isobel A. P.; Sharpe, Andrew G.; Gruber, Margaret Y.

    2014-01-01

    Coding sequences for major trichome regulatory genes, including the positive regulators GLABRA 1(GL1), GLABRA 2 (GL2), ENHANCER OF GLABRA 3 (EGL3), and TRANSPARENT TESTA GLABRA 1 (TTG1) and the negative regulator TRIPTYCHON (TRY), were cloned from wild Brassica villosa, which is characterized by dense trichome coverage over most of the plant. Transcript (FPKM) levels from RNA sequencing indicated much higher expression of the GL2 and TTG1 regulatory genes in B. villosa leaves compared with expression levels of GL1 and EGL3 genes in either B. villosa or the reference genome species, glabrous B. oleracea; however, cotyledon TTG1 expression was high in both species. RNA sequencing and Q-PCR also revealed an unusual expression pattern for the negative regulators TRY and CPC, which were much more highly expressed in trichome-rich B. villosa leaves than in glabrous B. oleracea leaves and in glabrous cotyledons from both species. The B. villosa TRY expression pattern also contrasted with TRY expression patterns in two diploid Brassica species, and with the Arabidopsis model for expression of negative regulators of trichome development. Further unique sequence polymorphisms, protein characteristics, and gene evolution studies highlighted specific amino acids in GL1 and GL2 coding sequences that distinguished glabrous species from hairy species and several variants that were specific for each B. villosa gene. Positive selection was observed for GL1 between hairy and non-hairy plants, and as expected the origin of the four expressed positive trichome regulatory genes in B. villosa was predicted to be from B. oleracea. In particular the unpredicted expression patterns for TRY and CPC in B. villosa suggest additional characterization is needed to determine the function of the expanded families of trichome regulatory genes in more complex polyploid species within the Brassicaceae. PMID:24755905

  6. Botulinum toxin for treatment of glandular hypersecretory disorders.

    LENUS (Irish Health Repository)

    Laing, T A

    2012-02-03

    SUMMARY: The use of botulinum toxin to treat disorders of the salivary glands is increasing in popularity in recent years. Recent reports of the use of botulinum toxin in glandular hypersecretion suggest overall favourable results with minimal side-effects. However, few randomised clinical trials means that data are limited with respect to candidate suitability, treatment dosages, frequency and duration of treatment. We report a selection of such cases from our own department managed with botulinum toxin and review the current data on use of the toxin to treat salivary gland disorders such as Frey\\'s syndrome, excessive salivation (sialorrhoea), focal and general hyperhidrosis, excessive lacrimation and chronic rhinitis.

  7. Method for determination of the mean fraction of glandular tissue in individual female breasts using mammography

    International Nuclear Information System (INIS)

    Jansen, J T M; Veldkamp, W J H; Thijssen, M A O; Woudenberg, S van; Zoetelief, J

    2005-01-01

    The nationwide breast cancer screening programme using mammography has been in full operation in the Netherlands since 1997. Quality control of the screening programme has been assigned to the National Expert and Training Centre for Breast Cancer Screening. Limits are set to the mean glandular dose and the centre monitors these for all facilities engaged in the screening programme. This procedure is restricted to the determination of the entrance dose on a 5 cm thick polymethylmethacrylate (PMMA) phantom. The mean glandular dose for a compressed breast is estimated from these data. Individual breasts may deviate largely from this 5 cm PMMA breast model. Not only may the compressed breast size vary from 2 to 10 cm, but breast composition varies also. The mean glandular dose is dependent on the fraction of glandular tissue (glandularity) of the breast. To estimate the risk related to individual mammograms requires the development of a method for determination of the glandularity of individual breasts. A method has been developed to derive the glandularity using the attenuation of mammography x-rays in the breast. The method was applied to a series of mammograms at a screening unit. The results, i.e., a glandularity of 93% within the range of 0 to 1, were comparable with data in the literature. The glandularity as a function of compressed breast thickness is similar to results from other investigators using differing methods

  8. Comparative genetic analysis of trichome-less and normal pod genotypes of Mucuna pruriens (Fabaceae).

    Science.gov (United States)

    Dhawan, S S; Rai, G K; Darokar, M P; Lal, R K; Misra, H O; Khanuja, S P S

    2011-09-15

    Velvet bean (Mucuna pruriens) seeds contain the catecholic amino acid L-DoPA (L-3,4-dihydroxyphenylalanine), which is a neurotransmitter precursor and used for the treatment of Parkinson's disease and mental disorders. The great demand for L-DoPA is largely met by the pharmaceutical industry through extraction of the compound from wild populations of this plant; commercial exploitation of this compound is hampered because of its limited availability. The trichomes present on the pods can cause severe itching, blisters and dermatitis, discouraging cultivation. We screened genetic stocks of velvet bean for the trichome-less trait, along with high seed yield and L-DoPA content. The highest yielding trichome-less elite strain was selected and indentified on the basis of a PCR-based DNA fingerprinting method (RAPD), using deca-nucleotide primers. A genetic similarity index matrix was obtained through multivariant analysis using Nei and Li's coefficient. The similarity coefficients were used to generate a tree for cluster analysis using the UPGMA method. Analysis of amplification spectra of 408 bands obtained with 56 primers allowed us to distinguish a trichome-less elite strain of M. pruriens.

  9. Lima bean – lady beetle interactions: hooked trichomes affect survival of Stethorus punctillum larvae

    Science.gov (United States)

    We tested the hypothesis that Lima bean Phaseolus lunatus L. (Henderson cultivar) trichome density affects the survival of the acariphagous lady beetle Stethorus punctillum Weise. When isolated throughout larval development, 10% or less of S. punctillum larvae reared on two-spotted spider mite Tetr...

  10. Expression of β-glucosidase increases trichome density and artemisinin content in transgenic Artemisia annua plants.

    Science.gov (United States)

    Singh, Nameirakpam Dolendro; Kumar, Shashi; Daniell, Henry

    2016-03-01

    Artemisinin is highly effective against multidrug-resistant strains of Plasmodium falciparum, the aetiological agent of the most severe form of malaria. However, a low level of accumulation of artemisinin in Artemisia annua is a major limitation for its production and delivery to malaria endemic areas of the world. While several strategies to enhance artemisinin have been extensively explored, enhancing storage capacity in trichome has not yet been considered. Therefore, trichome density was increased with the expression of β-glucosidase (bgl1) gene in A. annua through Agrobacterium-mediated transformation. Transgene (bgl1) integration and transcript were confirmed by molecular analysis. Trichome density increased up to 20% in leaves and 66% in flowers of BGL1 transgenic plants than Artemisia control plants. High-performance liquid chromatography, time of flight mass spectrometer data showed that artemisinin content increased up to 1.4% in leaf and 2.56% in flowers (per g DW), similar to the highest yields achieved so far through metabolic engineering. Artemisinin was enhanced up to five-fold in BGL1 transgenic flowers. This study opens the possibility of increasing artemisinin content by manipulating trichomes' density, which is a major reservoir of artemisinin. Combining biosynthetic pathway engineering with enhancing trichome density may further increase artemisinin yield in A. annua. Because oral feeding of Artemisia plant cells reduced parasitemia more efficiently than the purified drug, reduced drug resistance and cost of prohibitively expensive purification process, enhanced expression should play a key role in making this valuable drug affordable to treat malaria in a large global population that disproportionally impacts low-socioeconomic areas and underprivileged children. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

  11. Expression of Beta-glucosidase increases trichome density and artemisinin content in transgenic Artemisia annua plants

    Science.gov (United States)

    Singh, Nameirakpam Dolendro; Kumar, Shashi; Daniell, Henry

    2015-01-01

    Artemisinin is highly effective against multidrug-resistant strains of Plasmodium falciparum, the etiological agent of the most severe form of malaria. However, a low level of accumulation of artemisinin in Artemisia annua is a major limitation for its production and delivery to malaria endemic areas of the world. While several strategies to enhance artemisinin have been extensively explored, enhancing storage capacity in trichome has not yet been considered. Therefore, trichome density was increased with the expression of β glucosidase (bgl1) gene in A. annua through Agrobacterium-mediated transformation. Transgene (bgl1) integration and transcript was confirmed by molecular analysis. Trichome density increased up to 20% in leaves and 66% in flowers of BGL1 transgenic plants than Artemisia control plants. High-performance liquid chromatography (HPLC, MS-TOF) data showed that artemisinin content increased up to 1.4% in leaf and 2.56% in flowers (g-1DW), similar to the highest yields achieved so far through metabolic engineering. Artemisinin was enhanced up to 5-fold in BGL1 transgenic flowers. The present study opens the possibility of increasing artemisinin content by manipulating trichomes density, which is a major reservoir of artemisinin. Combining biosynthetic pathway engineering with enhancing trichome density may further increase artemisinin yield in A. annua. Because oral feeding of Artemisia plant cells reduced parasitemia more efficiently than the purified drug, reduced drug resistance and cost of prohibitively expensive purification process, enhanced expression should play a key role in making this valuable drug affordable to treat malaria in a large global population that disproportionally impacts low-socioeconomic areas and underprivileged children. PMID:26360801

  12. Glandular dose in breast tomosynthesis examinations: Preliminary study with a sample of patients; Dosis glandular en examenes de tomosintesis de mama: estudio preliminar con una muestra de pacientes

    Energy Technology Data Exchange (ETDEWEB)

    Castillo, M.; Chevalier, M.; Calzado, A.; Valverde, J.

    2013-07-01

    The aim of this study is to analyze the mean glandular dose administered to a group of patients with a tomography system (Selenia Dimensions) service installed on a large hospital in which routine tests are done and screening. (Author)

  13. Average glandular dose in digital mammography and breast tomosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Olgar, T. [Ankara Univ. (Turkey). Dept. of Engineering Physics; Universitaetsklinikum Leipzig AoeR (Germany). Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie; Kahn, T.; Gosch, D. [Universitaetsklinikum Leipzig AoeR (Germany). Klinik und Poliklinik fuer Diagnostische und Interventionelle Radiologie

    2012-10-15

    Purpose: To determine the average glandular dose (AGD) in digital full-field mammography (2 D imaging mode) and in breast tomosynthesis (3 D imaging mode). Materials and Methods: Using the method described by Boone, the AGD was calculated from the exposure parameters of 2247 conventional 2 D mammograms and 984 mammograms in 3 D imaging mode of 641 patients examined with the digital mammographic system Hologic Selenia Dimensions. The breast glandular tissue content was estimated by the Hologic R2 Quantra automated volumetric breast density measurement tool for each patient from right craniocaudal (RCC) and left craniocaudal (LCC) images in 2 D imaging mode. Results: The mean compressed breast thickness (CBT) was 52.7 mm for craniocaudal (CC) and 56.0 mm for mediolateral oblique (MLO) views. The mean percentage of breast glandular tissue content was 18.0 % and 17.4 % for RCC and LCC projections, respectively. The mean AGD values in 2 D imaging mode per exposure for the standard breast were 1.57 mGy and 1.66 mGy, while the mean AGD values after correction for real breast composition were 1.82 mGy and 1.94 mGy for CC and MLO views, respectively. The mean AGD values in 3 D imaging mode per exposure for the standard breast were 2.19 mGy and 2.29 mGy, while the mean AGD values after correction for the real breast composition were 2.53 mGy and 2.63 mGy for CC and MLO views, respectively. No significant relationship was found between the AGD and CBT in 2 D imaging mode and a good correlation coefficient of 0.98 in 3 D imaging mode. Conclusion: In this study the mean calculated AGD per exposure in 3 D imaging mode was on average 34 % higher than for 2 D imaging mode for patients examined with the same CBT.

  14. Average glandular dose in digital mammography and breast tomosynthesis

    International Nuclear Information System (INIS)

    Olgar, T.; Universitaetsklinikum Leipzig AoeR; Kahn, T.; Gosch, D.

    2012-01-01

    Purpose: To determine the average glandular dose (AGD) in digital full-field mammography (2 D imaging mode) and in breast tomosynthesis (3 D imaging mode). Materials and Methods: Using the method described by Boone, the AGD was calculated from the exposure parameters of 2247 conventional 2 D mammograms and 984 mammograms in 3 D imaging mode of 641 patients examined with the digital mammographic system Hologic Selenia Dimensions. The breast glandular tissue content was estimated by the Hologic R2 Quantra automated volumetric breast density measurement tool for each patient from right craniocaudal (RCC) and left craniocaudal (LCC) images in 2 D imaging mode. Results: The mean compressed breast thickness (CBT) was 52.7 mm for craniocaudal (CC) and 56.0 mm for mediolateral oblique (MLO) views. The mean percentage of breast glandular tissue content was 18.0 % and 17.4 % for RCC and LCC projections, respectively. The mean AGD values in 2 D imaging mode per exposure for the standard breast were 1.57 mGy and 1.66 mGy, while the mean AGD values after correction for real breast composition were 1.82 mGy and 1.94 mGy for CC and MLO views, respectively. The mean AGD values in 3 D imaging mode per exposure for the standard breast were 2.19 mGy and 2.29 mGy, while the mean AGD values after correction for the real breast composition were 2.53 mGy and 2.63 mGy for CC and MLO views, respectively. No significant relationship was found between the AGD and CBT in 2 D imaging mode and a good correlation coefficient of 0.98 in 3 D imaging mode. Conclusion: In this study the mean calculated AGD per exposure in 3 D imaging mode was on average 34 % higher than for 2 D imaging mode for patients examined with the same CBT.

  15. Enhancement of lymphocyte proliferation by mouse glandular kallikrein.

    Science.gov (United States)

    Hu, Z Q; Murakami, K; Ikigai, H; Shimamura, T

    1992-03-01

    Mouse glandular kallikrein (mGK) strongly enhanced the spontaneous and mitogen-induced proliferation of lymphocytes. Both blast formation and 3H-TdR incorporation were dose-dependently enhanced at the same time many cells were killed. The enhancing activity was independent of EGF, because EGF-binding proteins (mGK-9 in mGK-6,9 mixture and mGK-13), renal kallikrein (mGK-6) and human kallikrein all displayed the same enhancement. A serine proteinase inhibitor, diisopropyl fluorophosphate, could block the enhancement by mGK. The new function suggests that mGK is important in the immune system as a regulatory molecule.

  16. Herbivore handling of a plant's trichome: the case of Heliconius charithonia (L.) (Lepidoptera: Nymphalidae) and Passiflora lobata (Killip) Hutch. (Passifloraceae)

    Energy Technology Data Exchange (ETDEWEB)

    Cardoso, Marcio Z. [Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN (Brazil). Centro de Biociencias. Dept. de Botanica, Ecologia e Zoologia]. E-mail: mzc@cb.ufrn.br

    2008-05-15

    Trichomes reduce herbivore attack on plants by physically and/or chemically inhibiting movement or other activities. Despite evidence that herbivores are negatively affected by trichomes there also reports of insect counter-adaptations that circumvent the plant's defense. This paper reports on a study that investigated the likely mechanisms employed by larvae of the nymphalid butterfly, Heliconius charithonia (L.), that allow it to feed on a host that is presumably protected by hooked trichomes (Passiflora lobata (Killip) Hutch). Evidence were gathered using data from direct observations of larval movement and behavior, faeces analysis, scanning electron microscopy of plant surface and experimental analysis of larval movement on plants with and without trichomes (manually removed). The latter involved a comparison with a non specialist congener, Heliconius pachinus Salvin. Observations showed that H. charithonia larvae are capable of freeing themselves from entrapment on trichome tips by physical force. Moreover, wandering larvae lay silk mats on the trichomes and remove their tips by biting. In fact, trichome tips were found in the faeces. Experimental removal of trichomes aided in the movement of the non specialist but had no noticeable effect on the specialist larvae. These results support the suggestion that trichomes are capable of deterring a non specialist herbivore (H. pachinus). The precise mechanisms that allow the success of H. charithonia are not known, but I suggest that a blend of behavioral as well as physical resistance mechanisms is involved. Future studies should ascertain whether larval integument provides physical resistance to trichomes. (author)

  17. Efficiency of Trichome-Based Plant Defense in Phaseolus vulgaris Depends on Insect Behavior, Plant Ontogeny, and Structure

    Directory of Open Access Journals (Sweden)

    Zhenlong Xing

    2017-11-01

    Full Text Available Plant trichomes often function as physical barriers in preventing arthropod feeding and oviposition. Even though insects are frequently reported being entrapped and killed by trichome traps, the actual trapping behavior has not yet been described in detail. Capture experiments showed that capture efficiency during the plant's vegetative stage was considerably higher than in the fruiting and cotyledon stages. The ventral surface of the leaf was more effective in trapping flies than other parts of the plant. Capture-events monitoring showed that the mouthparts, legs, and ovipositor of Liriomyza trifolii adults are the body parts involved in entrapment by surface trichomes on Phaseolus vulgaris plants, and subsequently, deter their ability to feed, walk, and oviposit. Of the three main body parts normally affected, mouthparts was found to be the body part most susceptible to the trichomes. Entrapments were most often caused by landing, followed by puncturing or feeding, and occasionally by walking or fighting. Using scanning electron microscopy (SEM and optical microscopy, we determined the susceptible positions of each body part and found that the flies were all trapped by hooked trichomes. This study revealed the process by which leafminer flies are entrapped by surface trichomes of the host plant and evaluated the capture efficiency. The results will contribute to our understanding of physical defenses against herbivores.

  18. TCS1, a Microtubule-Binding Protein, Interacts with KCBP/ZWICHEL to Regulate Trichome Cell Shape in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Liangliang Chen

    2016-10-01

    Full Text Available How cell shape is controlled is a fundamental question in developmental biology, but the genetic and molecular mechanisms that determine cell shape are largely unknown. Arabidopsis trichomes have been used as a good model system to investigate cell shape at the single-cell level. Here we describe the trichome cell shape 1 (tcs1 mutants with the reduced trichome branch number in Arabidopsis. TCS1 encodes a coiled-coil domain-containing protein. Pharmacological analyses and observations of microtubule dynamics show that TCS1 influences the stability of microtubules. Biochemical analyses and live-cell imaging indicate that TCS1 binds to microtubules and promotes the assembly of microtubules. Further results reveal that TCS1 physically associates with KCBP/ZWICHEL, a microtubule motor involved in the regulation of trichome branch number. Genetic analyses indicate that kcbp/zwi is epistatic to tcs1 with respect to trichome branch number. Thus, our findings define a novel genetic and molecular mechanism by which TCS1 interacts with KCBP to regulate trichome cell shape by influencing the stability of microtubules.

  19. Breast Glandularity in Malaysian Women from a Full-Field Digital Mammography System

    International Nuclear Information System (INIS)

    Noriah Jamal; Humairah Samad Cheung; Siti Selina Abdul Hamid; Juliana Mahamad Napiah

    2014-01-01

    This study is undertaken to estimate breast glandularity in Malaysian women from a Full-Field Digital mammography System. This study involved 223 women (Malay=100;Chinese=101 and Indian=22) underwent voluntary screening mammography at Breast Centre, International Islamic University Malaysia (IIUM Breast Centre) for the first quarter of year 2009. Those are women aged between 31 to 69 years old (median age, 49 years). Data on miliampere-seconds, kilo voltage and compressed breast thickness for each cranio caudal view are used to estimate breast glandularity for an individual breast. Breast glandularity is calculated using the fitted equation reported earlier. The difference in breast glandularity among ethnic groups was tested for significance using the nonparametric Kruskal-Wallis test. The average breast glandularity estimated in our study, using FFDM system is 52.94±27.63 %. No significant difference was seen in breast glandularity among the ethnic groups (p>0.05, Kruskan Wallis test). Breast glandularity decrease as age increases, up to 60 years old. (author)

  20. Is nectar reabsorption restricted by the stalk cells of floral and extrafloral nectary trichomes?

    Science.gov (United States)

    Cardoso-Gustavson, P; Davis, A R

    2015-01-01

    Reabsorption is a phase of nectar dynamics that occurs concurrently with secretion; it has been described in floral nectaries that exude nectar through stomata or unicellular trichomes, but has not yet been recorded in extrafloral glands. Apparently, nectar reabsorption does not occur in multicellular secretory trichomes (MST) due to the presence of lipophilic impregnations - which resemble Casparian strips - in the anticlinal walls of the stalk cells. It has been assumed that these impregnations restrict solute movement within MST to occur unidirectionally and exclusively by the symplast, thereby preventing nectar reflux toward the underlying nectary tissues. We hypothesised that reabsorption is absent in nectaries possessing MST. The fluorochrome lucifer yellow (LYCH) was applied to standing nectar of two floral and extrafloral glands of distantly related species, and then emission spectra from nectary sections were systematically analysed using confocal microscopy. Passive uptake of LYCH via the stalk cells to the nectary tissues occurred in all MST examined. Moreover, we present evidence of nectar reabsorption in extrafloral nectaries, demonstrating that LYCH passed the stalk cells of MST, although it did not reach the deepest nectary tissues. Identical (control) experiments performed with neutral red (NR) demonstrated no uptake of this stain by actively secreting MST, whereas diffusion of NR did occur in plasmolysed MST of floral nectaries at the post-secretory phase, indicating that nectar reabsorption by MST is governed by stalk cell physiology. Interestingly, non-secretory trichomes failed to reabsorb nectar. The role of various nectary components is discussed in relation to the control of nectar reabsorption by secretory trichomes. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  1. Telomerase reverse transcriptase promoter mutations in glandular lesions of the urinary bladder.

    Science.gov (United States)

    Vail, Eric; Zheng, Xiaoyong; Zhou, Ming; Yang, Ximing; Fallon, John T; Epstein, Jonathan I; Zhong, Minghao

    2015-10-01

    Glandular lesions of the urinary bladder include a broad spectrum of entities ranging from completely benign to primary and secondary malignancies. The accurate diagnosis of these lesions is both important and challenging. Recently, studies suggest that telomerase reverse transcriptase (TERT) promoter mutations could be a biomarker for urothelial carcinoma (UC). We hypothesized that these mutations can distinguish UC with glandular differentiation from nephrogenic adenoma, primary adenocarcinoma of the urinary bladder (PAUB), or secondary malignancies. Twenty-five cases of benign glandular lesions (including nephrogenic adenoma); 29 cases of UC with glandular differentiation; 10 cases of PAUB; and 10 cases each of metastatic colon cancer, prostatic carcinoma, and carcinoma from Mullerian origin were collected. Slides were reviewed and selected to make sure the lesion was at least 10% to 20% of all tissue. Macrodissection was performed in some of cases, and genomic DNA was extracted from the tissue. Telomerase reverse transcriptase promoter mutations were determined by standard polymerase chain reaction sequencing. Twenty-one cases (72%) of UC with glandular differentiation were positive for TERT promoter mutations. However, none of the remaining cases (total 65 cases of benign lesions, PAUB, and metastatic carcinomas) was positive for TERT promoter mutation. Telomerase reverse transcriptase promoter mutations were highly associated with UC including UC with glandular differentiation but not other glandular lesions of bladder. Therefore, in conjunction with morphologic features, Immunohistochemistry stain profile, and clinical information, TERT promoter mutations could distinguish UC with glandular differentiation from other bladder glandular lesions. In addition, lack of TERT promoter mutations in primary adenocarcinoma of bladder suggests that this entity may have different origin or carcinogenesis from those of UC. Published by Elsevier Inc.

  2. FORTRAN Code for Glandular Dose Calculation in Mammography Using Sobol-Wu Parameters

    Directory of Open Access Journals (Sweden)

    Mowlavi A A

    2007-07-01

    Full Text Available Background: Accurate computation of the radiation dose to the breast is essential to mammography. Various the thicknesses of breast, the composition of the breast tissue and other variables affect the optimal breast dose. Furthermore, the glandular fraction, which refers to the composition of the breasts, as partitioned between radiation-sensitive glandular tissue and the adipose tissue, also has an effect on this calculation. Fatty or fibrous breasts would have a lower value for the glandular fraction than dense breasts. Breast tissue composed of half glandular and half adipose tissue would have a glandular fraction in between that of fatty and dense breasts. Therefore, the use of a computational code for average glandular dose calculation in mammography is a more effective means of estimating the dose of radiation, and is accurate and fast. Methods: In the present work, the Sobol-Wu beam quality parameters are used to write a FORTRAN code for glandular dose calculation in molybdenum anode-molybdenum filter (Mo-Mo, molybdenum anode-rhodium filter (Mo-Rh and rhodium anode-rhodium filter (Rh-Rh target-filter combinations in mammograms. The input parameters of code are: tube voltage in kV, half-value layer (HVL of the incident x-ray spectrum in mm, breast thickness in cm (d, and glandular tissue fraction (g. Results: The average glandular dose (AGD variation against the voltage of the mammogram X-ray tube for d = 4 cm, HVL = 0.34 mm Al and g=0.5 for the three filter-target combinations, as well as its variation against the glandular fraction of breast tissue for kV=25, HVL=0.34, and d=4 cm has been calculated. The results related to the average glandular absorbed dose variation against HVL for kV = 28, d=4 cm and g= 0.6 are also presented. The results of this code are in good agreement with those previously reported in the literature. Conclusion: The code developed in this study calculates the glandular dose quickly, and it is complete and

  3. Breast dose in mammography is about 30% lower when realistic heterogeneous glandular distributions are considered

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez, Andrew M., E-mail: amhern@ucdavis.edu [Biomedical Engineering Graduate Group, University of California Davis, Sacramento, California 95817 (United States); Seibert, J. Anthony; Boone, John M. [Departments of Radiology and Biomedical Engineering, Biomedical Engineering Graduate Group, University of California Davis, Sacramento, California 95817 (United States)

    2015-11-15

    Purpose: Current dosimetry methods in mammography assume that the breast is comprised of a homogeneous mixture of glandular and adipose tissues. Three-dimensional (3D) dedicated breast CT (bCT) data sets were used previously to assess the complex anatomical structure within the breast, characterizing the statistical distribution of glandular tissue in the breast. The purpose of this work was to investigate the effect of bCT-derived heterogeneous glandular distributions on dosimetry in mammography. Methods: bCT-derived breast diameters, volumes, and 3D fibroglandular distributions were used to design realistic compressed breast models comprised of heterogeneous distributions of glandular tissue. The bCT-derived glandular distributions were fit to biGaussian functions and used as probability density maps to assign the density distributions within compressed breast models. The MCNPX 2.6.0 Monte Carlo code was used to estimate monoenergetic normalized mean glandular dose “DgN(E)” values in mammography geometry. The DgN(E) values were then weighted by typical mammography x-ray spectra to determine polyenergetic DgN (pDgN) coefficients for heterogeneous (pDgN{sub hetero}) and homogeneous (pDgN{sub homo}) cases. The dependence of estimated pDgN values on phantom size, volumetric glandular fraction (VGF), x-ray technique factors, and location of the heterogeneous glandular distributions was investigated. Results: The pDgN{sub hetero} coefficients were on average 35.3% (SD, 4.1) and 24.2% (SD, 3.0) lower than the pDgN{sub homo} coefficients for the Mo–Mo and W–Rh x-ray spectra, respectively, across all phantom sizes and VGFs when the glandular distributions were centered within the breast phantom in the coronal plane. At constant breast size, increasing VGF from 7.3% to 19.1% lead to a reduction in pDgN{sub hetero} relative to pDgN{sub homo} of 23.6%–27.4% for a W–Rh spectrum. Displacement of the glandular distribution, at a distance equal to 10% of the

  4. Glandular dose in breast tomosynthesis examinations: Preliminary study with a sample of patients

    International Nuclear Information System (INIS)

    Castillo, M.; Chevalier, M.; Calzado, A.; Valverde, J.

    2013-01-01

    The aim of this study is to analyze the mean glandular dose administered to a group of patients with a tomography system (Selenia Dimensions) service installed on a large hospital in which routine tests are done and screening. (Author)

  5. Diagnostic and therapeutic dilemma associated with atypical glandular cells on liquid-based cervical cytology.

    LENUS (Irish Health Repository)

    Chummun, K

    2012-12-01

    In 2008, the management of women in Ireland with atypical glandular cells changed to immediate referral to colposcopy. The optimal management of these women is unclear. A balance between the detection of occult disease and overtreatment is required.

  6. Glandularity estimation in Japanese women by using a breast model made from mammographic findings of European women

    International Nuclear Information System (INIS)

    Kawaguchi, Ai; Matsunaga, Yuta; Chida, Koichi; Asada, Yasuki; Suzuki, Shoichi

    2016-01-01

    This study aimed to estimate breast glandularity in Japanese women using patient exposure conditions and tissue-equivalent materials by a conventional method. Typical glandularities in Japanese women were compared with those in European women to verify the validity of the average glandular dose estimation manual based on the EUREF protocol. Glandularity was estimated from the data of 600 patients and the model breast of the tissue-equivalent materials which had various amounts of glandular contents and thicknesses. The model breasts were measured to examine the relationships between the thickness of the glandular contents and tube loading by using an automatic exposure control system. Then, equations were established to determine glandularity from patient data. The mean glandularity in the highest compressed breast thickness (CBT) group of 36–45 mm was 72%. The mean CBT of the 184 (31%) patients with glandularities exceeding 100% was 31 mm. Glandularities in patients with CBT of 30–70 mm in the present study were higher compared to those in European women by approximately 10–20%. The results suggest that the model breast of European women might not be a suitable reference standard for more than 30% of Japanese women, who have breasts with lower CBT. (author)

  7. Mineral nutrient uptake from prey and glandular phosphatase activity as dual test of carnivory in semidesert plants with glandular leaves suspected of carnivory

    Czech Academy of Sciences Publication Activity Database

    Plachno, B.J.; Adamec, Lubomír; Huet, H.

    2009-01-01

    Roč. 104, č. 4 (2009), s. 649-654 ISSN 0305-7364 Institutional research plan: CEZ:AV0Z60050516 Keywords : mineral nutrient uptake * phosphatases * glandular leaves Subject RIV: EF - Botanics Impact factor: 3.501, year: 2009

  8. A calibration approach to glandular tissue composition estimation in digital mammography

    International Nuclear Information System (INIS)

    Kaufhold, J.; Thomas, J.A.; Eberhard, J.W.; Galbo, C.E.; Trotter, D.E. Gonzalez

    2002-01-01

    The healthy breast is almost entirely composed of a mixture of fatty, epithelial, and stromal tissues which can be grouped into two distinctly attenuating tissue types: fatty and glandular. Further, the amount of glandular tissue is linked to breast cancer risk, so an objective quantitative analysis of glandular tissue can aid in risk estimation. Highnam and Brady have measured glandular tissue composition objectively. However, they argue that their work should only be used for 'relative' tissue measurements unless a careful calibration has been performed. In this work, we perform such a 'careful calibration' on a digital mammography system and use it to estimate breast tissue composition of patient breasts. We imaged 0%, 50%, and 100% glandular-equivalent phantoms of varying thicknesses for a number of clinically relevant x-ray techniques on a digital mammography system. From these images, we extracted mean signal and noise levels and computed calibration curves that can be used for quantitative tissue composition estimation. In this way, we calculate the percent glandular composition of a patient breast on a pixelwise basis. This tissue composition estimation method was applied to 23 digital mammograms. We estimated the quantitative impact of different error sources on the estimates of tissue composition. These error sources include compressed breast height estimation error, residual scattered radiation, quantum noise, and beam hardening. Errors in the compressed breast height estimate contribute the most error in tissue composition--on the order of ±7% for a 4 cm compressed breast height. The spatially varying scattered radiation will contribute quantitatively less error overall, but may be significant in regions near the skinline. It is calculated that for a 4 cm compressed breast height, a residual scatter signal error is mitigated by approximately sixfold in the composition estimate. The error in composition due to the quantum noise, which is the limiting

  9. Investigation of mean glandular dose versus compressed breast thickness relationship for mammography

    International Nuclear Information System (INIS)

    Bor, D.; Tukel, S.; Olgar, T.; Toklu, T.; Aydin, E.; Akyol, O.

    2008-01-01

    The relationship between the mean glandular dose (MGD) and the compressed breast thickness (CBT) is commonly used for the presentation of mammographic dose survey results and could also be useful for the assessment of individual breast doses retrospectively in case of lack of necessary dosimetric instrumentation. The high data scattering from the best fit reduces the reliability of this technique. The aim of this study was to investigate the accuracy of this relationship using the data collected from a patient survey and phantom experiment. Patients were divided into three different groups according to their breast glandularities, which were predicted from the inspection of previous mammograms. X-ray beam qualities that will be used in patient examinations were determined according to breast thickness and predicted glandularities. The MGD versus CBT relationship for all the examined patients resulted in a poor correlation (R 2 = 0.28). This relationship was separately obtained for each glandularity group and also for sub-groups of specific beam qualities. The best correlation (R 2 = 0.73) was obtained for the fatty breast group and Mo/Mo combination. A low correlation (R 2 = 0.34) was observed in the mid-glandularity group due to inclusion of a wide range of glandularities in this group. In the case of the dense breast group, although the glandularity range was narrow, there were e still high data scattering (R 2 = 0.25). This was probably due to the use of Mo/Rh and Mo/Mo combinations. This is validated by obtaining the MGD-CBT relationship specific to Mo/Mo combination (R 2 = 0.61). (authors)

  10. Computation of the glandular radiation dose in digital tomosynthesis of the breast

    International Nuclear Information System (INIS)

    Sechopoulos, Ioannis; Suryanarayanan, Sankararaman; Vedantham, Srinivasan; D'Orsi, Carl; Karellas, Andrew

    2007-01-01

    Tomosynthesis of the breast is currently a topic of intense interest as a logical next step in the evolution of digital mammography. This study reports on the computation of glandular radiation dose in digital tomosynthesis of the breast. Previously, glandular dose estimations in tomosynthesis have been performed using data from studies of radiation dose in conventional planar mammography. This study evaluates, using Monte Carlo methods, the normalized glandular dose (D g N) to the breast during a tomosynthesis study, and characterizes its dependence on breast size, tissue composition, and x-ray spectrum. The conditions during digital tomosynthesis imaging of the breast were simulated using a computer program based on the Geant4 toolkit. With the use of simulated breasts of varying size, thickness and tissue composition, the D g N to the breast tissue was computed for varying x-ray spectra and tomosynthesis projection angle. Tomosynthesis projections centered about both the cranio-caudal (CC) and medio-lateral oblique (MLO) views were simulated. For each projection angle, the ratio of the glandular dose for that projection to the glandular dose for the zero degree projection was computed. This ratio was denoted the relative glandular dose (RGD) coefficient, and its variation under different imaging parameters was analyzed. Within mammographic energies, the RGD was found to have a weak dependence on glandular fraction and x-ray spectrum for both views. A substantial dependence on breast size and thickness was found for the MLO view, and to a lesser extent for the CC view. Although RGD values deviate substantially from unity as a function of projection angle, the RGD averaged over all projections in a complete tomosynthesis study varies from 0.91 to 1.01. The RGD results were fit to mathematical functions and the resulting equations are provided

  11. Normalized glandular dose (DgN) coefficients for flat-panel CT breast imaging

    International Nuclear Information System (INIS)

    Thacker, Samta C; Glick, Stephen J

    2004-01-01

    The development of new digital mammography techniques such as dual-energy imaging, tomosynthesis and CT breast imaging will require investigation of optimal camera design parameters and optimal imaging acquisition parameters. In optimizing these acquisition protocols and imaging systems it is important to have knowledge of the radiation dose to the breast. This study presents a methodology for estimating the normalized glandular dose to the uncompressed breast using the geometry proposed for flat-panel CT breast imaging. The simulation uses the GEANT 3 Monte Carlo code to model x-ray transport and absorption within the breast phantom. The Monte Carlo software was validated for breast dosimetry by comparing results of the normalized glandular dose (DgN) values of the compressed breast to those reported in the literature. The normalized glandular dose was then estimated for a range of breast diameters from 10 cm to 18 cm using an uncompressed breast model with a homogeneous composition of adipose and glandular tissue, and for monoenergetic x-rays from 10 keV to 120 keV. These data were fit providing expressions for the normalized glandular dose. Using these expressions for the DgN coefficients and input variables such as the diameter, height and composition of the breast phantom, the mean glandular dose for any spectra can be estimated. A computer program to provide normalized glandular dose values has been made available online. In addition, figures displaying energy deposition maps are presented to better understand the spatial distribution of dose in CT breast imaging

  12. Genome-wide identification of GLABRA3 downstream genes for anthocyanin biosynthesis and trichome formation in Arabidopsis.

    Science.gov (United States)

    Gao, Chenhao; Li, Dong; Jin, Changyu; Duan, Shaowei; Qi, Shuanghui; Liu, Kaige; Wang, Hanchen; Ma, Haoli; Hai, Jiangbo; Chen, Mingxun

    2017-04-01

    GLABRA3 (GL3), a bHLH transcription factor, has previously proved to be involved in anthocyanin biosynthesis and trichome formation in Arabidopsis, however, its downstream targeted genes are still largely unknown. Here, we found that GL3 was widely present in Arabidopsis vegetative and reproductive organs. New downstream targeted genes of GL3 for anthocyanin biosynthesis and trichome formation were identified in young shoots and expanding true leaves by RNA sequencing. GL3-mediated gene expression was tissue specific in the two biological processes. This study provides new clues to further understand the GL3-mediated regulatory network of anthocyanin biosynthesis and trichome formation in Arabidopsis. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Quantitative expression analysis of selected transcription factors in pavement, basal and trichome cells of mature leaves from Arabidopsis thaliana.

    Science.gov (United States)

    Schliep, Martin; Ebert, Berit; Simon-Rosin, Ulrike; Zoeller, Daniela; Fisahn, Joachim

    2010-05-01

    Gene expression levels of several transcription factors from Arabidopsis thaliana that were described previously to be involved in leaf development and trichome formation were analysed in trichome, basal and pavement cells of mature leaves. Single cell samples of these three cells types were collected by glass micro-capillaries. Real-time reverse transcription (RT)-PCR was used to analyse expression patterns of the following transcription factors: MYB23, MYB55, AtHB1, FILAMENTOUS FLOWER (FIL)/YABBY1 (YAB1), TRIPTYCHON (TRY) and CAPRICE (CPC). A difference in the expression patterns of TRY and CPC was revealed. Contrary to the CPC expression pattern, no transcripts of TRY could be detected in pavement cells. FIL/YAB1 was exclusively expressed in trichome cells. AtHB1 was highly expressed throughout all three cell types. MYB55 was higher expressed in basal cells than in trichome and pavement cells. MYB23 showed a pattern of low expression in pavement cells, medium in basal cells and high expression in trichomes. Expression patterns obtained by single cell sampling and real-time RT-PCR were compared to promoter GUS fusions of the selected transcription factors. Therefore, we regenerated two transgenic Arabidopsis lines that expressed the GUS reporter gene under control of the promoters of MYB55 and YAB1. In conclusion, despite their function in leaf morphogenesis, all six transcription factors were detected in mature leaves. Furthermore, single cell sampling and promoter GUS staining patterns demonstrated the predominant presence of MYB55 in basal cells as compared to pavement cells and trichomes.

  14. Evaluation of average glandular dose in mammography services in 10 cities of Colombia; Avaliacao de dose glandular media em servicos de mamografia de 10 cidades de Colombia

    Energy Technology Data Exchange (ETDEWEB)

    Alejo-Martinez, H.; Salazar-Hurtado, E.; Puerto-Jimenez, D. [Grupo de Prevencion Temprana Del Cancer, Instituto Nacional de Cancerologia, Bogota D.C. (Colombia)

    2016-07-01

    The objective of this study was to conduct an assessment of dose in 60 mammography services that have screening programs for breast cancer in 10 cities of Colombia. The third quartile of the average glandular dose was 2,29 mGy, range between 1,0 and 5,6 mGy, for the phantom equivalent to a standard breast. This study included mammography units with conventional and digital technology. (author)

  15. Evaluation of subject contrast and normalized average glandular dose by semi-analytical models

    International Nuclear Information System (INIS)

    Tomal, A.; Poletti, M.E.; Caldas, L.V.E.

    2010-01-01

    In this work, two semi-analytical models are described to evaluate the subject contrast of nodules and the normalized average glandular dose in mammography. Both models were used to study the influence of some parameters, such as breast characteristics (thickness and composition) and incident spectra (kVp and target-filter combination) on the subject contrast of a nodule and on the normalized average glandular dose. From the subject contrast results, detection limits of nodules were also determined. Our results are in good agreement with those reported by other authors, who had used Monte Carlo simulation, showing the robustness of our semi-analytical method.

  16. The European wool-carder bee (Anthidium manicatum) eavesdrops on plant volatile organic compounds (VOCs) during trichome collection.

    Science.gov (United States)

    Graham, Kelsey K; Brown, Steve; Clarke, Stephanie; Röse, Ursula S R; Starks, Philip T

    2017-11-01

    The plant-pollinator relationship is generally considered mutualistic. This relationship is less clear, however, when pollinators also cause tissue damage. Some Megachilidae bees collect plant material for nests from the plants they pollinate. In this study, we examined the relationship between Anthidium manicatum, the European wool-carder bee, and the source of its preferred nesting material - Stachys byzantina, lamb's ear. Female A. manicatum use their mandibles to trim trichomes from plants for nesting material (a behaviour dubbed "carding"). Using volatile organic compound (VOC) headspace analysis and behavioural observations, we explored (a) how carding effects S. byzantina and (b) how A. manicatum may choose specific S. byzantina plants. We found that removal of trichomes leads to a dissimilar VOC bouquet compared to intact leaves, with a significant increase in VOC detection following damage. A. manicatum also visit S. byzantina plants with trichomes removed at a greater frequency compared to plants with trichomes intact. Our data suggest that A. manicatum eavesdrop on VOCs produced by damaged plants, leading to more carding damage for individual plants due to increased detectability by A. manicatum. Accordingly, visitation by A. manicatum to S. byzantina may incur both a benefit (pollination) and cost (tissue damage) to the plant. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Epifluorescence and stereomicroscopy of trichomes associated with resistant and susceptible host plant genotypes of the Asian citrus psyllid (Hemiptera: Liviidae)

    Science.gov (United States)

    Epifluorescence, light and stereo-microscopy were used to characterize foliar trichomes associated with young flush leaves and stems of six plant genotypes that are hosts of the Asian citrus psyllid, Diaphorina citri, vector of the economically important citrus greening disease. These genotypes incl...

  18. A new quantitative classification of ecological types in the bromeliad genus Tillandsia (Bromeliaceae based on trichomes

    Directory of Open Access Journals (Sweden)

    Mosti Stefano

    2008-03-01

    Full Text Available Using collection specimens, we measured the density and wing area of trichomes in 37 species of the bromeliad genus Tillandsia, specifically the abaxial proximal, abaxial distal, adaxial proximal and adaxial distal parts of the leaf. The product of the trichome "wing" area by the number of trichomes (means produced a pure number (T that was correlated to ecological features. The correlation was positive with respect to arid environments (xeric Tillands and negative with respect to humid environments (mesic Tillands. Bulbous, and particularly myrmecophytic species and species with tanks, represented particular categories. Other intermediate types were identified based on the T number, totalling five ecological types. In comparison with other systems of ecological typification for Tillands and other Bromeliaceae, the present system offers measurable data whose analysis is reproducible. Rev. Biol. Trop. 56 (1: 191-203. Epub 2008 March 31.Medimos el número por milímetro cuadrado y el área del "ala" (parte móvil de los tricomas en las partes adaxial próxima y distal, y adaxial próxima y distal, de la hoja de 37 especies de bromelias del género Tillandsia. El producto del área del ala para el número de los tricomas (promedio produjo un número puro (T. Hallamos que T se correlaciona con las características ecológicas de las tilandsias investigadas. La correlación es positiva con respecto a ambientes áridos (especies xéricas y negativa con respecto a los ambientes húmedos (especies mésicas. Las especies con bulbo, y particularmente las asociadas con hormigas y especies con de tanque representan categorías particulares. Identificamos otros tipos intermedios, agradando así cinco tipos ecológicos. En comparación con otros sistemas de tipificación ecológica, este sistema ofrece la ventaja de ser reproducible y cuantitativo.

  19. Web services for transcriptomics

    NARCIS (Netherlands)

    Neerincx, P.

    2009-01-01

    Transcriptomics is part of a family of disciplines focussing on high throughput molecular biology experiments. In the case of transcriptomics, scientists study the expression of genes resulting in transcripts. These transcripts can either perform a biological function themselves or function as

  20. Method for the evaluation of a average glandular dose in mammography

    International Nuclear Information System (INIS)

    Okunade, Akintunde Akangbe

    2006-01-01

    This paper concerns a method for accurate evaluation of average glandular dose (AGD) in mammography. At different energies, the interactions of photons with tissue are not uniform. Thus, optimal accuracy in the estimation of AGD is achievable when the evaluation is carried out using the normalized glandular dose values, g(x,E), that are determined for each (monoenergetic) x-ray photon energy, E, compressed breast thickness (CBT), x, breast glandular composition, and data on photon energy distribution of the exact x-ray beam used in breast imaging. A generalized model for the values of g(x,E) that is for any arbitrary CBT ranging from 2 to 9 cm (with values that are not whole numbers inclusive, say, 4.2 cm) was developed. Along with other dosimetry formulations, this was integrated into a computer software program, GDOSE.FOR, that was developed for the evaluation of AGD received from any x-ray tube/equipment (irrespective of target-filter combination) of up to 50 kVp. Results are presented which show that the implementation of GDOSE.FOR yields values of normalized glandular dose that are in good agreement with values obtained from methodologies reported earlier in the literature. With the availability of a portable device for real-time acquisition of spectra, the model and computer software reported in this work provide for the routine evaluation of AGD received by a specific woman of known age and CBT

  1. Honey bee males and queens use glandular secretions to enhance sperm viability before and after storage

    DEFF Research Database (Denmark)

    Den Boer, Susanne Petronella A; Boomsma, Jacobus Jan; Baer, Boris

    2009-01-01

    Internal fertilization requires live sperm to be transferred from male to female before egg fertilization. Both males and females assist the insemination process by providing sperm with glandular secretions, which have been inferred to contain subsets of proteins that maintain sperm viability. He...

  2. Average glandular dose in digital mammography and digital breast tomosynthesis: comparison of phantom and patient data

    NARCIS (Netherlands)

    Bouwman, R. W.; van Engen, R. E.; Young, K. C.; den Heeten, G. J.; Broeders, M. J. M.; Schopphoven, S.; Jeukens, C. R. L. P. N.; Veldkamp, W. J. H.; Dance, D. R.

    2015-01-01

    For the evaluation of the average glandular dose (AGD) in digital mammography (DM) and digital breast tomosynthesis (DBT) phantoms simulating standard model breasts are used. These phantoms consist of slabs of polymethyl methacrylate (PMMA) or a combination of PMMA and polyethylene (PE). In the last

  3. Severe glandular tularemia in a patient treated with anti-tumour necrosis factor for psoriatic arthritis

    Directory of Open Access Journals (Sweden)

    Ruxandra Calin

    2017-07-01

    Full Text Available A case of severe glandular tularemia in a patient receiving anti-tumour necrosis factor (TNF therapy is reported here. The patient required prolonged treatment with doxycycline–ciprofloxacin due to early relapse after ciprofloxacin was stopped. Tularemia may have a more severe course in patients receiving anti-TNF. This may thus be an indication for more aggressive treatment.

  4. A Stochastic Polygons Model for Glandular Structures in Colon Histology Images.

    Science.gov (United States)

    Sirinukunwattana, Korsuk; Snead, David R J; Rajpoot, Nasir M

    2015-11-01

    In this paper, we present a stochastic model for glandular structures in histology images of tissue slides stained with Hematoxylin and Eosin, choosing colon tissue as an example. The proposed Random Polygons Model (RPM) treats each glandular structure in an image as a polygon made of a random number of vertices, where the vertices represent approximate locations of epithelial nuclei. We formulate the RPM as a Bayesian inference problem by defining a prior for spatial connectivity and arrangement of neighboring epithelial nuclei and a likelihood for the presence of a glandular structure. The inference is made via a Reversible-Jump Markov chain Monte Carlo simulation. To the best of our knowledge, all existing published algorithms for gland segmentation are designed to mainly work on healthy samples, adenomas, and low grade adenocarcinomas. One of them has been demonstrated to work on intermediate grade adenocarcinomas at its best. Our experimental results show that the RPM yields favorable results, both quantitatively and qualitatively, for extraction of glandular structures in histology images of normal human colon tissues as well as benign and cancerous tissues, excluding undifferentiated carcinomas.

  5. Estimation of the average glandular dose on a team of tomosynthesis; Estimacion de la dosis glandular media en un equipo de tomosintesis

    Energy Technology Data Exchange (ETDEWEB)

    Nunez Martinez, L. M. R.; Sanchez Jimenez, J.; Pizarro trigo, F.

    2013-07-01

    Seeking to improve the information that gives us an image of mammography the manufacturers have implemented tomosynthesis. With this method of acquisition and reconstruction of image we went from having a 2D to a 3D image image, in such a way that it reduces or eliminates the effect of overlap of tissues. The estimate of the dose, which is always a fundamental parameter in the control of quality of radiology equipment, is more in the case of mammography by the radiosensitivity of this body and the frequency of their use. The objective of this work is the determination of the mean in a team glandular dose of with tomosynthesis mammography. (Author)

  6. The effect of aluminium added filter on mean glandular dose using mammography machine in MINT Medical Physics Laboratory

    International Nuclear Information System (INIS)

    Asmaliza Hashim; Wan Hazlinda Ismail; Abd Aziz Mhd Ramli

    2005-01-01

    The effect of various thickness of aluminium added filter on mean glandular dose in mammography is investigated for a standard breast phantom, 4.2 cm Perspex. A mammography machine in Medical Physics Laboratory MINT, Bennett Model DMF-150 is used to provide radiation in various kV range under clinical condition. The mean glandular dose on the phantom were measured based on technique recommended by AAPM protocol (1990) report no 29. The mean glandular dose was found reducing with increasing thickness of added filter. A more detail results of this study is presented in this paper. (Author)

  7. Monte Carlo simulation for the estimation of the glandular breast dose for a digital breast tomosynthesis system

    International Nuclear Information System (INIS)

    Rodrigues, Leonardo; Braz, Delson; Goncalves Magalhaes, Luis Alexandre

    2015-01-01

    Digital breast tomosynthesis (DBT) is a screening and diagnostic modality that acquires images of the breast at multiple angles during a short scan. The Selenia Dimensions (Hologic, Bedford, Mass) DBT system can perform both full-field digital mammography and DBT. The system acquires 15 projections over a 15 deg. angular range (from -7.5 deg. to +7.5 deg.). An important factor in determining the optimal imaging technique for breast tomosynthesis is the radiation dose. In breast imaging, the radiation dose of concern is that deposited in the glandular tissue of the breast because this is the tissue that has a risk of developing cancer. The concept of the normalised mean glandular dose (DgN) has been introduced as the metric for the dose in breast imaging. The DgN is difficult to measure. The Monte Carlo techniques offer an alternative method for a realistic estimation of the radiation dose. The purpose of this work was to use the Monte Carlo code MCNPX technique to generate monoenergetic glandular dose data for estimating the breast tissue dose in tomosynthesis for arbitrary spectra as well as to observe the deposited radiation dose by projection on the glandular portion of the breast in a Selenia Dimensions DBT system. A Monte Carlo simulation of the system was developed to compute the DgN in a craniocaudal view. Monoenergetic X-ray beams from 10 to 49 keV in 1-keV increments were used. The simulation utilised the assumption of a homogeneous breast composition and three compositions (0 % glandular, 50 % glandular and 100 % glandular). The glandular and adipose tissue compositions were specified according ICRU Report 44. A skin layer of 4 mm was assumed to encapsulate the breast on all surfaces. The breast size was varied using the chest wall-to-nipple distance (CND) and compressed breast thickness (t). In this work, the authors assumed a CND of 5 cm and the thicknesses ranged from 2 to 8 cm, in steps of 2 cm. The fractional energy absorption increases (up to 44

  8. Trichomes of tobacco excrete zinc as zinc-substituted calcium carbonate and other zinc-containing compounds

    International Nuclear Information System (INIS)

    Sarret, G.; Harada, E.; Choi, Y-E.; Isaure, M.-P.; Geoffroy, N.; Fakra, S.; Marcus, M.A.; Birschwilks, M.; Clemens, S.; Manceau, A.

    2006-01-01

    Tobacco (Nicotiana tabacum L. cv Xanthi) plants were exposed to toxic levels of zinc (Zn). Zn exposure resulted in toxicity signs in plants, and these damages were partly reduced by a calcium (Ca) supplement. Confocal imaging of intracellular Zn using Zinquin showed that Zn was preferentially accumulated in trichomes. Exposure to Zn and Zn + Ca increased the trichome density and induced the production of Ca/Zn mineral grains on the head cells of trichomes. These grains were aggregates of submicrometer-sized crystals and poorly crystalline material and contained Ca as major element, along with subordinate amounts of Zn, manganese, potassium, chlorine, phosphorus, silicon, and magnesium. Micro x-ray diffraction revealed that the large majority of the grains were composed essentially of metal-substituted calcite (CaCO3). CaCO3 polymorphs (aragonite and vaterite) and CaC2O4 (Ca oxalate) mono- and dihydrate also were identified, either as an admixture to calcite or in separate grains. Some grains did not diffract, although they contained Ca, suggesting the presence of amorphous form of Ca. The presence of Zn-substituted calcite was confirmed by Zn K-edge micro-extended x-ray absorption fine structure spectroscopy. Zn bound to organic compounds and Zn-containing silica and phosphate were also identified by this technique. The proportion of Zn-substituted calcite relative to the other species increased with Ca exposure. The production of Zn-containing biogenic calcite and other Zn compounds through the trichomes is a novel mechanism involved in Zn detoxification. This study illustrates the potential of laterally resolved x-ray synchrotron radiation techniques to study biomineralization and metal homeostasis processes in plants

  9. Trichome density and its UV-B protective potential are affected by shading and leaf position on the canopy

    International Nuclear Information System (INIS)

    Liakoura, V.; Stefanou, M.; Manetas, Y.; Cholevas, C.; Karabourniotis, G.

    1997-01-01

    In Olea europaea trichome density and UV-B absorbing compounds of leaf hairs and the lamina proper of leaves located in south-facing, north-facing and the internal of the canopy were positively correlated to the UV-B midday instant irradiance measured in September at these three different positions of the canopy. The correlation between these three parameters and the receiving photosynthetically active radiation (PAR), however, was weaker. In Quercus ilex, trichome density and its UV-B absorbing capacity were considerably higher in the exposed, south-facing leaves, compared to the deeply shaded ones; the UV-B absorbing capacity of the de-haired lamina, however, was the same. In the broad-leaved, alpine rosette of Verbascum speciosum, one could distinguish two areas on the leaves, one exposed and one shaded by the superimposed lamina. Although trichome density and the UV-B absorbing compounds of the de-haired leaf were the same in the two areas, the UV-B absorbing capacity of hairs was considerably increased in the exposed region. In V. speciosum, exposure induced also qualitative changes in the UV-B absorbance profile, apparently due to the formation of new flavonoid compounds absorbing maximally at 345–350 nm. In all other cases, the differences were mainly quantitative. The results support the postulate of a function of leaf hairs as a UV-B radiation screen and suggest that trichome density and/or its UV-B absorbing capacity may depend on irradiance during leaf development

  10. Next-generation transcriptome assembly

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey A.; Wang, Zhong

    2011-09-01

    Transcriptomics studies often rely on partial reference transcriptomes that fail to capture the full catalog of transcripts and their variations. Recent advances in sequencing technologies and assembly algorithms have facilitated the reconstruction of the entire transcriptome by deep RNA sequencing (RNA-seq), even without a reference genome. However, transcriptome assembly from billions of RNA-seq reads, which are often very short, poses a significant informatics challenge. This Review summarizes the recent developments in transcriptome assembly approaches - reference-based, de novo and combined strategies-along with some perspectives on transcriptome assembly in the near future.

  11. Evaluation of average glandular dose in digital and conventional systems of the mammography; Avaliacao da dose glandular media em sistemas digitais e convencionais de mamografia

    Energy Technology Data Exchange (ETDEWEB)

    Xavier, Aline C.S.; Barros, Vinicius S.M.; Khoury, Hellen J., E-mail: alinecx90@gmail.com, E-mail: vsmdbarros@gmail.com, E-mail: hjkhoury@gmail.com [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear; Mello, Francisca A. de, E-mail: francissamello@yahoo.com.br [Hospital das Clinicas do Recife (HCR/UFPE), PE (Brazil)

    2014-07-01

    Mammography is currently the most effective method of diagnosis and detection of breast pathologies. The main interest in this kid of exam comes from the high incidence rate of breast cancer and necessity of high quality images for accurate diagnosis. Digital mammography systems have several advantages compared to conventional systems, however the use of digital imaging systems is not always integrated to an image acquisition protocol. Therefore, it is questionable if digital systems truly reduce the dose received by the patient, because many times is introduced in the clinics without optimization of the image acquisition protocols. The aim of this study is to estimate the value of incident air Kerma and average glandular dose (AGD) in patients undergoing conventional and digital mammography systems in Recife. This study was conducted with 650 patients in three hospitals. The value of incident air Kerma was estimated from the measurement of the yield of equipment and irradiation parameters used for each patient. From these results and using the methodology proposed by Dance et al. the value of the average glandular dose was calculated. The results obtained show that the lowest value of AGD was found with conventional screen-film system, indicating that the parameters for image acquisition with digital systems are not optimized. It was also observed that the institutions with digital systems use lower breast compression values than the conventional. (author)

  12. Computer Vision for High-Throughput Quantitative Phenotyping: A Case Study of Grapevine Downy Mildew Sporulation and Leaf Trichomes.

    Science.gov (United States)

    Divilov, Konstantin; Wiesner-Hanks, Tyr; Barba, Paola; Cadle-Davidson, Lance; Reisch, Bruce I

    2017-12-01

    Quantitative phenotyping of downy mildew sporulation is frequently used in plant breeding and genetic studies, as well as in studies focused on pathogen biology such as chemical efficacy trials. In these scenarios, phenotyping a large number of genotypes or treatments can be advantageous but is often limited by time and cost. We present a novel computational pipeline dedicated to estimating the percent area of downy mildew sporulation from images of inoculated grapevine leaf discs in a manner that is time and cost efficient. The pipeline was tested on images from leaf disc assay experiments involving two F 1 grapevine families, one that had glabrous leaves (Vitis rupestris B38 × 'Horizon' [RH]) and another that had leaf trichomes (Horizon × V. cinerea B9 [HC]). Correlations between computer vision and manual visual ratings reached 0.89 in the RH family and 0.43 in the HC family. Additionally, we were able to use the computer vision system prior to sporulation to measure the percent leaf trichome area. We estimate that an experienced rater scoring sporulation would spend at least 90% less time using the computer vision system compared with the manual visual method. This will allow more treatments to be phenotyped in order to better understand the genetic architecture of downy mildew resistance and of leaf trichome density. We anticipate that this computer vision system will find applications in other pathosystems or traits where responses can be imaged with sufficient contrast from the background.

  13. Second-harmonic generation as a DNA malignancy indicator of prostate glandular epithelial cells

    International Nuclear Information System (INIS)

    Zheng-Fei, Zhuang; Han-Ping, Liu; Zhou-Yi, Guo; Xiao-Yuan, Deng; Shuang-Mu, Zhuo; Bi-Ying, Yu

    2010-01-01

    This paper first demonstrates second-harmonic generation (SHG) in the intact cell nucleus, which acts as an optical indicator of DNA malignancy in prostate glandular epithelial cells. Within a scanning region of 2.7 μm×2.7 μm in cell nuclei, SHG signals produced from benign prostatic hyperplasia (BPH) and prostate carcinoma (PC) tissues (mouse model C57BL/6) have been investigated. Statistical analyses (t test) of a total of 405 measurements (204 nuclei from BPH and 201 nuclei from PC) show that SHG signals from BPH and PC have a distinct difference (p < 0.05), suggesting a potential optical method of revealing very early malignancy in prostate glandular epithelial cells based upon induced biochemical and/or biophysical modifications in DNA. (geophysics, astronomy and astrophysics)

  14. Ultrastructure of the apical glandular region of the scolex of Proteocephalus torulosus (Cestoda: Proteocephalidae)

    Czech Academy of Sciences Publication Activity Database

    Žďárská, Zdeňka; Scholz, Tomáš; Nebesářová, Jana

    2004-01-01

    Roč. 51, č. 4 (2004), s. 333-338 ISSN 0015-5683 R&D Projects: GA ČR GA524/04/0342; GA AV ČR KSK6005114 Institutional research plan: CEZ:AV0Z6022909 Keywords : Cestoda * Proteocephalus torulosus * apical glandular region Subject RIV: GJ - Animal Vermins ; Diseases, Veterinary Medicine Impact factor: 0.837, year: 2004

  15. Evaluation of average glandular dose in mammography services in 10 cities of Colombia

    International Nuclear Information System (INIS)

    Alejo-Martinez, H.; Salazar-Hurtado, E.; Puerto-Jimenez, D.

    2016-01-01

    The objective of this study was to conduct an assessment of dose in 60 mammography services that have screening programs for breast cancer in 10 cities of Colombia. The third quartile of the average glandular dose was 2,29 mGy, range between 1,0 and 5,6 mGy, for the phantom equivalent to a standard breast. This study included mammography units with conventional and digital technology. (author)

  16. Severe glandular tularemia in a patient treated with anti-tumour necrosis factor for psoriatic arthritis.

    Science.gov (United States)

    Calin, Ruxandra; Caumes, Eric; Reibel, Florence; Ali Mohamed, Anzime; Brossier, Florence; Foltz, Violaine; Boussouar, Samia; Fautrel, Bruno; Maurin, Max; Katlama, Christine; Pourcher, Valérie

    2017-07-01

    A case of severe glandular tularemia in a patient receiving anti-tumour necrosis factor (TNF) therapy is reported here. The patient required prolonged treatment with doxycycline-ciprofloxacin due to early relapse after ciprofloxacin was stopped. Tularemia may have a more severe course in patients receiving anti-TNF. This may thus be an indication for more aggressive treatment. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. MORPHOLOGIC CONSIDERATIONS ABOUT THE WALL OF THE GLANDULAR STOMACH OF YOUNG RABBITS (Oryctolagus cuniculus)

    OpenAIRE

    de Oliveira, Larissa Renata; Molinari, Sonia Lucy; Natali, Maria Raquel Marçal; Michelan, Andrea Cristiane; Scapinello, Claúdio

    2001-01-01

    The morphology of the stomach may vary between species as a function of feeding habits, differences on the cellular composition of the mucosa of the stomach wall and the different functions it carries out. Morphofunctional variations of the stomach of several animals along phylogeny led us to investigate the morphology of the wall of the glandular stomach of rabbits. We used the stomachs of 32 young rabbits (Oryctolagus cuniculus) from the White New Zealand strain, coming from the Experimenta...

  18. Long acting β2-agonist and corticosteroid restore airway glandular cell function altered by bacterial supernatant

    Directory of Open Access Journals (Sweden)

    Nawrocki-Raby Béatrice

    2010-01-01

    Full Text Available Abstract Background Staphylococcus aureus releases virulence factors (VF that may impair the innate protective functions of airway cells. The aim of this study was to determine whether a long-acting β2 adrenergic receptor agonist (salmeterol hydroxynaphthoate, Sal combined with a corticosteroid (fluticasone propionate, FP was able to regulate ion content and cytokine expression by airway glandular cells after exposure to S. aureus supernatant. Methods A human airway glandular cell line was incubated with S. aureus supernatant for 1 h and then treated with the combination Sal/FP for 4 h. The expression of actin and CFTR proteins was analyzed by immunofluorescence. Videomicroscopy was used to evaluate chloride secretion and X-ray microanalysis to measure the intracellular ion and water content. The pro-inflammatory cytokine expression was assessed by RT-PCR and ELISA. Results When the cells were incubated with S. aureus supernatant and then with Sal/FP, the cellular localisation of CFTR was apical compared to the cytoplasmic localisation in cells incubated with S. aureus supernatant alone. The incubation of airway epithelial cells with S. aureus supernatant reduced by 66% the chloride efflux that was fully restored by Sal/FP treatment. We also observed that Sal/FP treatment induced the restoration of ion (Cl and S and water content within the intracellular secretory granules of airway glandular cells and reduced the bacterial supernatant-dependent increase of pro-inflammatory cytokines IL8 and TNFα. Conclusions Our results demonstrate that treatment with the combination of a corticosteroid and a long-acting β2 adrenergic receptor agonist after bacterial infection restores the airway glandular cell function. Abnormal mucus induced by defective ion transport during pulmonary infection could benefit from treatment with a combination of β2 adrenergic receptor agonist and glucocorticoid.

  19. Effect of the glandular composition on digital breast tomosynthesis image quality and dose optimisation

    International Nuclear Information System (INIS)

    Marques, T.; Di Maria, S.; Vaz, P.; Ribeiro, A.; Belchior, A.; Cardoso, J.; Matela, N.; Oliveira, N.; Almeida, P.; Janeiro, L.

    2015-01-01

    In the image quality assessment for digital breast tomosynthesis (DBT), a breast phantom with an average percentage of 50 % glandular tissue is seldom used, which may not be representative of the breast tissue composition of the women undergoing such examination. This work aims at studying the effect of the glandular composition of the breast on the image quality taking into consideration different sizes of lesions. Monte Carlo simulations were performed using the state-of-the-art computer program PENELOPE to validate the image acquisition system of the DBT equipment as well as to calculate the mean glandular dose for each projection image and for different breast compositions. The integrated PENELOPE imaging tool (PenEasy) was used to calculate, in mammography, for each clinical detection task the X-ray energy that maximises the figure of merit. All the 2D cranial-caudal projections for DBT were simulated and then underwent the reconstruction process applying the Simultaneous Algebraic Reconstruction Technique. Finally, through signal-to-noise ratio analysis, the image quality in DBT was assessed. (authors)

  20. Atypical squamous and glandular cells of undetermined significance (ASCUS and AGUS) of the uterine cervix.

    Science.gov (United States)

    Cenci, M; Vecchione, A

    2000-01-01

    ASCUS (Atypical Squamous Cells of Undetermined Significance) and AGUS (Atypical Glandular Cells of Undetermined Significance), or AGCUS, are two acronyms introduced in 1988 by The Bethesda System (TBS) for reporting borderline cytological changes in cervical cytology. ASCUS and AGUS categories should be subclassified. Five ASCUS subgroups were proposed: 1) ASCUS due to processing defects, 2) with "mature" cytoplasm, 3) in post-menopausal women (a--in the setting of atrophy and b--with estrogen stimulation), 4) atypical metaplasia, and 5) ASCUS with keratinized cytoplasm. AGUS subgroups may be subcategorized in endometrial or endocervical on the basis of origin. Endocervical AGUS should be further qualified, but the analysis of atypical glandular cells may be really difficult and the conclusive diagnosis is frequently "AGUS not otherwise specified". The subclassification of ASCUS and AGUS is useful for an appropriate clinical management, but pertinent patient information (such as age, date of last menstrual period, mechanical therapies, tamoxifen therapy, and others) is needed to avoid an overdiagnosis and consequently an overtreatment. In fact various subgroups require different clinical management. Therefore, an effective communication between cytopathologists and referring physicians is essential in the analysis of squamous and glandular atypias.

  1. CT measurement of breast glandular tissue and its association with testicular cancer

    Energy Technology Data Exchange (ETDEWEB)

    Klang, Eyal [Tel Aviv University, Department of Radiology, Chaim Sheba Medical Center, Tel Aviv (Israel); The Chaim Sheba Medical Center, Tel Hashomer (Israel); Rozendorn, Noa; Raskin, Steve; Portnoy, Orith; Sklair, Miri; Marom, Edith M.; Konen, Eli; Amitai, Michal M. [Tel Aviv University, Department of Radiology, Chaim Sheba Medical Center, Tel Aviv (Israel)

    2017-02-15

    To evaluate the associations between breast glandular tissues diameters as determined by CT and b-hCG levels, histological types, tumour spread and prognosis in patients with testicular germ cell tumour. Ninety-four patients with pre-treatment CT scan and markers (b-hCG, AFP, LDH) were retrospectively collected. A radiologist measured diameters in all CT examinations and correlation between diameters and log (b-hCG) was assessed (Pearson's coefficient). The ability of measured diameters to predict lymphatic and distant haematogenous metastatic spread was evaluated (ROC curves). The associations between measured diameter cut-off values of 20 and 25 mm and International Germ Cell Cancer Collaborative Group (IGCCCG) classification, lymphatic and distant haematogenous metastatic spread and histological subtypes were evaluated (chi squared test). Breast glandular diameters correlated to log(b-hCG) (r = 0.579) and predicted distant haematogenous metastatic spread (AUC = 0.78). Worse prognosis (intermediate or poor IGCCCG) was shown for 20 mm (27.3 vs. 4.2 %, p = 0.005) and 25 mm (33.3 vs. 6.1 %, p = 0.014). A diameter of 25 mm was associated with non-seminoma (91.7 vs. 48.8 %, p = 0.005). Breast glandular tissue diameters correlated with log(b-hCG) and predicted distant haematogenous metastases. Twenty and 25 mm were associated with worse prognosis and 25 mm was able to distinguish between seminoma and non-seminoma. (orig.)

  2. Antibacterial, modulatory activity of antibiotics and toxicity from Rhinella jimi (Stevaux, 2002) (Anura: Bufonidae) glandular secretions.

    Science.gov (United States)

    Sales, Débora Lima; Morais-Braga, Maria Flaviana Bezerra; Santos, Antonia Thassya Lucas Dos; Machado, Antonio Judson Targino; Araujo Filho, João Antonio de; Dias, Diógenes de Queiroz; Cunha, Francisco Assis Bezerra da; Saraiva, Rogério de Aquino; Menezes, Irwin Rose Alencar de; Coutinho, Henrique Douglas Melo; Costa, José Galberto Martins; Ferreira, Felipe Silva; Alves, Rômulo Romeu da Nóbrega; Almeida, Waltécio de Oliveira

    2017-08-01

    The increase in microorganisms with resistance to medications has caused a strong preoccupation within the medical and scientific community. Animal toxins studies, such as parotoid glandular secretions from amphibians, possesses a great potential in the development of drugs, such as antimicrobials, as these possess bioactive compounds. It was evaluated Rhinella jimi (Stevaux, 2002) glandular secretions against standard and multi-resistant bacterial strains; the effect of secretions combined with drugs; and determined the toxicity using two biologic in vivo models, and a in vitro model with mice livers. Standard strains were used for the determination of the Minimum Inhibitory Concentration (MIC), while for the modulatory activity of antibiotics, the clinical isolates Escherichia coli 06, Pseudomonas aeruginosa 03 and Staphylococcus aureus 10 were used. Modulatory activity was evaluated by the broth microdilution method with aminoglycosides and β-lactams as target antibiotics. The secretions in association with the antibiotics have a significant reduction in MIC, both the aminoglycosides and β-lactams. The toxicity and cytotoxicity results were lower than the values used in the modulation. R. jimi glandular secretions demonstrated clinically relevant results regarding the modulation of the tested antimicrobials. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  3. Radioimmunoassay of glandular kallikrein in human plasma after partial purification by immunoaffinity column

    International Nuclear Information System (INIS)

    Nishimura, Kazutaka; Inoue, Yoshikazu; Kokubu, Tatsuo

    1987-01-01

    Glandular kallikrein in human plasma was partially purified by immunoaffinity column and was measured by a radioimmunoassay (RIA). Plasma was diluted with an equal volume of 10 mmol/l sodium phosphate buffer, pH 7.4, containing 0.9% NaCl (PBS) and was applied to an immunoaffinity column from which glandular kallikrein was eluted with 3 mol/l NaSCN (20 ml). The enzymic fraction was concentrated with an Amicon PM 10 filter and dialyzed against PBS. The final recovery of the enzyme was 51.6 ± 1.6%, determined by using [ 125 I]kallikrein. The usable range of the standard curve covered 2.5-100 ng/tube. The coefficient of variation within the series was 5.9%, and the coefficient of variation between the series was 7.6%. In healthy controls, the plasma content of glandular kallikrein was 1.36 ± 0.39 ng/ml. In patients with acute pancreatitis, the plasma concentration was 8.02 ± 6.15 ng/ml, significantly different from the control group. (Auth.)

  4. Impact of digitalization of mammographic units on average glandular doses in the Flemish Breast Cancer Screening Program

    OpenAIRE

    De Hauwere, An; Thierens, Hubert

    2012-01-01

    The impact of digitalization on the average glandular doses in 49 mammographic units participating in the Flemish Breast Cancer Screening Program was studied. Screen-film was changed to direct digital radiography and computed radiography in 25 and 24 departments respectively. Average glandular doses were calculated before and after digitalization for different PMMA-phantom thicknesses and for groups of 50 successive patients. For the transition from screen-film to computed radiography both ph...

  5. Characterization of fibrillar collagens and extracellular matrix of glandular benign prostatic hyperplasia nodules.

    Directory of Open Access Journals (Sweden)

    Tyler M Bauman

    Full Text Available Recent studies have associated lower urinary tract symptoms (LUTS in men with prostatic fibrosis, but a definitive link between collagen deposition and LUTS has yet to be demonstrated. The objective of this study was to evaluate ECM and collagen content within normal glandular prostate tissue and glandular BPH, and to evaluate the association of clinical parameters of LUTS with collagen content.Fibrillar collagen and ECM content was assessed in normal prostate (48 patients and glandular BPH nodules (24 patients using Masson's trichrome stain and Picrosirius red stain. Second harmonic generation (SHG imaging was used to evaluate collagen content. Additional BPH tissues (n = 47 were stained with Picrosirius red and the association between clinical parameters of BPH/LUTS and collagen content was assessed.ECM was similar in normal prostate and BPH (p = 0.44. Total collagen content between normal prostate and glandular BPH was similar (p = 0.27, but a significant increase in thicker collagen bundles was observed in BPH (p = 0.045. Using SHG imaging, collagen content in BPH (mean intensity = 62.52; SEM = 2.74 was significantly higher than in normal prostate (51.77±3.49; p = 0.02. Total collagen content was not associated with treatment with finasteride (p = 0.47 or α-blockers (p = 0.52, pre-TURP AUA symptom index (p = 0.90, prostate-specific antigen (p = 0.86, post-void residual (PVR; p = 0.32, prostate size (p = 0.21, or post-TURP PVR (p = 0.51. Collagen content was not associated with patient age in patients with BPH, however as men aged normal prostatic tissue had a decreased proportion of thick collagen bundles.The proportion of larger bundles of collagen, but not total collagen, is increased in BPH nodules, suggesting that these large fibers may play a role in BPH/LUTS. Total collagen content is independent of clinical parameters of BPH and LUTS. If fibrosis and overall ECM deposition are

  6. Calculation of Absorbed Glandular Dose using a FORTRAN Program Based on Monte Carlo X-ray Spectra in Mammography

    Directory of Open Access Journals (Sweden)

    Ali Asghar Mowlavi

    2011-03-01

    Full Text Available Introduction: Average glandular dose calculation in mammography with Mo-Rh target-filter and dose calculation for different situations is accurate and fast. Material and Methods: In this research, first of all, x-ray spectra of a Mo target bombarded by a 28 keV electron beam with and without a Rh filter were calculated using the MCNP code. Then, we used the Sobol-Wu parameters to write a FORTRAN code to calculate average glandular dose. Results: Average glandular dose variation was calculated against the voltage of the mammographic x-ray tube for d = 5 cm, HVL= 0.35 mm Al, and different value of g. Also, the results related to average glandular absorbed dose variation per unit roentgen radiation against the glandular fraction of breast tissue for kV = 28 and HVL = 0.400 mmAl and different values of d are presented. Finally, average glandular dose against d for g = 60% and three values of kV (23, 27, 35 kV with corresponding HVLs have been calculated. Discussion and Conclusion: The absorbed dose computational program is accurate, complete, fast and user friendly. This program can be used for optimization of exposure dose in mammography. Also, the results of this research are in good agreement with the computational results of others.

  7. Preliminary results of the average glandular dose to the breast with TLDS measure is computed as the conversion factors; Resultados preliminares da dose glandular media na mama medida com TLDS e calculada atraves de fatores de conversao

    Energy Technology Data Exchange (ETDEWEB)

    Sardo, Luiz T.L.; Almeida, Claudio D.; Coutinho, Celia M.C., E-mail: ltsardo@yahoo.com.br, E-mail: claudio@ird.gov.br, E-mail: celia@ird.gov.br [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

    2013-07-01

    At mammography exams there is a risk of a breast cancer induced from the absorbed dose by the glandular tissue. According to the National Institute of Cancer, INCA, breast cancer is the second type most frequent in the world and the most common among women, therefore the necessity of monitoring the mean glandular dose, D{sub G}. Measuring methods of D{sub G} were established by some authors. Among the established methods the method of Dance is one of the most known. In this study was utilized a measurement method realized with TL dosimeters inserted in a breast tissue equivalent phantom, BTE, with 46% of glandularity and exposed using Mo/Mo and Mo/Rh target/filter combination and 28kV. To ensure this measurement method the results were compared with a calculation method, used by Dance, of D{sub G} from the measurement of incident air kerma, K{sub i}, and conversion factors to consider mainly the beam quality, the compressed thickness and the glandularity of the breast. The results of the comparison of the D{sub G} measurement with the obtained dose by the method of Dance demonstrated that for the thickness of 4.0 and 6.0 cm the doses were consistent. For the thickness of 5.0 cm the difference was higher, indicating that the glandularity may influence, suggesting further investigation. (author)

  8. Assessment of mean glandular dose to patients from digital mammography systems

    International Nuclear Information System (INIS)

    Pwamang, Caroline K.

    2016-07-01

    Mean glandular dose assessment of patients undergoing digital mammography examination has been done. A total of 297 patient data was used for the study. Basic Quality Control tests were done to ascertain the performance of the equipment used. The results of Quality Control tests indicated that the three Mammography units used for this study were functioning within the internationally acceptable performance criteria. Patients with a breast thickness of 30 mm within the two age groups of 40-49 yrs and 50-64 yrs received doses slightly higher than the acceptable dose levels. A patient in the category 40-49 yrs with breast thickness of 30 mm received 1.83 mGy as calculated Mean Glandular Dose, 2.10 mGy was the recorded dose and 1.58 mGy was recorded under the age group 50-64 yrs. These values have deviated by -22%, -40%, and -5.33% respectively from 1.5 mGy which is the recommended dose for a breast thickness of 30 mm. Also patients with breast thickness of 70 mm under the age group 40–49 yrs had a recorded dose of 6.58 mGy, which deviated by -1.21% from the recommended value of 6.5 mGy for that breast thickness. Aside these values, all the other values were within the recommended dose values. The percentage deviation between the recommended values and the calculated values was within ±25% which was a working limit that was set for this work. Doses delivered by the Full-field Digital mammography equipment were higher than doses delivered by the Computered Radiography equipment. The calculated Mean Glandular Doses for the three facilities were within recommended dose values. (author)

  9. NTL8 Regulates Trichome Formation in Arabidopsis by Directly Activating R3 MYB Genes TRY and TCL1.

    Science.gov (United States)

    Tian, Hainan; Wang, Xianling; Guo, Hongyan; Cheng, Yuxin; Hou, Chunjiang; Chen, Jin-Gui; Wang, Shucai

    2017-08-01

    The NAM, ATAF1/2, and CUC (NAC) are plant-specific transcription factors that regulate multiple aspects of plant growth and development and plant response to environmental stimuli. We report here the identification of NTM1-LIKE8 (NTL8), a membrane-associated NAC transcription factor, as a novel regulator of trichome formation in Arabidopsis ( Arabidopsis thaliana ). From an activation-tagged Arabidopsis population, we identified a dominant, gain-of-function mutant with glabrous inflorescence stem. By using plasmid rescue and RT-PCR analyses, we found that NTL8 was tagged; thus, the mutant was named ntl8-1 Dominant ( ntl8-1D ). Recapitulation experiment further confirmed that the phenotype observed in the ntl8-1D mutant was caused by elevated expression of NTL8 Quantitative RT-PCR results showed that the expression level of the single-repeat R3 MYB genes TRIPTYCHON ( TRY ) and TRICHOMELESS1 ( TCL1 ) was elevated in the ntl8-1D mutant. Genetic analyses demonstrated that NTL8 acts upstream of TRY and TCL1 in the regulation of trichome formation. When recruited to the promoter region of the reporter gene Gal4:GUS by a fused GAL4 DNA-binding domain, NTL8 activated the expression of the reporter gene. Chromatin immunoprecipitation results indicated that TRY and TCL1 are direct targets of NTL8. However, NTL8 did not interact with SQUAMOSA PROMOTER BINDING PROTEIN LIKE9, another transcription factor that regulates the expression of TRY and TCL1 , in yeast and plant cells. Taken together, our results suggest that NTL8 negatively regulates trichome formation in Arabidopsis by directly activating the expression of TRY and TCL1 . © 2017 American Society of Plant Biologists. All Rights Reserved.

  10. Foliar trichome- and aquaporin-aided water uptake in a drought-resistant epiphyte Tillandsia ionantha Planchon.

    Science.gov (United States)

    Ohrui, T; Nobira, H; Sakata, Y; Taji, T; Yamamoto, C; Nishida, K; Yamakawa, T; Sasuga, Y; Yaguchi, Y; Takenaga, H; Tanaka, Shigeo

    2007-12-01

    The atmospheric epiphyte Tillandsia ionantha is capable of surviving drought stress for 6 months or more without any exogenous water supply via an as of yet to be determined mechanism. When plants were soaked in water for 3 h, leaves absorbed a remarkably large amount of water (30-40% on the basis of fresh weight), exhibiting a bimodal absorption pattern. Radiolabeled water was taken up by the leaves by capillary action of the epidermal trichomes within 1 min (phase 1) and then transported intracellularly to leaf tissues over 3 h (phase 2). The removal of epidermal trichome wings from leaves as well as rinsing leaves with water significantly lowered the extracellular accumulation of water on leaf surfaces. The intracellular transport of water was inhibited by mercuric chloride, implicating the involvement of a water channel aquaporin in second-phase water absorption. Four cDNA clones (TiPIP1a, TiPIP1b, TiPIP1c, and TiPIP2a) homologous to PIP family aquaporins were isolated from the leaves, and RT-PCR showed that soaking plants in water stimulated the expression of TiPIP2a mRNA, suggesting the reinforcement in ability to rapidly absorb a large amount of water. The expression of TiPIP2a complementary RNA in Xenopus oocytes enhanced permeability, and treatment with inhibitors suggested that the water channel activity of TiPIP2a protein was regulated by phosphorylation. Thus, the high water uptake capability of T. ionantha leaves surviving drought is attributable to a bimodal trichome- and aquaporin-aided water uptake system based on rapid physical collection of water and subsequent, sustained chemical absorption.

  11. Estimation of the average glandular dose on a team of tomosynthesis

    International Nuclear Information System (INIS)

    Nunez Martinez, L. M. R.; Sanchez Jimenez, J.; Pizarro trigo, F.

    2013-01-01

    Seeking to improve the information that gives us an image of mammography the manufacturers have implemented tomosynthesis. With this method of acquisition and reconstruction of image we went from having a 2D to a 3D image image, in such a way that it reduces or eliminates the effect of overlap of tissues. The estimate of the dose, which is always a fundamental parameter in the control of quality of radiology equipment, is more in the case of mammography by the radiosensitivity of this body and the frequency of their use. The objective of this work is the determination of the mean in a team glandular dose of with tomosynthesis mammography. (Author)

  12. Estimate of average glandular dose (AGD) in national clinics of mammography

    International Nuclear Information System (INIS)

    Mora, Patricia; Segura, Helena

    2004-01-01

    The breast cancer represents the second cause of death by cancer in the femme population of our country. The specialized equipment for the obtaining of the mammographic images is higher every day and its use increases daily. The quality of the radiographic study is linked to the dose that this tissue intrinsically sensible receives to the ionizing radiations. The present work makes the first national study to quantify the average glandular doses and to connect them with the diagnostic quality and the recommendations to international scale. (Author) [es

  13. Preliminary results of the average glandular dose to the breast with TLDS measure is computed as the conversion factors

    International Nuclear Information System (INIS)

    Sardo, Luiz T.L.; Almeida, Claudio D.; Coutinho, Celia M.C.

    2013-01-01

    At mammography exams there is a risk of a breast cancer induced from the absorbed dose by the glandular tissue. According to the National Institute of Cancer, INCA, breast cancer is the second type most frequent in the world and the most common among women, therefore the necessity of monitoring the mean glandular dose, D G . Measuring methods of D G were established by some authors. Among the established methods the method of Dance is one of the most known. In this study was utilized a measurement method realized with TL dosimeters inserted in a breast tissue equivalent phantom, BTE, with 46% of glandularity and exposed using Mo/Mo and Mo/Rh target/filter combination and 28kV. To ensure this measurement method the results were compared with a calculation method, used by Dance, of D G from the measurement of incident air kerma, K i , and conversion factors to consider mainly the beam quality, the compressed thickness and the glandularity of the breast. The results of the comparison of the D G measurement with the obtained dose by the method of Dance demonstrated that for the thickness of 4.0 and 6.0 cm the doses were consistent. For the thickness of 5.0 cm the difference was higher, indicating that the glandularity may influence, suggesting further investigation. (author)

  14. Penetration of UV-A, UV-B and blue light through the leaf trichome layers of two xeromorphic plants, olive and oak, measured by optical fibre microprobes

    International Nuclear Information System (INIS)

    Karabourniotis, G.; Bornman, J.F.

    1999-01-01

    Quartz fibre-optic microprobes were used to monitor the light microenvironment beneath trichome layers of the xeromorphic leaves of two Mediterranean evergreen sclerophylls, Olea europaea and Quercus ilex. Young developing leaves of both plants were densely pubescent on both surfaces of the lamina, whereas the mature leaves were pubescent only on the abaxial side. Trichome layers of young as well as of mature leaves of both plants attenuated almost all incident ultraviolet (UV)-B (310 nm) and UV-A (360 nm) radiation and a considerable portion of blue light (430 nm). Abaxial trichome layers of young leaves were more effective in screening out the incident radiation compared to the adaxial ones of the same leaves and also compared to the abaxial layer of the mature leaves. The abaxial epidermis of dehaired mature leaves of O. europaea was ineffective in absorbing most of the incident UV-B and UV-A radiation. UV and visible spectra beneath trichome layers of O. europaea in mature leaves confirmed that the light microenvironment on the epidermis was deprived in the UV-B, UV-A and partly in the blue spectral regions. It is proposed that the occurrence of a dense trichome layer, especially in young leaves, may play a protective role against not only UV-B radiation damage, but also against high visible irradiance. This function is performed irrespective of the differing anatomy of individual hairs of both plants. The protection provided by the trichomes could afford advantages under stress conditions, especially during leaf development. (author)

  15. Functional characterization of TRICHOMELESS2, a new single-repeat R3 MYB transcription factor in the regulation of trichome patterning in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Gan Lijun

    2011-12-01

    Full Text Available Abstract Background Single-repeat R3 MYB transcription factors (single-repeat MYBs play important roles in controlling trichome patterning in Arabidopsis. It was proposed that single-repeat MYBs negatively regulate trichome formation by competing with GLABRA1 (GL1 for binding GLABRA3/ENHANCER OF GLABRA3 (GL3/EGL3, thus inhibiting the formation of activator complex TTG1(TRANSPARENT TESTA GLABRA1-GL3/EGL3-GL1 that is required for the activation of GLABRA2 (GL2, whose product is a positive regulator of trichome formation. Previously we identified a novel single-repeat MYB transcription factor, TRICHOMELESS1 (TCL1, which negatively regulates trichome formation on the inflorescence stems and pedicels by directly suppressing the expression of GL1. Results We analyzed here the role of TRICHOMELESS2 (TCL2, a previously-uncharacterized single-repeat MYB transcription factor in trichome patterning in Arabidopsis. We showed that TCL2 is closely related to TCL1, and like TCL1 and other single-repeat MYBs, TCL2 interacts with GL3. Overexpression of TCL2 conferred glabrous phenotype while knockdown of TCL2 via RNAi induced ectopic trichome formation on the inflorescence stems and pedicels, a phenotype that was previously observed in tcl1 mutants. These results suggested that TCL2 may have overlapping function with TCL1 in controlling trichome formation on inflorescences. On the other hand, although the transcription of TCL2, like TCL1, is not controlled by the activator complex formed by GL1 and GL3, and TCL2 and TCL1 proteins are more than 80% identical at the amino acid level, the expression of TCL2 under the control of TCL1 promoter only partially recovered the mutant phenotype of tcl1, implying that TCL2 and TCL1 are not fully functional equivalent. Conclusions TCL2 function redundantly with TCL1 in controlling trichome formation on inflorescences, but they are not fully functional equivalent. Transcription of TCL2 is not controlled by activator complex

  16. Glandular differentiation in dedifferentiated chondrosarcoma: molecular evidence of a rare phenomenon.

    Science.gov (United States)

    Jour, George; Liu, Yajuan; Ricciotti, Robert; Pritchard, Colin; Hoch, Benjamin L

    2015-09-01

    Epithelial glandular differentiation in dedifferentiated chondrosarcoma has not been described. Our patient was a 64-year-old man with a history of prostate cancer status post-radiation and hormonal therapy. On screening bone scan, he was found to have increased uptake in his right femoral shaft. Biopsy revealed intermediate-grade conventional chondrosarcoma. Subsequent femoral resection was remarkable for an intermediate-grade chondrosarcomatous component juxtaposed to an area composed of anastomosing nests and cords of malignant epithelial cells showing nuclear atypia and increased mitotic activity. A fibroblastic-appearing spindle cell population was intimately associated with the epithelial cells. The epithelial cells labeled with 34bE12, AE1/AE3, EMA, and Vimentin (both spindled and epithelial components) while being negative for prostate-specific antigen, prostate specific acid phosphatase, cytokeratin 20, thyroid transcription factor-1, and CDX2. The patient developed local recurrence 9 months after the initial resection but has had no metastatic disease and consistently undetectable prostate-specific antigen levels. Deep parallel sequencing of the dedifferentiated component showed a nonsynonymous mutation at exon 4 of IDH1 gene at codon R132 leading to a substitution of arginine, with serine confirming glandular differentiation in dedifferentiated chondrosarcoma. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Evaluation of average glandular dose in digital and conventional systems of the mammography

    International Nuclear Information System (INIS)

    Xavier, Aline C.S.; Barros, Vinicius S.M.; Khoury, Hellen J.

    2014-01-01

    Mammography is currently the most effective method of diagnosis and detection of breast pathologies. The main interest in this kid of exam comes from the high incidence rate of breast cancer and necessity of high quality images for accurate diagnosis. Digital mammography systems have several advantages compared to conventional systems, however the use of digital imaging systems is not always integrated to an image acquisition protocol. Therefore, it is questionable if digital systems truly reduce the dose received by the patient, because many times is introduced in the clinics without optimization of the image acquisition protocols. The aim of this study is to estimate the value of incident air Kerma and average glandular dose (AGD) in patients undergoing conventional and digital mammography systems in Recife. This study was conducted with 650 patients in three hospitals. The value of incident air Kerma was estimated from the measurement of the yield of equipment and irradiation parameters used for each patient. From these results and using the methodology proposed by Dance et al. the value of the average glandular dose was calculated. The results obtained show that the lowest value of AGD was found with conventional screen-film system, indicating that the parameters for image acquisition with digital systems are not optimized. It was also observed that the institutions with digital systems use lower breast compression values than the conventional. (author)

  18. Average glandular dose in routine mammography screening using a Sectra Microdose Mammography unit

    International Nuclear Information System (INIS)

    Hemdal, B.; Herrnsdorf, L.; Andersson, I.; Bengtsson, G.; Heddson, B.; Olsson, M.

    2005-01-01

    The Sectra MicroDose Mammography system is based on direct photon counting (with a solid-state detector), and a substantially lower dose to the breast than when using conventional system can be expected. In this work absorbed dose measurements have been performed for the first unit used in routine mammography screening (at the Hospitals of Helsingborg (Sweden)). Two European protocols on dosimetry in mammography have been followed. Measurement of half value layer (HVL) cannot be performed as prescribed, but this study has demonstrated than non-invasive measurements of HVL can be performed accurately with a sensitive and well collimated solid-state detector with simultaneous correction for the energy dependence. The average glandular dose for a 50 mm standard breast with 50% glandularity, simulated by 45 mm polymethylmethacrylate, was found to be 0.21 and 0.28 mGy in March and December 2004, respectively. These values are much lower than for any other mammography system on the market today. It has to be stressed that the measurement were made using the current clinical settings and that no systematic optimisation of the relationship between absorbed dose and diagnostic image quality has been performed within the present study. In order to further increase the accuracy of absorbed dose measurements for this unit, the existing dose protocols should be revised to account also for the tungsten/aluminium anode/filter combination, the multi-slit pre-collimator device and the occurrence of a dose profile in the scanning direction. (authors)

  19. Gynecomastia: glandular-liposculpture through a single transaxillary one hole incision.

    Science.gov (United States)

    Lee, Yung Ki; Lee, Jun Hee; Kang, Sang Yoon

    2018-04-01

    Gynecomastia is characterized by the benign proliferation of breast tissue in men. Herein, we present a new method for the treatment of gynecomastia, using ultrasound-assisted liposuction with both conventional and reverse-cutting edge tip cannulas in combination with a pull-through lipectomy technique with pituitary forceps through a single transaxillary incision. Thirty patients were treated with this technique at the author's institution from January 2010 to January 2015. Ten patients were treated with conventional surgical excision of the glandular/fibrous breast tissue combined with liposuction through a periareolar incision before January 2010. Medical records, clinical photographs and linear analog scale scores were analyzed to compare the surgical results and complications. The patients were required to rate their cosmetic outcomes based on the linear analog scale with which they rated their own surgical results; the mean overall average score indicated a good or high level of satisfaction. There were no incidences of skin necrosis, hematoma, infection and scar contracture; however, one case each of seroma and nipple inversion did occur. Operative time was reduced overall using the new technique since it is relatively simple and straightforward. According to the evaluation by the four independent researchers, the patients treated with this new technique showed statistically significant improvements in scar and nipple-areolar complex (NAC) deformity compared to those who were treated using the conventional method. Glandular liposculpture through a single transaxillary incision is an efficient and safe technique that can provide aesthetically satisfying and consistent results.

  20. A study on the image quality of mammography and the average glandular dose

    International Nuclear Information System (INIS)

    Lee, In Ja; Kim, Hak Sung; Kim, Sung Soo; Huh, Joon

    2002-01-01

    We came to the following conclusion as the results of experiment on the image quality of mammography and the average glandular dose using 4 apparatuses at 3 hospital in Seoul. Whereas the measurement of half value layer showed no differences among the apparatuses, the measurement by an attenuation curve method showed some differences by 5.9%. There were 9.1% differences in the measurement by aluminum conversion method. The basic density of an automatic exposure control unit must be D = 1.40, but there was no automatic exposure unit adjusted precisely at any hospital. The unit at the B hospital exceeded the allowable limit by ± 0.15. In the photographing using an automatic exposure control unit and the management of an automatic film processor using a sensitometer, most automatic film processors were well kept. But in some cases the mean value of a fluctuation coefficient exceeded the allowable limit. There is a need for more cautious management. The image quality of breast phantom photography was affected by the screen/film system among the hospital. The average glandular dose at a breast of 4.2 cm thickness depended on the tube voltage, In the case of Mo/Mo, it was measured 0.26 ∼ 1.39 mGy less than ACR standard 3.0 mGy

  1. TCW: transcriptome computational workbench.

    Science.gov (United States)

    Soderlund, Carol; Nelson, William; Willer, Mark; Gang, David R

    2013-01-01

    The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. The Transcriptome Computational Workbench (TCW) provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms). The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina) or assembling long sequences (e.g. Sanger, 454, transcripts), annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the transcriptome. TCW is freely available from www.agcol.arizona.edu/software/tcw.

  2. Estimation of average glandular dose depending on the thickness of the breast; Estimativa da dose glandular media em funcao da espessura da mama

    Energy Technology Data Exchange (ETDEWEB)

    Real, Jessica V.; Luz, Renata M. da, E-mail: jessica.real@pucrs.br, E-mail: renata.luz@pucrs.br [Hospital Sao Lucas (HSL/PUCRS), Porto Alegre, RS (Brazil); Fröhlich, Bruna D.; Pertile, Alessandra S.; Silva, Ana Maria Marques da, E-mail: bruna.frohlich@acad.pucrs.br, E-mail: lessandra.pertile@acad.pucrs.br, E-mail: ana.marques@pucrs.br [Pontificia Universidade Catolica do Rio Grande do Sul (PUCRS), Porto Alegre, RS (Brazil)

    2014-07-01

    Breast cancer is the most common type of cancer in women worldwide. Mammography is, to date, the most efficient method for detecting an abnormality in the patient's breast. It is a technique of imaging diagnostic that requires special care because radiographs without adequate quality may lead to a false diagnosis and lead to the need for a repeat examination, increasing the dose of radiation in the patient. This study aimed to evaluate the average glandular dose (AGD), depending on the breast thickness in patients undergoing routine tests, with a digital computer radiography processing system. Analyzed 30 exhibitions in patients aged (65 ± 12) years, in the right and left caudal skull projections, for breasts with thicknesses between 45 mm and 50 mm. The calculated value of the AGD for this track thickness was (1.600 ± 0.009) mGy. The performance of mammography quality control tests was satisfactory and the AGD values obtained for the chosen thickness range is acceptable, since the threshold achievable is 1.6 mGy and the acceptable is 2 mGy. In Brazil, it is only required the input dose calculation in skin for 45 mm breasts. However, the calculation of AGD is required for different thicknesses of the breast, to identify the best mammographic pattern aiming at better image quality at the lowest dose provided the patient.

  3. TU-F-18C-05: Evaluation of a Method to Calculate Patient-Oriented MGD Coefficients Using Estimates of Glandular Tissue Distribution

    International Nuclear Information System (INIS)

    Porras-Chaverri, M; Galavis, P; Bakic, P; Vetter, J

    2014-01-01

    Purpose: Evaluate mammographic mean glandular dose (MGD) coefficients for particular known tissue distributions using a novel formalism that incorporates the effect of the heterogeneous glandular tissue distribution, by comparing them with MGD coefficients derived from the corresponding anthropomorphic computer breast phantom. Methods: MGD coefficients were obtained using MCNP5 simulations with the currently used homogeneous assumption and the heterogeneously-layered breast (HLB) geometry and compared against those from the computer phantom (ground truth). The tissue distribution for the HLB geometry was estimated using glandularity map image pairs corrected for the presence of non-glandular fibrous tissue. Heterogeneity of tissue distribution was quantified using the glandular tissue distribution index, Idist. The phantom had 5 cm compressed breast thickness (MLO and CC views) and 29% whole breast glandular percentage. Results: Differences as high as 116% were found between the MGD coefficients with the homogeneous breast core assumption and those from the corresponding ground truth. Higher differences were found for cases with more heterogeneous distribution of glandular tissue. The Idist for all cases was in the [−0.8 − +0.3] range. The use of the methods presented in this work results in better agreement with ground truth with an improvement as high as 105 pp. The decrease in difference across all phantom cases was in the [9 − 105] pp range, dependent on the distribution of glandular tissue and was larger for the cases with the highest Idist values. Conclusion: Our results suggest that the use of corrected glandularity image pairs, as well as the HLB geometry, improves the estimates of MGD conversion coefficients by accounting for the distribution of glandular tissue within the breast. The accuracy of this approach with respect to ground truth is highly dependent on the particular glandular tissue distribution studied. Predrag Bakic discloses current

  4. Arabidopsis ketoacyl-CoA synthase 16 (KCS16) forms C36 /C38 acyl precursors for leaf trichome and pavement surface wax.

    Science.gov (United States)

    Hegebarth, Daniela; Buschhaus, Christopher; Joubès, Jérôme; Thoraval, Didier; Bird, David; Jetter, Reinhard

    2017-09-01

    The aliphatic waxes sealing plant surfaces against environmental stress are generated by fatty acid elongase complexes, each containing a β-ketoacyl-CoA synthase (KCS) enzyme that catalyses a crucial condensation forming a new C─C bond to extend the carbon backbone. The relatively high abundance of C 35 and C 37 alkanes derived from C 36 and C 38 acyl-CoAs in Arabidopsis leaf trichomes (relative to other epidermis cells) suggests differences in the elongation machineries of different epidermis cell types, possibly involving KCS16, a condensing enzyme expressed preferentially in trichomes. Here, KCS16 was found expressed primarily in Arabidopsis rosette leaves, flowers and siliques, and the corresponding protein was localized to the endoplasmic reticulum. The cuticular waxes on young leaves and isolated leaf trichomes of ksc16 loss-of-function mutants were depleted of C 35 and C 37 alkanes and alkenes, whereas expression of Arabidopsis KCS16 in yeast and ectopic overexpression in Arabidopsis resulted in accumulation of C 36 and C 38 fatty acid products. Taken together, our results show that KCS16 is the sole enzyme catalysing the elongation of C 34 to C 38 acyl-CoAs in Arabidopsis leaf trichomes and that it contributes to the formation of extra-long compounds in adjacent pavement cells. © 2017 John Wiley & Sons Ltd.

  5. Evaluation of mean glandular dose in a full-field digital mammography unit in Tabriz (IR)

    International Nuclear Information System (INIS)

    Riabi, H. A.; Mehnati, P.; Mesbahi, A.

    2010-01-01

    This study was aimed at evaluating the mean glandular dose (MGD) and affecting factors during mammography examinations by a full-field digital mammography unit. An extensive quality control program was performed to assure that the unit is properly working. Required information including compressed breast thickness (CBT), breast parenchymal pattern and technical factors used for imaging were recorded. An entrance skin exposure measurement was also performed using slabs of polymethylmethacrylate with 2-8 cm thickness. On the basis of recorded information and measured data, the MGD was estimated for 1145 mammography examinations obtained from 298 patients. Mean CBTs of 4.9 and 5.8 cm and MGDs of 2 and 2.4 mGy were observed for cranio-caudal and medio-lateral oblique views, respectively. Significant correlation was seen between MGD and CBT, breast parenchymal pattern and applied kVp and mAs. (authors)

  6. Mean glandular dose measurement on various breast phantom using mammography machine in MINT Medical Physics Laboratory

    International Nuclear Information System (INIS)

    Wan Hazlinda Ismail; Asmaliza Hashim; Abd Aziz Mhd Ramli

    2005-01-01

    Until recently, mammography have been the primary means of detecting early breast cancer. Although there is a risk of radiation- induced carcinogenesis associated with the x-ray examination of the female breast, but this risk is small compared to its benefits with modern equipment and technique. Therefore, it is important to determine the dose of the tissue at risk from radiation exposure by measuring the mean glandular dose (MGD). This can help minimize the risk to the patient. This paper describe the MGD measurement done on various types and thickness of breast phantom using a Bennett mammography machine model DMF-150 in the Medical Physics laboratory at the Malaysian Institute for Nuclear Technology Research (MINT). Results of this study are discussed in this paper. (Author)

  7. Human papillomavirus prevalence and type-distribution in cervical glandular neoplasias

    DEFF Research Database (Denmark)

    Holl, Katsiaryna; Nowakowski, Andrzej M; Powell, Ned

    2015-01-01

    Cervical glandular neoplasias (CGN) present a challenge for cervical cancer prevention due to their complex histopathology and difficulties in detecting preinvasive stages with current screening practices. Reports of human papillomavirus (HPV) prevalence and type-distribution in CGN vary, providing...... uncertain evidence to support prophylactic vaccination and HPV screening. This study [108288/108290] assessed HPV prevalence and type-distribution in women diagnosed with cervical adenocarcinoma in situ (AIS, N = 49), adenosquamous carcinoma (ASC, N = 104), and various adenocarcinoma subtypes (ADC, N = 461...... of CGN are HPV16/18/45-positive, the incorporation of prophylactic vaccination and HPV testing in cervical cancer screening are important prevention strategies. Our results suggest that special attention should be given to certain rarer ADC subtypes as most appear to be unrelated to HPV....

  8. Relationship of Compressed Breast Thickness and Average Glandular Dose According to Focus/Filter

    International Nuclear Information System (INIS)

    Lee, In Ja

    2009-01-01

    The study examined the relationship between the compressed breast thickness and Average Glandular Dose (AGD) among 1,969 outpatients who went through breast X-ray in a university hospital for 10 months from July 1st, 2007 to April 30th, 2008. Then it analyzed the result acquired from 3,900 cases of Cranio-Caudal (CC) view, especially, when the breasts were compressed (13-15daN). The following is the conclusion driven from the relationship analysis. 1. The subjects aged in 40s and 50s were 2,679 out of 3,900 cases and this figure was 68.69% in all. 2. In terms of distribution depending on focus/filter, 41.0% was Mo/Mo, 34.8% was Mo/Rh, and 24.2% was Rh/Rh. 3. In terms of compressed breast thickness depending on focus/filter, the average thickness was 26.91 mm at Mo/Mo, 38.84 mm at Mo/Rh, and 48.80 mm at Rh/Rh. The average thickness of the entire cases was shown to be 36.27 mm. 4. AGD depending on focus/filter was 1.27 mGy at Mo/Mo, 1.55 mGy at Mo/Rh, and 1.42 mGy at Rh/Rh. The average glandular dose of the entire cases was shown to be 1.43 mGy. 5. The relationship of AGD depending on compressed breast thickness at Mo/Mo was y=0.0318x + 0.470 while it was y=0.0206x + 0.709 at Mo/Rh and y=0.0248x + 0.335 at Mo/Rh. It was highly influenced by the compressed breast thickness, however, more variation was detected at Mo/Mo depending on breast thickness.

  9. Determination of mean glandular dose on patients and phantom in X-ray mammography

    International Nuclear Information System (INIS)

    Avramova-Cholakova, S.; Vassileva, J.

    2008-01-01

    The statistics of breast cancer rate in Bulgaria show a tendency towards increase of the morbidity from this disease. Last years campaigns against breast cancer are organized yearly. This leads to an increased number of screening and diagnostic mammograms that are made in the country. The dose associated with the examination is very low but not slightingly small. The glandular tissue in the breast is considered to be the most sensitive in relation to the radiation exposure. Several publications propose different methods, measurement set up or conversion coefficients for the calculation of the mean glandular dose (MGD) delivered to the breast during the X-ray examination. The question about the standardization of the measurement procedures arises since the differences in the results obtained using different methodologies may be quite big. The aim of this work is to develop a standard procedure for the measurement of MGD based on the recommendations mentioned in the European protocol on dosimetry in mammography, the European protocol for the quality control of the physical and technical aspects of mammography screening and the Code of practice: TRS 457 of the IAEA. Five contemporary film-screen mammography units were included in this study. Attention should be paid to the measurement set up. The reference point is chosen 6 cm from the chest wall edge laterally centered. If an ionization chamber is used for dose measurements the compression plate should be placed in close contact with it. If solid state detectors are used the compression plate should be put away from the detector and the output recalculated like if the plate is near the detector. The conversion coefficients for age dependence are not used in this study as not appropriate for the population included in it. PMMA measurements for the determination of diagnostic reference levels could be used but more correct results would be obtained with patient measurements

  10. Increased adrenocortical response to adrenocorticotropic hormone (ACTH) in sport horses with equine glandular gastric disease (EGGD).

    Science.gov (United States)

    Scheidegger, M D; Gerber, V; Bruckmaier, R M; van der Kolk, J H; Burger, D; Ramseyer, A

    2017-10-01

    This study tested the hypothesis that adrenocortical function would be altered in horses with equine gastric ulcer syndrome (EGUS). Twenty-six sport horses competing at national or international levels in eventing (n=15) or endurance (n=11) were subjected to a gastroscopic examination and an adrenocorticotropic hormone (ACTH) stimulation test. Salivary cortisol concentrations were measured before (baseline) and after (30, 60, 90, 120 and 150min) IV ACTH injection (1μg/kg bodyweight). Within EGUS, two distinct diseases, equine squamous gastric disease (ESGD) and equine glandular gastric disease (EGGD), can be distinguished. ESGD was diagnosed in 8/11 (73%; 95% confidence intervals [95%CI], 43-92%) endurance horses and 5/15 (33%; 95% CI, 14-58%) eventing horses. EGGD was observed in 9/11 (82%; 95% CI, 53-96%) endurance horses and 9/15 (60%; 95% CI, 35-81%) eventing horses. The presence or severity of ESGD was unrelated to the presence or severity of EGGD. ACTH stimulation induced a larger increase in cortisol concentration in horses with moderate EGGD than in horses with mild EGGD. Cortisol concentration during the entire sampling period (total increase in cortisol concentration during the entire sampling period [dAUC], 31.1±6.4ng/mL) and the highest measured concentration at a single time point (maximal increase in cortisol concentration [dMAX], 10.3±2.3ng/mL) were increased (P=0.005 and P=0.038, respectively), indicating that horses with glandular gastric disease exhibited increased adrenocortical responses to ACTH stimulation. These results suggest that EGGD might be associated with an enhanced adrenocortical sensitivity. Further investigations are warranted to confirm the association between adrenocortical sensitivity and EGGD and to elucidate the pathophysiological mechanisms involved. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Estimation of mean glandular dose for patients who undergo mammography and studying the factors affecting it

    Science.gov (United States)

    Barzanje, Sana L. N. H.; Harki, Edrees M. Tahir Nury

    2017-09-01

    The objective of this study was to determine mean glandular dose (MGD) during diagnostic mammography. This study was done in two hospitals in Hawler city in Kurdistan -region /Iraq, the exposure parameters kVp and mAs was recorded for 40 patients under go mammography. The MGD estimated by multiplied ESD with normalized glandular dose (Dn). The ESD measured indirectly by measuring output radiation mGy/mAs by using PalmRAD 907 as a suitable detector (Gigger detector).the results; shown that the mean and its standard deviation of MGD for Screen Film Mammography and Digital Mammography are (0.95±0.18)mGy and (0.99±0.26)mGy, respectively. And there is a significant difference between MGD for Screen Film Mammography and Digital Mammography views (p≤0. 05). Also the mean value and its standard deviation of MGD for screen film mammography is (0.96±0.21) for CC projection and (1.03±0.3) mGy for MLO projection, but mean value and its standard deviation evaluated of MGD for digital mammography is (0.92±0.17) mGy for CC projection and (0.98±0.2) mGy for MLO projection. As well as, the effect of kVp and mAs in MGD were studied, shows that in general as kVp and mAs increased the MGD increased accordingly in both of mammography systems.

  12. PTEN phosphatase-independent maintenance of glandular morphology in a predictive colorectal cancer model system.

    Science.gov (United States)

    Jagan, Ishaan C; Deevi, Ravi K; Fatehullah, Aliya; Topley, Rebecca; Eves, Joshua; Stevenson, Michael; Loughrey, Maurice; Arthur, Kenneth; Campbell, Frederick Charles

    2013-11-01

    Organotypic models may provide mechanistic insight into colorectal cancer (CRC) morphology. Three-dimensional (3D) colorectal gland formation is regulated by phosphatase and tensin homologue deleted on chromosome 10 (PTEN) coupling of cell division cycle 42 (cdc42) to atypical protein kinase C (aPKC). This study investigated PTEN phosphatase-dependent and phosphatase-independent morphogenic functions in 3D models and assessed translational relevance in human studies. Isogenic PTEN-expressing or PTEN-deficient 3D colorectal cultures were used. In translational studies, apical aPKC activity readout was assessed against apical membrane (AM) orientation and gland morphology in 3D models and human CRC. We found that catalytically active or inactive PTEN constructs containing an intact C2 domain enhanced cdc42 activity, whereas mutants of the C2 domain calcium binding region 3 membrane-binding loop (M-CBR3) were ineffective. The isolated PTEN C2 domain (C2) accumulated in membrane fractions, but C2 M-CBR3 remained in cytosol. Transfection of C2 but not C2 M-CBR3 rescued defective AM orientation and 3D morphogenesis of PTEN-deficient Caco-2 cultures. The signal intensity of apical phospho-aPKC correlated with that of Na(+)/H(+) exchanger regulatory factor-1 (NHERF-1) in the 3D model. Apical NHERF-1 intensity thus provided readout of apical aPKC activity and associated with glandular morphology in the model system and human colon. Low apical NHERF-1 intensity in CRC associated with disruption of glandular architecture, high cancer grade, and metastatic dissemination. We conclude that the membrane-binding function of the catalytically inert PTEN C2 domain influences cdc42/aPKC-dependent AM dynamics and gland formation in a highly relevant 3D CRC morphogenesis model system.

  13. PTEN Phosphatase-Independent Maintenance of Glandular Morphology in a Predictive Colorectal Cancer Model System

    Directory of Open Access Journals (Sweden)

    Ishaan C. Jagan

    2013-11-01

    Full Text Available Organotypic models may provide mechanistic insight into colorectal cancer (CRC morphology. Three-dimensional (3D colorectal gland formation is regulated by phosphatase and tensin homologue deleted on chromosome 10 (PTEN coupling of cell division cycle 42 (cdc42 to atypical protein kinase C (aPKC. This study investigated PTEN phosphatase-dependent and phosphatase-independent morphogenic functions in 3D models and assessed translational relevance in human studies. Isogenic PTEN-expressing or PTEN-deficient 3D colorectal cultures were used. In translational studies, apical aPKC activity readout was assessed against apical membrane (AM orientation and gland morphology in 3D models and human CRC. We found that catalytically active or inactive PTEN constructs containing an intact C2 domain enhanced cdc42 activity, whereas mutants of the C2 domain calcium binding region 3 membrane-binding loop (M-CBR3 were ineffective. The isolated PTEN C2 domain (C2 accumulated in membrane fractions, but C2 M-CBR3 remained in cytosol. Transfection of C2 but not C2 M-CBR3 rescued defective AM orientation and 3D morphogenesis of PTEN-deficient Caco-2 cultures. The signal intensity of apical phospho-aPKC correlated with that of Na+/H+ exchanger regulatory factor-1 (NHERF-1 in the 3D model. Apical NHERF-1 intensity thus provided readout of apical aPKC activity and associated with glandular morphology in the model system and human colon. Low apical NHERF-1 intensity in CRC associated with disruption of glandular architecture, high cancer grade, and metastatic dissemination. We conclude that the membrane-binding function of the catalytically inert PTEN C2 domain influences cdc42/aPKC-dependent AM dynamics and gland formation in a highly relevant 3D CRC morphogenesis model system.

  14. Dual-energy digital mammography: Calibration and inverse-mapping techniques to estimate calcification thickness and glandular-tissue ratio

    International Nuclear Information System (INIS)

    Kappadath, S. Cheenu; Shaw, Chris C.

    2003-01-01

    Breast cancer may manifest as microcalcifications in x-ray mammography. Small microcalcifications, essential to the early detection of breast cancer, are often obscured by overlapping tissue structures. Dual-energy imaging, where separate low- and high-energy images are acquired and synthesized to cancel the tissue structures, may improve the ability to detect and visualize microcalcifications. Transmission measurements at two different kVp values were made on breast-tissue-equivalent materials under narrow-beam geometry using an indirect flat-panel mammographic imager. The imaging scenario consisted of variable aluminum thickness (to simulate calcifications) and variable glandular ratio (defined as the ratio of the glandular-tissue thickness to the total tissue thickness) for a fixed total tissue thickness--the clinical situation of microcalcification imaging with varying tissue composition under breast compression. The coefficients of the inverse-mapping functions used to determine material composition from dual-energy measurements were calculated by a least-squares analysis. The linear function poorly modeled both the aluminum thickness and the glandular ratio. The inverse-mapping functions were found to vary as analytic functions of second (conic) or third (cubic) order. By comparing the model predictions with the calibration values, the root-mean-square residuals for both the cubic and the conic functions were ∼50 μm for the aluminum thickness and ∼0.05 for the glandular ratio

  15. Detection of cervical intraepithelial neoplasia in women with atypical squamous or glandular cells of undetermined significance cytology: a prospective study

    NARCIS (Netherlands)

    Wensveen, Celesta; Kagie, Marjolein; Veldhuizen, Roel; de Groot, Christianne; Denny, Lynette; Zwinderman, Koos; Trimbos, Baptist

    2003-01-01

    (1) To assess the prevalence of histologically confirmed cervical intraepithelial neoplasia in patients with cervical smears diagnosed as atypical squamous or glandular cells of undetermined significance. (2) To evaluate the role of colposcopy and the presence of human papillomavirus in detecting

  16. Estimates of Average Glandular Dose with Auto-modes of X-ray Exposures in Digital Breast Tomosynthesis

    Directory of Open Access Journals (Sweden)

    Izdihar Kamal

    2015-05-01

    Full Text Available Objectives: The aim of this research was to examine the average glandular dose (AGD of radiation among different breast compositions of glandular and adipose tissue with auto-modes of exposure factor selection in digital breast tomosynthesis. Methods: This experimental study was carried out in the National Cancer Society, Kuala Lumpur, Malaysia, between February 2012 and February 2013 using a tomosynthesis digital mammography X-ray machine. The entrance surface air kerma and the half-value layer were determined using a 100H thermoluminescent dosimeter on 50% glandular and 50% adipose tissue (50/50 and 20% glandular and 80% adipose tissue (20/80 commercially available breast phantoms (Computerized Imaging Reference Systems, Inc., Norfolk, Virginia, USA with auto-time, auto-filter and auto-kilovolt modes. Results: The lowest AGD for the 20/80 phantom with auto-time was 2.28 milliGray (mGy for two dimension (2D and 2.48 mGy for three dimensional (3D images. The lowest AGD for the 50/50 phantom with auto-time was 0.97 mGy for 2D and 1.0 mGy for 3D. Conclusion: The AGD values for both phantoms were lower against a high kilovolt peak and the use of auto-filter mode was more practical for quick acquisition while limiting the probability of operator error.

  17. Monte Carlo simulation studies for the determination of microcalcification thickness and glandular ratio through dual-energy mammography

    Science.gov (United States)

    Del Lama, L. S.; Godeli, J.; Poletti, M. E.

    2017-08-01

    The majority of breast carcinomas can be associated to the presence of calcifications before the development of a mass. However, the overlapping tissues can obscure the visualization of microcalcification clusters due to the reduced contrast-noise ratio (CNR). In order to overcome this complication, one potential solution is the use of the dual-energy (DE) technique, in which two different images are acquired at low (LE) and high (HE) energies or kVp to highlight specific lesions or cancel out tissue background. In this work, the DE features were computationally studied considering simulated acquisitions from a modified PENELOPE Monte Carlo code. The employed irradiation geometry considered typical distances used in digital mammography, a CsI detection system and an updated breast model composed of skin, microcalcifications and glandular and adipose tissues. The breast thickness ranged from 2 to 6 cm with glandularities of 25%, 50% and 75%, where microcalcifications with dimensions from 100 up to 600 μm were positioned. In general, results pointed an efficiency index better than 87% for the microcalcification thicknesses and better than 95% for the glandular ratio. The simulations evaluated in this work can be used to optimize the elements from the DE imaging chain, in order to become a complementary tool for the conventional single-exposure images, especially for the visualization and estimation of calcification thicknesses and glandular ratios.

  18. Abnormal ion content, hydration and granule expansion of the secretory granules from cystic fibrosis airway glandular cells

    International Nuclear Information System (INIS)

    Baconnais, S.; Delavoie, F.; Zahm, J.M.; Milliot, M.; Terryn, C.; Castillon, N.; Banchet, V.; Michel, J.; Danos, O.; Merten, M.; Chinet, T.; Zierold, K.; Bonnet, N.; Puchelle, E.; Balossier, G.

    2005-01-01

    The absence or decreased expression of cystic fibrosis transmembrane conductance regulator (CFTR) induces increased Na + absorption and hyperabsorption of the airway surface liquid (ASL) resulting in a dehydrated and hyperviscous ASL. Although the implication of abnormal airway submucosal gland function has been suggested, the ion and water content in the Cystic Fibrosis (CF) glandular secretory granules, before exocytosis, is unknown. We analyzed, in non-CF and CF human airway glandular cell lines (MM-39 and KM4, respectively), the ion content in the secretory granules by electron probe X-ray microanalysis and the water content by quantitative dark field imaging on freeze-dried cryosections. We demonstrated that the ion content (Na + , Mg 2+ , P, S and Cl - ) is significantly higher and the water content significantly lower in secretory granules from the CF cell line compared to the non-CF cell line. Using videomicroscopy, we observed that the secretory granule expansion was deficient in CF glandular cells. Transfection of CF cells with CFTR cDNA or inhibition of non-CF cells with CFTR inh -172, respectively restored or decreased the water content and granule expansion, in parallel with changes in ion content. We hypothesize that the decreased water and increased ion content in glandular secretory granules may contribute to the dehydration and increased viscosity of the ASL in CF

  19. Estimation of glandular content rate and statistical analysis of the influence of age group and compressed breast thickness on the estimated value

    International Nuclear Information System (INIS)

    Ohmori, Naoki; Ashida, Kenji; Fujita, Osamu

    2003-01-01

    Because the glandular content rate is an important factor in evaluating breast cancer detection and average glandular dose, it is important in mammography research to estimate and analyze this rate. The purpose of this study was to obtain a formula for statistical estimation of the glandular content rate, to clarify statistically the influence of age group and compressed breast thickness (CBT) on estimating the glandular content rate, and to show statistically the general relation between glandular content rate and the factors of age and CBT. The subjects were 740 Japanese women aged 20-91 years (mean±SD: 48.3±12.8 years) who had undergone mammography. In our study, the glandular content rate was statistically estimated from age group, mAs-value, and CBT when subjects underwent mammography, from a phantom simulation, and from MR images of the breast. In addition, multivariate analysis was carried to examine statistically the influence of age group and CBT on glandular content rate. The mean glandular content rate as estimated by age group was as follows: 35.6% for those in their 20s, 33.4% in the 30s, 27.5% in the 40s, 23.8% in the 50s, and 21.8% in those 60 and over. The rate for the subjects as a whole was 27.1%. This study indicated that overestimation occurred if the estimated value of the glandular content rate was not corrected in the 3D-measurement by MRI. In addition, this study showed that the statistical influence on glandular content rate was significantly larger for CBT than age. (author)

  20. TCW: transcriptome computational workbench.

    Directory of Open Access Journals (Sweden)

    Carol Soderlund

    Full Text Available BACKGROUND: The analysis of transcriptome data involves many steps and various programs, along with organization of large amounts of data and results. Without a methodical approach for storage, analysis and query, the resulting ad hoc analysis can lead to human error, loss of data and results, inefficient use of time, and lack of verifiability, repeatability, and extensibility. METHODOLOGY: The Transcriptome Computational Workbench (TCW provides Java graphical interfaces for methodical analysis for both single and comparative transcriptome data without the use of a reference genome (e.g. for non-model organisms. The singleTCW interface steps the user through importing transcript sequences (e.g. Illumina or assembling long sequences (e.g. Sanger, 454, transcripts, annotating the sequences, and performing differential expression analysis using published statistical programs in R. The data, metadata, and results are stored in a MySQL database. The multiTCW interface builds a comparison database by importing sequence and annotation from one or more single TCW databases, executes the ESTscan program to translate the sequences into proteins, and then incorporates one or more clusterings, where the clustering options are to execute the orthoMCL program, compute transitive closure, or import clusters. Both singleTCW and multiTCW allow extensive query and display of the results, where singleTCW displays the alignment of annotation hits to transcript sequences, and multiTCW displays multiple transcript alignments with MUSCLE or pairwise alignments. The query programs can be executed on the desktop for fastest analysis, or from the web for sharing the results. CONCLUSION: It is now affordable to buy a multi-processor machine, and easy to install Java and MySQL. By simply downloading the TCW, the user can interactively analyze, query and view their data. The TCW allows in-depth data mining of the results, which can lead to a better understanding of the

  1. Cervical squamous and glandular intraepithelial neoplasia: identification and current management approaches Neoplasia intraepitelial cervical escamosa y glandular: identificación y estrategias de manejo

    Directory of Open Access Journals (Sweden)

    V Cecil Wright

    2003-01-01

    realiza mediante la biopsia de cono, y el espécimen debe tener márgenes negativos para enfermedad. La histerectomía es un tratamiento probable, a menos que la fertilidad esté siendo buscada. La escisión, particularmente por electrocirugía (loop, puede interferir con la interpretación histológica en algunos casos o de ambos, particularmente en enfermedades escamosas y adenocarcinoma in situ. En este artículo se describe ampliamente el manejo de la neoplasia intraepitelial escamosa y glandular.

  2. Células glandulares atípicas em esfregaços cervicovaginais: significância e aspectos atuais Atypical glandular cells in cervical smears: significance and current aspects

    Directory of Open Access Journals (Sweden)

    Adriana Bittencourt Campaner

    2007-02-01

    Full Text Available Células glandulares atípicas (AGC em esfregaços cervicovaginais são achados citológicos raros, porém de significado representativo. Sua incidência varia, na literatura, de 0,08% a 0,81%. O sistema Bethesda de 2001 classifica estas lesões glandulares como AGCs sem outras especificações, AGCs provavelmente neoplásicas, adenocarcinoma cervical in situ (AIS e adenocarcinoma invasivo. Das mulheres portadoras de AGC, grande parte não apresentará qualquer tipo de alteração histológica em avaliação subseqüente. Entretanto, em 17,4% a 62,2% dos casos serão encontradas lesões histológicas significativas, como neoplasias intra-epiteliais cervicais, AIS, neoplasias escamosas e glandulares, cervicais e endometriais, bem como neoplasias de outras localizações. O risco de doença significativa está relacionado à subdivisão de AGC encontrada. Em virtude da elevada probabilidade de anormalidades histológicas significativas em casos de AGC, a simples repetição citológica é insuficiente para o seguimento dessa condição. Esta atualização descreve a epidemiologia, a avaliação e a conduta das pacientes portadoras dessa anormalidade citológica.Atypical glandular cells (AGC on cervical smears are unusual but important cytologic diagnosis. The incidence of AGC ranges from 0.08% to 0.81 % of all cervical smears tests. The 2001 Bethesda System nomenclature classifies these glandular lesions as AGC not otherwise specified, AGC favor neoplasia, endocervical adenocarcinoma in situ (AIS and invasive adenocarcinoma. Of women with AGC smears, a great number will have no histologic abnormalities on further evaluation. However, 17.4% to 62.2% are found to have significant histologic lesions such as cervical intraepithelial neoplasia, AIS, squamous and glandular cancers from sites farther the cervix and endometrium. The risk of significant disease is related to the AGC subclassification that was found. Because of the high likelihood that AGC

  3. Differentiating between endocervical glandular neoplasia and high grade squamous intraepithelial lesions in endocervical crypts: cytological features in ThinPrep and SurePath cervical cytology samples.

    Science.gov (United States)

    Thiryayi, Sakinah A; Marshall, Janet; Rana, Durgesh N

    2009-05-01

    A recent audit at our institution revealed a higher number of cases diagnosed as endocervical glandular neoplasia on ThinPrep (TP) cervical cytology samples (9 cases) as opposed to SurePath (SP) (1 case), which on histology showed only high-grade cervical intraepithelial neoplasia (CIN) with endocervical crypt involvement (CI). We attempted to ascertain the reasons for this finding by reviewing the available slides of these cases, as well as slides of cases diagnosed as glandular neoplasia on cytology and histology; cases diagnosed as high-grade squamous intraepithelial lesions (HSIL) on cytology which had CIN with CI on histology and cases with mixed glandular and squamous abnormalities diagnosed both cytologically and histologically. Single neoplastic glandular cells and short pseudostratified strips were more prevalent in SP than TP with the cell clusters in glandular neoplasia 3-4 cells thick, in contrast to the dense crowded centre of cell groups in HSIL with CI. The cells at the periphery of groups can be misleading. Cases with HSIL and glandular neoplasia have a combination of the features of each entity in isolation. The diagnosis of glandular neoplasia remains challenging and conversion from conventional to liquid based cervical cytology requires a period of learning and adaptation, which can be facilitated by local audit and review of the cytology slides in cases with a cytology-histology mismatch. (c) 2009 Wiley-Liss, Inc.

  4. Assessment of Mean Glandular Dose in Mammography System with Different Anode-Filter Combinations Using MCNP Code.

    Science.gov (United States)

    Gholamkar, Lida; Mowlavi, Ali Asghar; Sadeghi, Mahdi; Athari, Mitra

    2016-10-01

    X-ray mammography is one of the general methods for early detection of breast cancer. Since glandular tissue in the breast is sensitive to radiation and it increases the risk of cancer, the given dose to the patient is very important in mammography. The aim of this study was to determine the average absorbed dose of X-ray radiation in the glandular tissue of the breast during mammography examinations as well as investigating factors that influence the mean glandular dose (MGD). One of the precise methods for determination of MGD absorbed by the breast is Monte Carlo simulation method which is widely used to assess the dose. We studied some different X-ray sources and exposure factors that affect the MGD. "Midi-future" digital mammography system with amorphous-selenium detector was simulated using the Monte Carlo N-particle extended (MCNPX) code. Different anode/filter combinations such as tungsten/silver (W/Ag), tungsten/rhodium (W/Rh), and rhodium/aluminium (Rh/Al) were simulated in this study. The voltage of X-ray tube ranged from 24 kV to 32 kV with 2 kV intervals and the breast phantom thickness ranged from 3 to 8 cm, and glandular fraction g varied from 10% to 100%. MGD was measured for different anode/filter combinations and the effects of changing tube voltage, phantom thickness, combination and glandular breast tissue on MGD were studied. As glandular g and X-ray tube voltage increased, the breast dose increased too, and the increase of breast phantom thickness led to the decrease of MGD. The obtained results for MGD were consistent with the result of Boone et al. that was previously reported. By comparing the results, we saw that W/Rh anode/filter combination is the best choice in breast mammography imaging because of the lowest delivered dose in comparison with W/Ag and Rh/Al. Moreover, breast thickness and g value have significant effects on MGD.

  5. Assessment of mean glandular dose for patients in mammography in some Hospitals in Khartoum state

    International Nuclear Information System (INIS)

    Abu Elmola, Alaa Mahdi

    2016-12-01

    A mammography examination facilitates the early detection of breast cancer. However, the potential risk of radiation- induced carcinogenesis is also increased with such a procedure. Thus assessment of the breast dose is important. The objective of this study was to determine the mean glandular dose (MGD) resulting from cranio caudal(CC) and mediolateral oblique (MLO) views in one breast and the total dose per woman in Sudan, and to identify the factors affecting it. Measurements were performed to estimate mean glandular doses for 60 patients who underwent mammography examination in two clinics in Khartoum, Sudan.Doses were studied in RCH and NDC, centers which were using computed radiography(CR)devices. The piranha system was used for determining the MGD in this work. The characteristics of the radiographic equipment and the exposure data of each patient were recorded using designed format. The MGD was calculated from the measured incident Air kerma using appropriate conversion coefficients. The range of CBT was (1-7)cm for two projections. The respective averages for the CC and MLO projections were (4.55±1.38)mGy and (4.15±1.33) mGy, respectively. The average MGD per image was (4.3±1.35)mGy. The MGD per women was (8.6±1.35)mGy. The mean±SD MGD per image in the present study was lower than most of similar reports. The average MGD values recorded in this study were above the limiting value of the Institute of Physical Sciences in Medicine(2.0 mGy) and American College of Radiology (3.0 mGy recommendation. This suggests that mammography x-ray generators in this case are not capable of achieving acceptable dose levels for patients safety. Therefore, with consideration of all other factors, quality control program tests must be carried out periodically and frequently of the mammography equipment.(Author)

  6. A Monte Carlo model for mean glandular dose evaluation in spot compression mammography.

    Science.gov (United States)

    Sarno, Antonio; Dance, David R; van Engen, Ruben E; Young, Kenneth C; Russo, Paolo; Di Lillo, Francesca; Mettivier, Giovanni; Bliznakova, Kristina; Fei, Baowei; Sechopoulos, Ioannis

    2017-07-01

    To characterize the dependence of normalized glandular dose (DgN) on various breast model and image acquisition parameters during spot compression mammography and other partial breast irradiation conditions, and evaluate alternative previously proposed dose-related metrics for this breast imaging modality. Using Monte Carlo simulations with both simple homogeneous breast models and patient-specific breasts, three different dose-related metrics for spot compression mammography were compared: the standard DgN, the normalized glandular dose to only the directly irradiated portion of the breast (DgNv), and the DgN obtained by the product of the DgN for full field irradiation and the ratio of the mid-height area of the irradiated breast to the entire breast area (DgN M ). How these metrics vary with field-of-view size, spot area thickness, x-ray energy, spot area and position, breast shape and size, and system geometry was characterized for the simple breast model and a comparison of the simple model results to those with patient-specific breasts was also performed. The DgN in spot compression mammography can vary considerably with breast area. However, the difference in breast thickness between the spot compressed area and the uncompressed area does not introduce a variation in DgN. As long as the spot compressed area is completely within the breast area and only the compressed breast portion is directly irradiated, its position and size does not introduce a variation in DgN for the homogeneous breast model. As expected, DgN is lower than DgNv for all partial breast irradiation areas, especially when considering spot compression areas within the clinically used range. DgN M underestimates DgN by 6.7% for a W/Rh spectrum at 28 kVp and for a 9 × 9 cm 2 compression paddle. As part of the development of a new breast dosimetry model, a task undertaken by the American Association of Physicists in Medicine and the European Federation of Organizations of Medical Physics

  7. Glandular dose and image quality control in mammography facilities with computerized radiography systems

    International Nuclear Information System (INIS)

    Dantas, Marcelino Vicente de Almeida

    2010-01-01

    Breast cancer is the most common cancer among women, and early detection is critical to its diagnosis and treatment. To date, the most effective method for early detection of breast cancer has been x-ray mammography for which the screen/film (SF) technique has been the gold standard. However, even though SF combinations have been improved and optimized over the years for breast imaging, there are some critical limitations, including a narrow exposure range, image artifacts, film processing problems, and inflexibility in image processing and film management. In recent years, digital mammography has been introduced in cancer screening programmes with the screen/film techniques gradually being phased out. Computed radiography (CR), also commonly known as photostimulable phosphor (PSP) imaging or storage phosphor, employs reusable imaging plates and associated hardware and software to acquire and to display digital projection radiographs. In this work, a protocol model was tested for performing image quality control and average glandular dose (AGD) evaluation in 19 institutions with computed radiography systems for mammography. The protocol was validated through tests at the Laboratorio de Radioprotecao Aplicada a Mamografia (LARAM) from the Centro de Desenvolvimento da Tecnologia Nuclear (CDTN). The image quality visual evaluation of CDMAM phantom showed that 53% of the facilities were able to produce images of excellent quality. Furthermore, the automated evaluation of image quality, using the analyze software cdcom.exe, showed that 57% of the images were considered to be of good quality. The detector linearity test showed that the CR response is very linear, where 95% of facilities evaluated were considered to be compliant. For the image noise was found that only 20% of facilities are in agreement with the parameters established for this test. The average glandular doses, which patients may be getting to perform an examination, were below the action levels

  8. Establishing Substantial Equivalence: Transcriptomics

    Science.gov (United States)

    Baudo, María Marcela; Powers, Stephen J.; Mitchell, Rowan A. C.; Shewry, Peter R.

    Regulatory authorities in Western Europe require transgenic crops to be substantially equivalent to conventionally bred forms if they are to be approved for commercial production. One way to establish substantial equivalence is to compare the transcript profiles of developing grain and other tissues of transgenic and conventionally bred lines, in order to identify any unintended effects of the transformation process. We present detailed protocols for transcriptomic comparisons of developing wheat grain and leaf material, and illustrate their use by reference to our own studies of lines transformed to express additional gluten protein genes controlled by their own endosperm-specific promoters. The results show that the transgenes present in these lines (which included those encoding marker genes) did not have any significant unpredicted effects on the expression of endogenous genes and that the transgenic plants were therefore substantially equivalent to the corresponding parental lines.

  9. Células glandulares atípicas e câncer de colo uterino: revisão sistemática Atypical glandular cells and cervical cancer: systematic review

    Directory of Open Access Journals (Sweden)

    Juliana Pedrosa de Holanda Marques

    2011-04-01

    Full Text Available Atipias de células glandulares em esfregaços cervicovaginais é um achado citológico na rotina de rastreamento do câncer cervical, que aumentou nas últimas décadas. Sua constatação é importante clinicamente, pois é alta a percentagem de casos associados com doença cervical e endometrial de alto grau e câncer. Este trabalho avaliou, por meio de uma revisão sistemática, estudos que investigaram o perfil das lesões de colo uterino em avaliações histológicas de seguimento de pacientes já diagnosticadas com células glandulares atípicas. Foram excluídos os estudos cuja investigação diagnóstica não incluísse o diagnóstico histopatológico. Realizou-se uma busca abrangente de publicações no período de 1966 a 2009, nas bases do LILACS, SciELO, PubMed/Medline e Old Medline. Os artigos omitidos na busca eletrônica também foram incluídos. Estavam de acordo com os critérios de inclusão 19 artigos, que foram selecionados. Este estudo tem como objetivo avaliar se a atipia celular glandular observada inicialmente na citologia relacionava-se histologicamente com a presença de lesões benignas, pré-neoplásicas ou neoplásicas. Dos 19 estudos selecionados, 11 mostraram maior correlação entre atipia glandular com patologias benignas e seis com lesões escamosas pré-malignas.Atypical glandular cells are a common finding in cervical cytology in cervical cancer screening and its occurrence has increased in the last decades. The identification of these cells is clinically very important due to its association with cervical and endometrial dysplasic lesions and cancer. Using a systematic approach, this article reviewed studies investigating cervical lesions that are characteristic in patients previously diagnosed as having atypical glandular cells. Studies in which diagnostic investigation did not include histopathological diagnosis were excluded. A comprehensive search for available material in LILACS, SciELO, PubMed/ Medline

  10. Developmental transcriptome of Aplysia californica'

    KAUST Repository

    Heyland, Andreas; Vue, Zer; Voolstra, Christian R.; Medina, Mó nica; Moroz, Leonid L.

    2010-01-01

    developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms

  11. Estimation of average glandular dose depending on the thickness of the breast

    International Nuclear Information System (INIS)

    Real, Jessica V.; Luz, Renata M. da; Fröhlich, Bruna D.; Pertile, Alessandra S.; Silva, Ana Maria Marques da

    2014-01-01

    Breast cancer is the most common type of cancer in women worldwide. Mammography is, to date, the most efficient method for detecting an abnormality in the patient's breast. It is a technique of imaging diagnostic that requires special care because radiographs without adequate quality may lead to a false diagnosis and lead to the need for a repeat examination, increasing the dose of radiation in the patient. This study aimed to evaluate the average glandular dose (AGD), depending on the breast thickness in patients undergoing routine tests, with a digital computer radiography processing system. Analyzed 30 exhibitions in patients aged (65 ± 12) years, in the right and left caudal skull projections, for breasts with thicknesses between 45 mm and 50 mm. The calculated value of the AGD for this track thickness was (1.600 ± 0.009) mGy. The performance of mammography quality control tests was satisfactory and the AGD values obtained for the chosen thickness range is acceptable, since the threshold achievable is 1.6 mGy and the acceptable is 2 mGy. In Brazil, it is only required the input dose calculation in skin for 45 mm breasts. However, the calculation of AGD is required for different thicknesses of the breast, to identify the best mammographic pattern aiming at better image quality at the lowest dose provided the patient

  12. 20-year Follow-up of Recurrent Glandular Odontogenic Cyst Mimicking a Periapical Lesion.

    Science.gov (United States)

    de Freitas Silva, Brunno Santos; Yamamoto-Silva, Fernanda Paula; Sena-Filho, Marcondes; Silva Sant'Ana, Simone Sousa; Mariano-Júnior, Wilson José; de Almeida, Oslei Paes; Estrela, Carlos

    2017-11-01

    Periapical lesions usually are caused by root canal infection; nevertheless, other pathologies may eventually involve the tooth apex, making the correct diagnosis more difficult. Glandular odontogenic cysts (GOCs) are uncommon and, despite their cystic nature, may present an aggressive behavior and a high recurrence rate. This report describes a recurrent GOC mimicking a periapical lesion that was followed up for 20 years. A 45-year-old woman described tooth discomfort for several years in the anterior region of the mandible that was not exacerbated during eating or occlusion. Clinical examination revealed no signs of swelling, redness, or inflammation in the gingival or surrounding soft tissue. Nevertheless, periapical radiography showed a well-defined large radiolucent lesion in the periapical region of teeth #22, #23, #24, and #25. The pulp test confirmed that all these teeth were vital. An incisional biopsy was performed, and with the histopathological diagnosis of an odontogenic cyst, the lesion was enucleated surgically. After recurrence, the extensive periapical multilocular lesions were again surgically removed. Based on the microscopic findings, the final diagnosis was GOC. One year later, there were no signs of recurrence. GOCs associated with the root apex may mimic periapical inflammatory diseases. Clinical, radiographic, and histopathological findings are essential for the diagnosis of inconclusive radiolucent findings in the periapical region. Biopsy specimens should be sent to a specialized oral pathology laboratory. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  13. Glandular odontogenic cyst mimicking ameloblastoma in a 78 year old female: A case report

    International Nuclear Information System (INIS)

    Lee, Byung Do; Lee, Wan; Kwon, Kyung Hwan; Choi, Moon Ki; Choi, Eun Joo; Yoon, Jung Hoon

    2014-01-01

    Glandular odontogenic cyst (GOC) is a rare, potentially aggressive jaw lesion. The common radiographic features include a well-defined radiolucency with distinct borders, presenting a uni- or multilocular appearance. A cystic lesion in the posterior mandible of a 78-year-old female was incidentally found. Radiographs showed a unilocular lesion with a scalloped margin, external root resorption of the adjacent tooth, and cortical perforation. This lesion had changed from a small ovoid shape to a more expanded lesion in a period of four years. The small lesion showed unilocularity with a smooth margin and a well-defined border, but the expanded lesion produced cortical perforation and a lobulated margin. The provisional diagnosis was an ameloblastoma, whereas the histopathological examination revealed a GOC. This was a quite rare case, given that this radiographic change was observed in the posterior mandible of an elderly female. This case showed that a GOC can grow even in people in their seventies, changing from the unilocular form to an expanded, lobulated lesion. Here, we report a case of GOC with characteristic radiographic features.

  14. Comparison of anode/filter combinations in digital mammography with respect to the average glandular dose

    International Nuclear Information System (INIS)

    Uhlenbrock, D.F.; Mertelmeier, Thomas

    2009-01-01

    To investigate the average glandular dose (AGD) applied for clinical digital mammograms acquired with the anode/filter combinations molybdenum/molybdenum (Mo/Mo), molybdenum/rhodium (Mo/Rh), and tungsten/rhodium (W/Rh). Using the method of Dance, the AGD was evaluated from the exposure data of 4867 digital mammograms at two sites equipped with a full-field digital mammography (FFDM) system based on an amorphous selenium detector. 1793 images were acquired and analyzed with Mo/Mo, 643 with Mo/Rh, and 2431 with W/Rh. In the Mo/Mo cases the mean compressed breast thickness was 46 ± 10 mm with an average AGD of 2.29 ± 1.31 mGy. For the Mo/Rh cases with a mean compressed thickness of 64 ± 9 mm, we obtained 2.76 ± 1.31 mGy. The W/Rh cases with a mean compressed thickness of 52 ± 13 mm resulted in 1.26 ± 0.44 mGy. The image quality was assessed as normal and adequate for diagnostic purposes in all cases. (orig.)

  15. Glandular odontogenic cyst mimicking ameloblastoma in a 78 year old female: A case report

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Byung Do; Lee, Wan; Kwon, Kyung Hwan; Choi, Moon Ki; Choi, Eun Joo [College of Dentistry, Wonkwang University, Iksan (Korea, Republic of); Yoon, Jung Hoon [Dept. of Oral and Maxillofacial Pathology, College of Dentistry, Daejeon Dental Hospital, Wonkwang University, Daejeon (Korea, Republic of)

    2014-09-15

    Glandular odontogenic cyst (GOC) is a rare, potentially aggressive jaw lesion. The common radiographic features include a well-defined radiolucency with distinct borders, presenting a uni- or multilocular appearance. A cystic lesion in the posterior mandible of a 78-year-old female was incidentally found. Radiographs showed a unilocular lesion with a scalloped margin, external root resorption of the adjacent tooth, and cortical perforation. This lesion had changed from a small ovoid shape to a more expanded lesion in a period of four years. The small lesion showed unilocularity with a smooth margin and a well-defined border, but the expanded lesion produced cortical perforation and a lobulated margin. The provisional diagnosis was an ameloblastoma, whereas the histopathological examination revealed a GOC. This was a quite rare case, given that this radiographic change was observed in the posterior mandible of an elderly female. This case showed that a GOC can grow even in people in their seventies, changing from the unilocular form to an expanded, lobulated lesion. Here, we report a case of GOC with characteristic radiographic features.

  16. The Jasmonate-ZIM-domain proteins interact with the WD-Repeat/bHLH/MYB complexes to regulate Jasmonate-mediated anthocyanin accumulation and trichome initiation in Arabidopsis thaliana.

    Science.gov (United States)

    Qi, Tiancong; Song, Susheng; Ren, Qingcuo; Wu, Dewei; Huang, Huang; Chen, Yan; Fan, Meng; Peng, Wen; Ren, Chunmei; Xie, Daoxin

    2011-05-01

    Jasmonates (JAs) mediate plant responses to insect attack, wounding, pathogen infection, stress, and UV damage and regulate plant fertility, anthocyanin accumulation, trichome formation, and many other plant developmental processes. Arabidopsis thaliana Jasmonate ZIM-domain (JAZ) proteins, substrates of the CORONATINE INSENSITIVE1 (COI1)-based SCF(COI1) complex, negatively regulate these plant responses. Little is known about the molecular mechanism for JA regulation of anthocyanin accumulation and trichome initiation. In this study, we revealed that JAZ proteins interact with bHLH (Transparent Testa8, Glabra3 [GL3], and Enhancer of Glabra3 [EGL3]) and R2R3 MYB transcription factors (MYB75 and Glabra1), essential components of WD-repeat/bHLH/MYB transcriptional complexes, to repress JA-regulated anthocyanin accumulation and trichome initiation. Genetic and physiological evidence showed that JA regulates WD-repeat/bHLH/MYB complex-mediated anthocyanin accumulation and trichome initiation in a COI1-dependent manner. Overexpression of the MYB transcription factor MYB75 and bHLH factors (GL3 and EGL3) restored anthocyanin accumulation and trichome initiation in the coi1 mutant, respectively. We speculate that the JA-induced degradation of JAZ proteins abolishes the interactions of JAZ proteins with bHLH and MYB factors, allowing the transcriptional function of WD-repeat/bHLH/MYB complexes, which subsequently activate respective downstream signal cascades to modulate anthocyanin accumulation and trichome initiation.

  17. The Jasmonate-ZIM-Domain Proteins Interact with the WD-Repeat/bHLH/MYB Complexes to Regulate Jasmonate-Mediated Anthocyanin Accumulation and Trichome Initiation in Arabidopsis thaliana[C][W

    Science.gov (United States)

    Qi, Tiancong; Song, Susheng; Ren, Qingcuo; Wu, Dewei; Huang, Huang; Chen, Yan; Fan, Meng; Peng, Wen; Ren, Chunmei; Xie, Daoxin

    2011-01-01

    Jasmonates (JAs) mediate plant responses to insect attack, wounding, pathogen infection, stress, and UV damage and regulate plant fertility, anthocyanin accumulation, trichome formation, and many other plant developmental processes. Arabidopsis thaliana Jasmonate ZIM-domain (JAZ) proteins, substrates of the CORONATINE INSENSITIVE1 (COI1)–based SCFCOI1 complex, negatively regulate these plant responses. Little is known about the molecular mechanism for JA regulation of anthocyanin accumulation and trichome initiation. In this study, we revealed that JAZ proteins interact with bHLH (Transparent Testa8, Glabra3 [GL3], and Enhancer of Glabra3 [EGL3]) and R2R3 MYB transcription factors (MYB75 and Glabra1), essential components of WD-repeat/bHLH/MYB transcriptional complexes, to repress JA-regulated anthocyanin accumulation and trichome initiation. Genetic and physiological evidence showed that JA regulates WD-repeat/bHLH/MYB complex-mediated anthocyanin accumulation and trichome initiation in a COI1-dependent manner. Overexpression of the MYB transcription factor MYB75 and bHLH factors (GL3 and EGL3) restored anthocyanin accumulation and trichome initiation in the coi1 mutant, respectively. We speculate that the JA-induced degradation of JAZ proteins abolishes the interactions of JAZ proteins with bHLH and MYB factors, allowing the transcriptional function of WD-repeat/bHLH/MYB complexes, which subsequently activate respective downstream signal cascades to modulate anthocyanin accumulation and trichome initiation. PMID:21551388

  18. [Treatment of gynecomastia by a combined method of liposuction and semicircular periareolar incision glandular organ partial resection].

    Science.gov (United States)

    Liu, Su; Kuang, Ruixia; Chen, Zhenyu; Li, Huichao; Zhang, Weina; Wang, Zhiguo; Miao, Yuanxin; Chen, Lu

    2008-12-01

    To evaluate the effect of the combined method of liposuction and semicircular periareolar incision glandular organ partial resection in the treatment of gynecomastia. From June 2004 to June 2006, 40 patients, aged 11-41 years old, were treated, with no-nodule (n = 10), nodule (n = 22) and female-breast-like with nodules (n = 8). Three patients were unilateral and 37 ones were bilateral. The levels of serum prolactin, luteinizing hormone, follicle stimulating hormone, estradiol, testosterone and cortisol were normal in 38 patients, while in the other 2 patients, the levels of serum prolactin, luteinizing hormone, follicle stimulating hormone and estradiol were higher than normal, and the testosterone level was lower. Liposuction alone was performed in 10 no-nodule patients (lipo-type), and combined liposuction and semicircular periareolar incision glandular organ partial resection were conducted in the other 30 patients (lipo-glandular type). RESULTS; Except for 2 cases in which hematoma and a small amount of effusion were found on the first and second day postoperatively and then obtained healing by first intention right after hematoma removal in time, all the other patients incisions obtained healing by first intention. Nipple numbness occurred in 3 cases on the first day postoperatively and no special treatment was conducted. There was still nipple hypesthesia in these 3 cases after 6-month follow-up. There were no complications such as hematoma, effusion, nipple and mammary areola necrosis, and nipple hypesthesia in other patients. All the 40 patients were followed up for 6-24 months (13 months on average). They were satisfied with their chest figures and no recurrence was observed. The combined method of liposuction and semicircular periareolar incision glandular organ partial resection in the treatment of gynecomastia has many advantages, such as safe, micro-scars, natural and beautiflhl male breast figures as well as high patients' satisfaction.

  19. Comparison of average glandular dose in screen-film and digital mammography using breast tissue-equivalent phantom

    International Nuclear Information System (INIS)

    Shin, Gwi Soon; Kim, Jung Min; Kim, You Hyun; Choi, Jong Hak; Kim, Chang Kyun

    2007-01-01

    In recent years, mammography system is changed rapidly from conventional screen-film system to digital system for application to screening and diagnosis. Digital mammography system provides several advantages over screen-film mammography system. According to the information provided by the manufacturer, digital mammography system offers radiation dose reduction in comparison with screen-film mammography system, because of digital detector, particularly direct digital detector has higher x-ray absorption efficiency than screen-film combination or imaging plate (IP). We measured average glandular doses (ADG) in screen-film mammography (SFM) system with slow screen-film combination, computed mammography (CM) system, indirect digital mammography (IDM) system and direct digital mammography (DDM) system using breast tissue-equivalent phantom (glandularity 30%, 50% and 70%). The results were shown as follows: AGD values for DDM system were highest than those for other systems. Although automatic exposure control (AEC) mode was selected, the curve of the AGD values against thickness or glandularity increased significantly for the SFM system with the uniform target/filter (Mo/Mo) combination. Therefore, the AGD values for the high energy examinations were highest in the SFM system, and those for the low energy examinations were highest in the DDM system. But the curve of the AGD values against thickness and glandularity increased gently for CM system with the automatic selection of the target/filter combination (from Mo/Mo to Mo/Rh or from Mo/Rh to Rh/Rh), and the AGD values were lowest. Consequently, the parameters in mammography for each exposure besides detection efficiency play an important role in order to estimate a patient radiation dose

  20. Fibroblast growth factor 10-fibroblast growth factor receptor 2b mediated signaling is not required for adult glandular stomach homeostasis.

    Directory of Open Access Journals (Sweden)

    Allison L Speer

    Full Text Available The signaling pathways that are essential for gastric organogenesis have been studied in some detail; however, those that regulate the maintenance of the gastric epithelium during adult homeostasis remain unclear. In this study, we investigated the role of Fibroblast growth factor 10 (FGF10 and its main receptor, Fibroblast growth factor receptor 2b (FGFR2b, in adult glandular stomach homeostasis. We first showed that mouse adult glandular stomach expressed Fgf10, its receptors, Fgfr1b and Fgfr2b, and most of the other FGFR2b ligands (Fgf1, Fgf7, Fgf22 except for Fgf3 and Fgf20. Fgf10 expression was mesenchymal whereas FGFR1 and FGFR2 expression were mostly epithelial. Studying double transgenic mice that allow inducible overexpression of Fgf10 in adult mice, we showed that Fgf10 overexpression in normal adult glandular stomach increased epithelial proliferation, drove mucous neck cell differentiation, and reduced parietal and chief cell differentiation. Although a similar phenotype can be associated with the development of metaplasia, we found that Fgf10 overexpression for a short duration does not cause metaplasia. Finally, investigating double transgenic mice that allow the expression of a soluble form of Fgfr2b, FGF10's main receptor, which acts as a dominant negative, we found no significant changes in gastric epithelial proliferation or differentiation in the mutants. Our work provides evidence, for the first time, that the FGF10-FGFR2b signaling pathway is not required for epithelial proliferation and differentiation during adult glandular stomach homeostasis.

  1. Brassica napusGLABRA3-1 promotes anthocyanin biosynthesis and trichome formation in true leaves when expressed in Arabidopsis thaliana.

    Science.gov (United States)

    Gao, C; Guo, Y; Wang, J; Li, D; Liu, K; Qi, S; Jin, C; Duan, S; Gong, J; Li, Z; Chen, M

    2018-01-01

    Previous studies have shown that GLABRA3 (AtGL3), a bHLH transcription factor, plays essential roles in anthocyanin biosynthesis and trichome formation in Arabidopsis thaliana. However, there have been no such studies of a homologue, BnGL3, from the closely related crop, Brassica napus. Here, we analysed the BnGL3-1 coding domain sequence from the B. napus cultivar QINYOU Seven, identified conserved protein domains and performed a phylogenetic analysis to elucidate its relationship with homologues form a range of plant species. When expressed in tobacco leaves as a fusion protein with green fluorescent protein, BnGL3-1 accumulated in the nucleus, consistent with its predicted function as a transcription factor. Ectopic expression of the BnGL3-1 gene in the A. thaliana gl3-3 mutant resulted in levels of anthocyanins and numbers of trichomes in true leaves that were higher than in wild-type plants. Moreover, overexpression of BnGL3-1 in gl3-3 compensated for the promotion and repression of genes involved in anthocyanin biosynthesis and trichome formation, respectively, that has been reported in gl3-3 young shoots and expanding true leaves. This study provides new insights into GL3 function in anthocyanin biosynthesis and trichome formation in crucifers, and represents a promising target for genetic manipulation of B. napus. © 2017 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

  2. CINtec PLUS immunocytochemistry as a tool for the cytologic diagnosis of glandular lesions of the cervix uteri.

    Science.gov (United States)

    Ravarino, Alberto; Nemolato, Sonia; Macciocu, Elena; Fraschini, Matteo; Senes, Giancarlo; Faa, Gavino; Negri, Giovanni

    2012-11-01

    Cytologic findings of glandular lesions of the cervix uteri are often difficult to evaluate. We studied the usefulness of CINtec PLUS p16/Ki-67 double stain (mtm laboratories, Heidelberg, Germany) for the diagnosis of glandular lesions. The study included 47 abnormal results on liquid-based cytologic tests with a subsequent histologic diagnosis of adenocarcinoma in situ or with early invasion, and 16 samples with negative results on follow-up. All samples were stained with CINtec PLUS p16/Ki-67 double stain. Of the neoplastic samples, 7 were excluded because of insufficient residual cellularity or loss of neoplastic cells. Of the samples that were adequate, 92.5% were stained with CINtec PLUS, whereas 7.5% were judged inconclusive. All inconclusive cases were at least 3 years old. Of the 16 negative samples, 15 (93.8%) stained negative and only 1 (6.2%) showed several positive clusters of cells. Our study shows that CINtec PLUS is a robust and useful tool for the diagnosis of glandular lesions of the cervix uteri.

  3. [Markers of stromal invasion during background and precancerous changes of the glandular epithelium and in adenocarcinoma of the cervix uteri].

    Science.gov (United States)

    Danilova, N V; Andreeva, Iu Iu; Zavalishina, L É; Mal'kov, P G

    2012-01-01

    It is very difficult to identify stromal invasion when the glandular epithelium of the cervix uteri is involved. It is necessary to draw a clear distinction between its glandular structures and adenocarcinoma in situ, involving the preexisting crypts and invasive glands. An attempt was made to assess the possibilities of using as markers of invasion the following stromal proteins and adhesion molecules: CD44, E-cadherin, beta-catenin, tenascin, and laminin. Fifty-three cases of benign glandular changes, 66 cases of dysplasias and adenocarcinomas in situ, and 47 cases of invasive adenocarcinoma were examined. An immunohistochemical study was performed according to the standard protocol using the antibodies to CD44, laminin, tenascin, E-cadherin, and beta-catenin and a semiquantitative assessment of results was made. CD44 was found to be redistributed from the cells to the tumor stroma. CD44 was not detected in the stroma surrounding the intact glands, so were benign epithelial changes. In the tumor environment, there was, on the contrary, a reaction with CD44 in 74.5% of invasive adenocarcinomas cases (p 0.05). CD44 and tenascin are of great diagnostic value in examining invasive and microinvasive adenocarcinomas of the cervix uteri. E-cadherin and beta-catenin are of no diagnostic value in the study groups of pathological processes. Laminin is a potential marker of stromal invasion; however, its expression calls for further investigation.

  4. Genetics and biochemistry of collagen binding-triggered glandular differentiation in a human colon carcinoma cell line

    International Nuclear Information System (INIS)

    Pignatelli, M.; Bodmer, W.F.

    1988-01-01

    The authors have examined the interaction between collagen binding and epithelial differentiation by using a human colon carcinoma cell line (SW1222) that can differentiate structurally when grown in a three-dimensional collagen gel to form glandular structures. As much as 66% inhibition of glandular differentiation can be achieved by addition to the culture of a synthetic peptide containing the Arg-Gly-Asp-Thr (RGDT) sequence, which is a cell recognition site found in collagen. Arg-Gly-Asp-Thr also inhibited the cell attachment to collagen-coated plates. Chromosome 15 was found in all human-mouse hybrid clones that could differentiate in the collagen gel and bind collagen. Both binding to collagen and glandular differentiation of the hybrid cells were also inhibited by Arg-Gly-Asp-Thr as for the parent cell line SW1222. The ability of SW1222 cells to express the differentiated phenotype appears, therefore, to be determined by an Arg-Gly-Asp-directed collagen receptor on the cell surface that is controlled by a gene on chromosome 15

  5. Oncoplastic Resection of Retroareolar Breast Cancer: Central Quadrantectomy and Reconstruction by Local Skin-Glandular Flap

    International Nuclear Information System (INIS)

    Naguib, S.F.

    2006-01-01

    Background: Patients with central breast neoplasms account for 5 to 20% of breast cancer cases and, for a long time, they have been denied Breast Conservation Surgery (BCS) and conventionally treated with mastectomy. The high incidence of Nipple-Areola-Complex (NAC) involvement usually associated with these tumors necessitates nipple and areolar resection together with an adequate safety margin around the tumor, which yields an unacceptable cosmetic result. With the help of Oncoplastic Surgical Techniques, BCS can be offered to these patients. In this study central quadrantectomy and breast reconstruction by an infero-Iaterally based pedicled flap were evaluated. Patients and Methods: This study comprised 23 women with central breast tumors treated at the National Cancer Institute (NC]), Cairo University and at the Aswan Cancer Center, Egyptian Ministry of Health. Their ages ranged from 31 to 62 years (mean: 48.4±10.2 years). Twenty-two had a palpable mass, while only I had Paget's disease of the nipple without mass. The size of their tumors ranged from 4 to 33mm (mean: 16.9±8.6mm). Only 9 women showed clinical suspicion of NAC involvement in the form of nipple retraction. Seventeen cases had their tumors strictly in the retro-areolar region, while 5 had tumors extending for a maximum of I.5Cm beyond the areolar edge. All patients underwent central quadrantec-tomy with NAC resection removing a cylinder of breast tissue reaching down to the pectoral muscle together with axillary dissection. Advancement of an infero-Iaterally based skin-glandular flap was then carried out. All patients received adjuvant radiotherapy with or without chemotherapy or hormonal therapy. Results: Fourteen patients showed pathological evidence of nipple infiltration (60.8%). The free safety margin (SM) ranged from 9 to 13mm (mean: 10. 0.9mm). This could be accomplished from the first attempt in 18 patients; however, in 5 patients a second wider excision was needed to obtain an adequate

  6. Results of a 2011 national questionnaire for investigation of mean glandular dose from mammography in Japan.

    Science.gov (United States)

    Asada, Y; Suzuki, S; Minami, K; Shirakawa, S

    2014-03-01

    Diagnostic reference levels (DRLs) for mammography have yet to be created in Japan. A national questionnaire investigation into radiographic conditions in Japan was carried out for the purpose of creating DRLs. Items investigated included the following: tube voltage; tube current; current-time product; source-image distance; craniocaudal view; automatic exposure control (AEC) settings; name of mammography unit; image receptor system (computed radiography (CR), flat panel detector (FPD), or film/screen (F/S)); and supported or unsupported monitor diagnosis (including monitor resolution). Estimation of the mean glandular dose (MGD) for mammography was performed and compared with previous investigations. The MGD was 1.58(0.48) mGy, which did not significantly differ from a 2007 investigation. In relation to image receptors, although no difference in average MGD values was observed between CR and FPD systems, F/S systems had a significantly decreased value compared to both CR and FPDs. Concerning digital systems (FPDs), the MGD value of the direct conversion system was significantly higher than the indirect conversion system. No significant difference in MGD value was evident concerning type of monitor diagnosis for either the CR or the FPD digital systems; however, hard copies were used more often in CR. No significant difference in the MGD value was found in relation to monitor resolution. This report suggests ways to lower the doses patients undergoing mammography receive in Japan, and serves as reference data for 4.2 cm compressed breast tissue of 50% composition DRLs. Furthermore, our findings suggest that further optimisation of FPD settings can promote a reduction in the MGD value.

  7. Average glandular dose in digital mammography and digital breast tomosynthesis: comparison of phantom and patient data

    International Nuclear Information System (INIS)

    Bouwman, R W; Van Engen, R E; Den Heeten, G J; Broeders, M J M; Veldkamp, W J H; Young, K C; Dance, D R; Schopphoven, S; Jeukens, C R L P N

    2015-01-01

    For the evaluation of the average glandular dose (AGD) in digital mammography (DM) and digital breast tomosynthesis (DBT) phantoms simulating standard model breasts are used. These phantoms consist of slabs of polymethyl methacrylate (PMMA) or a combination of PMMA and polyethylene (PE). In the last decades the automatic exposure control (AEC) increased in complexity and became more sensitive to (local) differences in breast composition. The question is how well the AGD estimated using these simple dosimetry phantoms agrees with the average patient AGD. In this study the AGDs for both dosimetry phantoms and for patients have been evaluated for 5 different x-ray systems in DM and DBT modes. It was found that the ratios between patient and phantom AGD did not differ considerably using both dosimetry phantoms. These ratios averaged over all breast thicknesses were 1.14 and 1.15 for the PMMA and PMMA-PE dosimetry phantoms respectively in DM mode and 1.00 and 1.02 in the DBT mode. These ratios were deemed to be sufficiently close to unity to be suitable for dosimetry evaluation in quality control procedures. However care should be taken when comparing systems for DM and DBT since depending on the AEC operation, ratios for particular breast thicknesses may differ substantially (0.83–1.96). Although the predictions of both phantoms are similar we advise the use of PMMA  +  PE slabs for both DM and DBT to harmonize dosimetry protocols and avoid any potential issues with the use of spacers with the PMMA phantoms. (paper)

  8. High Throughput Transcriptomics @ USEPA (Toxicology ...

    Science.gov (United States)

    The ideal chemical testing approach will provide complete coverage of all relevant toxicological responses. It should be sensitive and specific It should identify the mechanism/mode-of-action (with dose-dependence). It should identify responses relevant to the species of interest. Responses should ideally be translated into tissue-, organ-, and organism-level effects. It must be economical and scalable. Using a High Throughput Transcriptomics platform within US EPA provides broader coverage of biological activity space and toxicological MOAs and helps fill the toxicological data gap. Slide presentation at the 2016 ToxForum on using High Throughput Transcriptomics at US EPA for broader coverage biological activity space and toxicological MOAs.

  9. Transcriptome-enabled marker discovery and mapping of plastochron-related genes in Petunia spp.

    Science.gov (United States)

    Guo, Yufang; Wiegert-Rininger, Krystle E; Vallejo, Veronica A; Barry, Cornelius S; Warner, Ryan M

    2015-09-24

    Petunia (Petunia × hybrida), derived from a hybrid between P. axillaris and P. integrifolia, is one of the most economically important bedding plant crops and Petunia spp. serve as model systems for investigating the mechanisms underlying diverse mating systems and pollination syndromes. In addition, we have previously described genetic variation and quantitative trait loci (QTL) related to petunia development rate and morphology, which represent important breeding targets for the floriculture industry to improve crop production and performance. Despite the importance of petunia as a crop, the floriculture industry has been slow to adopt marker assisted selection to facilitate breeding strategies and there remains a limited availability of sequences and molecular markers from the genus compared to other economically important members of the Solanaceae family such as tomato, potato and pepper. Here we report the de novo assembly, annotation and characterization of transcriptomes from P. axillaris, P. exserta and P. integrifolia. Each transcriptome assembly was derived from five tissue libraries (callus, 3-week old seedlings, shoot apices, flowers of mixed developmental stages, and trichomes). A total of 74,573, 54,913, and 104,739 assembled transcripts were recovered from P. axillaris, P. exserta and P. integrifolia, respectively and following removal of multiple isoforms, 32,994 P. axillaris, 30,225 P. exserta, and 33,540 P. integrifolia high quality representative transcripts were extracted for annotation and expression analysis. The transcriptome data was mined for single nucleotide polymorphisms (SNP) and simple sequence repeat (SSR) markers, yielding 89,007 high quality SNPs and 2949 SSRs, respectively. 15,701 SNPs were computationally converted into user-friendly cleaved amplified polymorphic sequence (CAPS) markers and a subset of SNP and CAPS markers were experimentally verified. CAPS markers developed from plastochron-related homologous transcripts

  10. Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes

    International Nuclear Information System (INIS)

    Pascal, Laura E; Liu, Alvin Y; Vêncio, Ricardo ZN; Page, Laura S; Liebeskind, Emily S; Shadle, Christina P; Troisch, Pamela; Marzolf, Bruz; True, Lawrence D; Hood, Leroy E

    2009-01-01

    Prostate cancer cells in primary tumors have been typed CD10 - /CD13 - /CD24 hi /CD26 + /CD38 lo /CD44 - /CD104 - . This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. CD26 + cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types

  11. Image quality, threshold contrast and mean glandular dose in CR mammography

    International Nuclear Information System (INIS)

    Jakubiak, R R; Gamba, H R; Neves, E B; Peixoto, J E

    2013-01-01

    In many countries, computed radiography (CR) systems represent the majority of equipment used in digital mammography. This study presents a method for optimizing image quality and dose in CR mammography of patients with breast thicknesses between 45 and 75 mm. Initially, clinical images of 67 patients (group 1) were analyzed by three experienced radiologists, reporting about anatomical structures, noise and contrast in low and high pixel value areas, and image sharpness and contrast. Exposure parameters (kV, mAs and target/filter combination) used in the examinations of these patients were reproduced to determine the contrast-to-noise ratio (CNR) and mean glandular dose (MGD). The parameters were also used to radiograph a CDMAM (version 3.4) phantom (Artinis Medical Systems, The Netherlands) for image threshold contrast evaluation. After that, different breast thicknesses were simulated with polymethylmethacrylate layers and various sets of exposure parameters were used in order to determine optimal radiographic parameters. For each simulated breast thickness, optimal beam quality was defined as giving a target CNR to reach the threshold contrast of CDMAM images for acceptable MGD. These results were used for adjustments in the automatic exposure control (AEC) by the maintenance team. Using optimized exposure parameters, clinical images of 63 patients (group 2) were evaluated as described above. Threshold contrast, CNR and MGD for such exposure parameters were also determined. Results showed that the proposed optimization method was effective for all breast thicknesses studied in phantoms. The best result was found for breasts of 75 mm. While in group 1 there was no detection of the 0.1 mm critical diameter detail with threshold contrast below 23%, after the optimization, detection occurred in 47.6% of the images. There was also an average MGD reduction of 7.5%. The clinical image quality criteria were attended in 91.7% for all breast thicknesses evaluated in both

  12. Validation of mean glandular dose values provided by a digital breast tomosynthesis system in Brazil

    International Nuclear Information System (INIS)

    Beraldo O, B.; Paixao, L.; Donato da S, S.; Araujo T, M. H.; Nogueira, M. S.

    2014-08-01

    Digital breast tomosynthesis (DBT) is an emerging imaging modality that provides quasi-three-dimensional structural information of the breast and has strong promise to improve the differentiation of normal tissue and suspicious masses reducing the tissue overlaps. DBT images are reconstructed from a sequence of low-dose X-ray projections of the breast acquired at a small number of angles over a limited angular range. The Ho logic Selen ia Dimensions system is equipped with an amorphous Selenium (a-Se) detector layer of 250 μm thickness and a 70 μm pixel pitch. Studies are needed to determine the radiation dose of patients that are undergoing this emerging procedure to compare with the results obtained in DBT images. The mean glandular dose (D G ) is the dosimetric quantity used in quality control of the mammographic systems. The aim of this work is to validate D G values for different breast thicknesses provided by a Ho logic Selen ia Dimensions system using a DBT mode in comparison with the same results obtained by a calibrated 90 X 5-6M-model Radcal ionization chamber. D G values were derived from the incident air kerma (K i ) measurements and tabulated conversion coefficients that are dependent on the half value layer (HVL) of the X-ray spectrum. Voltage and tube loading values were recorded in irradiations using W/Al anode/filter combination, automatic exposure control mode and polymethyl methacrylate (PMMA) slabs which simulate different breast thicknesses. For K i measurements, the ionization chamber was positioned at 655 mm from the focus and the same radiographic technique values were selected with the manual mode. D G values for a complete procedure ranged from 0.9 ± 0.1 to 3.7 ± 0.4 mGy. The results for different breast thicknesses are in accordance with values obtained by DBT images and with acceptable levels established by the Commission of the European Communities (Cec) and the International Atomic Energy Agency (IAEA). This work contributes to

  13. Validation of mean glandular dose values provided by a digital breast tomosynthesis system in Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Beraldo O, B.; Paixao, L.; Donato da S, S. [Centro de Desenvolvimento da Tecnologia Nuclear / CNEN, Post-graduation in Sciences and Technology of Radiations Minerals and Materials, Pte. Antonio Carlos 6627, 31270-901 Belo Horizonte (Brazil); Araujo T, M. H. [Dr Maria Helena Araujo Teixeira Clinic, Guajajaras 40, 30180-100 Belo Horizonte (Brazil); Nogueira, M. S., E-mail: bbo@cdtn.br [Centro de Desenvolvimento da Tecnologia Nuclear / CNEN, Pte. Antonio Carlos 6627, 31270-901 Belo Horizonte (Brazil)

    2014-08-15

    Digital breast tomosynthesis (DBT) is an emerging imaging modality that provides quasi-three-dimensional structural information of the breast and has strong promise to improve the differentiation of normal tissue and suspicious masses reducing the tissue overlaps. DBT images are reconstructed from a sequence of low-dose X-ray projections of the breast acquired at a small number of angles over a limited angular range. The Ho logic Selen ia Dimensions system is equipped with an amorphous Selenium (a-Se) detector layer of 250 μm thickness and a 70 μm pixel pitch. Studies are needed to determine the radiation dose of patients that are undergoing this emerging procedure to compare with the results obtained in DBT images. The mean glandular dose (D{sub G}) is the dosimetric quantity used in quality control of the mammographic systems. The aim of this work is to validate D{sub G} values for different breast thicknesses provided by a Ho logic Selen ia Dimensions system using a DBT mode in comparison with the same results obtained by a calibrated 90 X 5-6M-model Radcal ionization chamber. D{sub G} values were derived from the incident air kerma (K{sub i}) measurements and tabulated conversion coefficients that are dependent on the half value layer (HVL) of the X-ray spectrum. Voltage and tube loading values were recorded in irradiations using W/Al anode/filter combination, automatic exposure control mode and polymethyl methacrylate (PMMA) slabs which simulate different breast thicknesses. For K{sub i} measurements, the ionization chamber was positioned at 655 mm from the focus and the same radiographic technique values were selected with the manual mode. D{sub G} values for a complete procedure ranged from 0.9 ± 0.1 to 3.7 ± 0.4 mGy. The results for different breast thicknesses are in accordance with values obtained by DBT images and with acceptable levels established by the Commission of the European Communities (Cec) and the International Atomic Energy Agency (IAEA

  14. Effect of 935-MHz phone-simulating electromagnetic radiation on endometrial glandular cells during mouse embryo implantation.

    Science.gov (United States)

    Liu, Wenhui; Zheng, Xinmin; Qu, Zaiqing; Zhang, Ming; Zhou, Chun; Ma, Ling; Zhang, Yuanzhen

    2012-10-01

    This study examined the impact of 935MHz phone-simulating electromagnetic radiation on embryo implantation of pregnant mice. Each 7-week-old Kunming (KM) female white mouse was set up with a KM male mouse in a single cage for mating overnight after induction of ovulation. In the first three days of pregnancy, the pregnant mice was exposed to electromagnetic radiation at low-intensity (150 μW/cm(2), ranging from 130 to 200 μW/cm(2), for 2- or 4-h exposure every day), mid-intensity (570 μW/cm(2), ranging from 400 to 700 μW/cm(2), for 2- or 4-h exposure every day) or high-intensity (1400 μW/cm(2), ranging from 1200 to 1500 μW/cm(2), for 2- or 4-h exposure every day), respectively. On the day 4 after gestation (known as the window of murine embryo implantation), the endometrium was collected and the suspension of endometrial glandular cells was made. Laser scanning microscopy was employed to detect the mitochondrial membrane potential and intracellular calcium ion concentration. In high-intensity, 2- and 4-h groups, mitochondrial membrane potential of endometrial glandular cells was significantly lower than that in the normal control group (Pelectromagnetic radiation and longer length of the radiation are required to inflict a remarkable functional and structural damage to mitochondrial membrane. Our data demonstrated that electromagnetic radiation with a 935-MHz phone for 4 h conspicuously decreased mitochondrial membrane potential and lowered the calcium ion concentration of endometrial glandular cells. It is suggested that high-intensity electromagnetic radiation is very likely to induce the death of embryonic cells and decrease the chance of their implantation, thereby posing a high risk to pregnancy.

  15. SU-F-I-01: Normalized Mean Glandular Dose Values for Dedicated Breast CT Using Realistic Breast-Shaped Phantoms

    Energy Technology Data Exchange (ETDEWEB)

    Hernandez, A [Department of Radiology, Biomedical Engineering Graduate Group, University of California Davis, Sacramento, CA (United States); Boone, J [Departments of Radiology and Biomedical Engineering, Biomedical Engeering Graduate Group, University of California Davis, Sacramento, CA (United States)

    2016-06-15

    Purpose: To estimate normalized mean glandular dose values for dedicated breast CT (DgN-CT) using breast CT-derived phantoms and compare to estimations using cylindrical phantoms. Methods: Segmented breast CT (bCT) volume data sets (N=219) were used to measure effective diameter profiles and were grouped into quintiles by volume. The profiles were averaged within each quintile to represent the range of breast sizes found clinically. These profiles were then used to generate five voxelized computational phantoms (V1, V2, V3, V4, V5 for the small to large phantom sizes, respectively), and loaded into the MCNP6 lattice geometry to simulate normalized mean glandular dose coefficients (DgN-CT) using the system specifications of the Doheny-prototype bCT scanner in our laboratory. The DgN-CT coefficients derived from the bCT-derived breast-shaped phantoms were compared to those generated using a simpler cylindrical phantom using a constant volume, and the following constraints: (1) Length=1.5*radius; (2) radius determined at chest wall (Rcw), and (3) radius determined at the phantom center-of-mass (Rcm). Results: The change in Dg-NCT coefficients averaged across all phantom sizes, was - 0.5%, 19.8%, and 1.3%, for constraints 1–3, respectively. This suggests that the cylindrical assumption is a good approximation if the radius is taken at the breast center-of-mass, but using the radius at the chest wall results in an underestimation of the glandular dose. Conclusion: The DgN-CT coefficients for bCT-derived phantoms were compared against the assumption of a cylindrical phantom and proved to be essentially equivalent when the cylinder radius was set to r=1.5/L or Rcm. While this suggests that for dosimetry applications a patient’s breast can be approximated as a cylinder (if the correct radius is applied), this assumes a homogenous composition of breast tissue and the results may be different if the realistic heterogeneous distribution of glandular tissue is considered

  16. Transgenerational effects of the endocrine disruptor vinclozolin on the prostate transcriptome and adult onset disease.

    Science.gov (United States)

    Anway, Matthew D; Skinner, Michael K

    2008-04-01

    The ability of an endocrine disruptor exposure during gonadal sex determination to promote a transgenerational prostate disease phenotype was investigated in the current study. Exposure of an F0 gestating female rat to the endocrine disruptor vinclozolin during F1 embryo gonadal sex determination promoted a transgenerational adult onset prostate disease phenotype. The prostate disease phenotype and physiological parameters were determined for males from F1 to F4 generations and the prostate transcriptome was assessed in the F3 generation. Although the prostate in prepubertal animals develops normally, abnormalities involving epithelial cell atrophy, glandular dysgenesis, prostatitis, and hyperplasia of the ventral prostate develop in older animals. The ventral prostate phenotype was transmitted for four generations (F1-F4). Analysis of the ventral prostate transcriptome demonstrated 954 genes had significantly altered expression between control and vinclozolin F3 generation animals. Analysis of isolated ventral prostate epithelial cells identified 259 genes with significantly altered expression between control and vinclozolin F3 generation animals. Characterization of regulated genes demonstrated several cellular pathways were influenced, including calcium and WNT. A number of genes identified have been shown to be associated with prostate disease and cancer, including beta-microseminoprotein (Msp) and tumor necrosis factor receptor superfamily 6 (Fadd). The ability of an endocrine disruptor to promote transgenerational prostate abnormalities appears to involve an epigenetic transgenerational alteration in the prostate transcriptome and male germ-line. Potential epigenetic transgenerational alteration of prostate gene expression by environmental compounds may be important to consider in the etiology of adult onset prostate disease.

  17. The Human Pancreas Proteome Defined by Transcriptomics and Antibody-Based Profiling

    Science.gov (United States)

    Fagerberg, Linn; Hallström, Björn M.; Schwenk, Jochen M.; Uhlén, Mathias; Korsgren, Olle; Lindskog, Cecilia

    2014-01-01

    The pancreas is composed of both exocrine glands and intermingled endocrine cells to execute its diverse functions, including enzyme production for digestion of nutrients and hormone secretion for regulation of blood glucose levels. To define the molecular constituents with elevated expression in the human pancreas, we employed a genome-wide RNA sequencing analysis of the human transcriptome to identify genes with elevated expression in the human pancreas. This quantitative transcriptomics data was combined with immunohistochemistry-based protein profiling to allow mapping of the corresponding proteins to different compartments and specific cell types within the pancreas down to the single cell level. Analysis of whole pancreas identified 146 genes with elevated expression levels, of which 47 revealed a particular higher expression as compared to the other analyzed tissue types, thus termed pancreas enriched. Extended analysis of in vitro isolated endocrine islets identified an additional set of 42 genes with elevated expression in these specialized cells. Although only 0.7% of all genes showed an elevated expression level in the pancreas, this fraction of transcripts, in most cases encoding secreted proteins, constituted 68% of the total mRNA in pancreas. This demonstrates the extreme specialization of the pancreas for production of secreted proteins. Among the elevated expression profiles, several previously not described proteins were identified, both in endocrine cells (CFC1, FAM159B, RBPJL and RGS9) and exocrine glandular cells (AQP12A, DPEP1, GATM and ERP27). In summary, we provide a global analysis of the pancreas transcriptome and proteome with a comprehensive list of genes and proteins with elevated expression in pancreas. This list represents an important starting point for further studies of the molecular repertoire of pancreatic cells and their relation to disease states or treatment effects. PMID:25546435

  18. Oladipo and Ayo-Ayinde (7).cdr

    African Journals Online (AJOL)

    Timothy Ademakinwa

    Result also reveals that simple hooked bicellular and unicellular non glandular trichome is diagnostic of Commelinabenghalensisand Aneilema aequinoctialerespectively. Similarities exist in foliar epidermal characters like the trichome and stomata types among other characters between the genera Commelina and ...

  19. Trans-nipple removal of fibro-glandular tissue in gynaecomastia surgery without additional scars: An innovative approach

    Directory of Open Access Journals (Sweden)

    R K Mishra

    2014-01-01

    Full Text Available Context: The established techniques that have been used to treat gynaecomastia are said to have relatively less patient satisfaction rate as they leave some visible scars or mild elevation over the nipple areola complex, resulting in aesthetically unsatisfactory results. Even the slightest elevation or smallest scar over nipple areola complex leave patients extremely self conscious and in a dilemma of having a second intervention to get rid of that blemish. Aims: The aim of the study is to achieve - A flat chest without adding a scar and with no chances of re-occurrence of the condition. This article suggests an innovative approach to address the problem. Materials and Methods: The author presents trans-nipple incision approach for the delivery of fibro-glandular tissue component following liposuction for maximum patient satisfaction. This method consists of a unique small criss-cross incision right on the nipple itself for retrieving any volume of tough fibro-glandular tissues. Between the duration of January 2012 to October 2013, 28 male patients of different ages were operated with this technique. Results: The surgery resulted in well-shaped, symmetric chest contour without any visible elevation or additional scars on nipple areola complex. No complications were noticed in any of the patients. Conclusions: The presented technique is proved to have a high patient satisfaction rate and to be promising method to achieve good aesthetic results in gynaecomastia surgery.

  20. Comparative evaluation of average glandular dose and image of digital mammography and film mammography in Minas Gerais, Brazil

    International Nuclear Information System (INIS)

    Nogueira, M.; Leyton, F.; Rodrigue, L. L.C.; Oliveira, M.A.; Joana, G.S.; Silva, S.D.

    2015-01-01

    Breast cancer is the most common cancer among women, and early detection is critical to its diagnosis and treatment. Mammography is the best method for breast-cancer screening and is capable of reducing mortality rates To date, the most effective method for early detection of breast cancer has been x-ray mammography for which the screen/film (SF) technique has been the gold standard. Digital mammography has been proposed as a substitute for film mammography given the benefits inherent to digital technology. The purpose of our study was to compare the technical performance of digital mammographic and screen-film mammography. A PMMA phantom with objects to simulate breast structures. For the screen/film (SF) technique the results showed that 54% mammography units did not achieve the minimum acceptable performance as far the image quality. Besides, 67% services showed inadequate performance in their processing systems, which had significant influence on the image quality. At the mean glandular dose only 44% of digital systems evaluated were compliant in all thicknesses of PMMA. The average glandular dose AGD was 90 % higher than in screen/film systems. (authors)

  1. The effect of chrysanthemum leaf trichome density and prey spatial distribution on predation of Tetranychus urticae (Acari: Tetranychidae) by Phytoseiulus persimilis (Acari: Phytoseiidae).

    Science.gov (United States)

    Skirvin, D J; Stavrinides, M C; Skirvin, D J

    2003-08-01

    The effect of plant architecture, in terms of leaf hairiness, and prey spatial arrangement, on predation rate of eggs of the spider mite, Tetranychus urticae Koch, by the predatory mite Phytoseiulus persimilis Athias-Henriot was examined on cut stems of chrysanthemums. Three levels of leaf hairiness (trichome density) were obtained using two different chrysanthemum cultivars and two ages within one of the cultivars. The number of prey consumed by P. persimilis was inversely related to trichome density. At low prey densities (less than ten eggs per stem), prey consumption did not differ in a biologically meaningful way between treatments. The effect of prey spatial arrangement on the predation rate of P. persimilis was also examined. Predation rates were higher in prey patches on leaves adjacent to the release point of P. persimilis, but significantly greater numbers of prey were consumed in higher density prey patches compared to low density patches. The predators exhibited non-random searching behaviour, spending more time on leaves closest to the release point. The implications of these findings for biological control and predator-prey dynamics are discussed.

  2. False positive reaction due to endogenous biotin activity in glandular epithelium of decidua Reação falso positiva em epitélio glandular da decídua devido a atividade endógena de biotina

    Directory of Open Access Journals (Sweden)

    Liliana Cruz Spano

    2005-06-01

    Full Text Available Biotin-labeled probe was used in an in situ hybridisation assay to localize virus infection in formalin-fixed, paraffin embedded tissues taken from eleven abortion cases. Probes for human cytomegalovirus (HCMV, human Parvovirus B19 (B19 and human adenovirus type 2 (HAd2, were labeled with biotin-11-dUTP by nick-translation reaction. Streptavidin-alkaline-phosphatase (SAP was used to detect biotin, followed by 4-nitroblue tetrazolium/5-bromo-4-chloro-3-indolyl phosphate (NBT/BCIP solution. Positive reaction was observed in nucleus of glandular ephitelium cells of decidua either in positive or in negative control at first and second gestational trimester. The reaction was not inhibited with blocking solution for alkaline phosphatase endogenous activity and it persisted even with probes omission. The use of adequate negative control permitted to reveal the presence of nuclear biotin in glandular epithelium of decidua, responsible for false positivity in detection systems involving streptavidin biotin system (StrepABC. The stained cells resembled to cytophatic effect due to herpesvirus, which could induce further misinterpretation. The results obtained in this study strongly recommend that DNA detection by in situ hybridisation reaction in gestational endometrium should be done without using StrepABC system.Sondas marcadas com biotina foram utilizadas neste trabalho para detecção de infecção viral por hibridização in situ em tecidos fixados com formalina e embebidos em parafina de 11 casos obtidos de abortamento. Sondas para citomegalovírus humano (HCMV, parvovírus B19 humano (B19 e adenovírus humano tipo 2 (HAd2, foram marcadas com biotina-11-dUTP através da reação de nick-translation. Estreptavidina conjugada com fosfatase alcalina (SAP seguida por solução de 4-nitro-azul de tetrazolio/5-bromo-4-cloro-3-indolil fosfato (NBT/BCIP foram utilizadas para detecção da biotina após a reação de hibridização. Reação positiva foi

  3. Comportamento da dose glandular versus contraste do objeto em mamografia: determinação de formalismo semi-empírico para diferentes combinações alvo-filtro Behavior of subject contrast versus glandular dose in mammography: determination of a semi-empirical formalism for different target-filter combinations

    Directory of Open Access Journals (Sweden)

    Gabriela Hoff

    2006-06-01

    Full Text Available OBJETIVO: Verificar o efeito da mudança no contraste do objeto, tempo de exposição e dose de radiação quando diferentes espessuras de filtração de molibdênio (Mo e ródio (Rh são empregadas em mamógrafos. MATERIAIS E MÉTODOS: Realizaram-se medidas da exposição na entrada da pele com uma câmara de ionização para diferentes espessuras para os filtros de Mo e Rh. Para determinar a dose glandular média foi utilizado simulador de BR12 (50% tecido adiposo e 50% tecido glandular de diferentes espessuras (4 cm e 8 cm. Energias na faixa de 24 kVp a 34 kVp foram empregadas e filmes Kodak MinR 2000 foram utilizados. RESULTADOS: Os resultados evidenciaram dados de contraste do objeto, dose glandular e tempo de exposição para diferentes espessuras de filtros adicionais e diferentes tensões. Esses dados indicaram aumento nos valores de contraste do objeto e tempo de exposição, com o aumento da espessura dos filtros. A dose glandular apresentou comportamento com diferentes tendências para cada caso analisado. Equações foram definidas para possibilitar a estimativa do contraste do objeto, dose glandular e tempo de exposição para os casos estudados. CONCLUSÃO: Os resultados possibilitaram a estimativa de equações que auxiliam na verificação do comportamento do contraste do objeto e da dose glandular para simuladores com espessura de 4 cm e 8 cm e para os filtros de Rh e Mo. Dessa forma, torna-se possível estimar a figura de mérito (razão entre o contraste do objeto e a dose glandular, podendo auxiliar na análise da relação risco-benefício dos casos estudados.OBJECTIVE: Our purpose was to verify the effect of changes in subject contrast, exposure time and radiation dose when different thicknesses of molybdenum (Mo and rhodium (Rh filters are used in mammography equipments. MATERIALS AND METHODS: Entrance skin exposure measurements were performed with an ionization chamber for different thicknesses of Mo and Rh filters

  4. Salivary gland acinar cells regenerate functional glandular structures in modified hydrogels

    Science.gov (United States)

    Pradhan, Swati

    Xerostomia, a condition resulting from irradiation of the head and neck, affects over 40,000 cancer patients each year in the United States. Direct radiation damage of the acinar cells that secrete fluid and protein results in salivary gland hypofunction. Present medical management for xerostomia for patients treated for upper respiratory cancer is largely ineffective. Patients who have survived their terminal diagnosis are often left with a diminished quality of life and are unable to enjoy the simple pleasures of eating and drinking. This project aims to ultimately reduce human suffering by developing a functional implantable artificial salivary gland. The goal was to create an extracellular matrix (ECM) modified hyaluronic acid (HA) based hydrogel culture system that allows for the growth and differentiation of salivary acinar cells into functional acini-like structures capable of secreting large amounts of protein and fluid unidirectionally and to ultimately engineer a functional artificial salivary gland that can be implanted into an animal model. A tissue collection protocol was established and salivary gland tissue was obtained from patients undergoing head and neck surgery. The tissue specimen was assessed by histology and immunohistochemistry to establish the phenotype of normal salivary gland cells including the native basement membranes. Hematoxylin and eosin staining confirmed normal glandular tissue structures including intercalated ducts, striated ducts and acini. alpha-Amylase and periodic acid schiff stain, used for structures with a high proportion of carbohydrate macromolecules, preferentially stained acinar cells in the tissue. Intercalated and striated duct structures were identified using cytokeratins 19 and 7 staining. Myoepithelial cells positive for cytokeratin 14 were found wrapped around the serous and mucous acini. Tight junction components including ZO-1 and E-cadherin were present between both ductal and acinar cells. Ductal and acinar

  5. Automated Breast Density Computation in Digital Mammography and Digital Breast Tomosynthesis: Influence on Mean Glandular Dose and BIRADS Density Categorization.

    Science.gov (United States)

    Castillo-García, Maria; Chevalier, Margarita; Garayoa, Julia; Rodriguez-Ruiz, Alejandro; García-Pinto, Diego; Valverde, Julio

    2017-07-01

    The study aimed to compare the breast density estimates from two algorithms on full-field digital mammography (FFDM) and digital breast tomosynthesis (DBT) and to analyze the clinical implications. We selected 561 FFDM and DBT examinations from patients without breast pathologies. Two versions of a commercial software (Quantra 2D and Quantra 3D) calculated the volumetric breast density automatically in FFDM and DBT, respectively. Other parameters such as area breast density and total breast volume were evaluated. We compared the results from both algorithms using the Mann-Whitney U non-parametric test and the Spearman's rank coefficient for data correlation analysis. Mean glandular dose (MGD) was calculated following the methodology proposed by Dance et al. Measurements with both algorithms are well correlated (r ≥ 0.77). However, there are statistically significant differences between the medians (P density median values from FFDM are, respectively, 8% and 77% higher than DBT estimations. Both algorithms classify 35% and 55% of breasts into BIRADS (Breast Imaging-Reporting and Data System) b and c categories, respectively. There are no significant differences between the MGD calculated using the breast density from each algorithm. DBT delivers higher MGD than FFDM, with a lower difference (5%) for breasts in the BIRADS d category. MGD is, on average, 6% higher than values obtained with the breast glandularity proposed by Dance et al. Breast density measurements from both algorithms lead to equivalent BIRADS classification and MGD values, hence showing no difference in clinical outcomes. The median MGD values of FFDM and DBT examinations are similar for dense breasts (BIRADS d category). Published by Elsevier Inc.

  6. An audit of cervicovaginal cytology in a teaching hospital: Are atypical glandular cells under-recognised on cytological screening?

    Directory of Open Access Journals (Sweden)

    Crasta Julian

    2009-01-01

    Full Text Available Background: Cervical cytology screening for carcinoma of the cervix in India is mainly opportunistic in nature and is practiced mainly in urban centres. The effectiveness of cervical cytology screening depends on various factors. The quality of cervicovaginal cytology service is assessed by various quality indices and by cyto-histology correlation, which is the most important quality assurance measure. Aims: To describe the cervical cytology diagnoses, estimate the quality indices, and evaluate the discrepant cases on cytohistological correlation. Settings and Design: Retrospective observational study from a tertiary care centre in South India. Materials and Methods: Using a database search, all the cervicovaginal cytology reported during the period of 2002-2006 was retrieved and various diagnoses were described. The data was analysed to assess the quality indices. The cytohistologically discrepant cases were reviewed. Results: A total of 10,787 cases were retrieved, of which 98.14% were labeled negative and 1.36% were unsatisfactory for evaluation. A few (0.81% of the cases were labeled as squamous intraepithelial lesions and 0.38% as atypical squamous cells. The ASCUS: SIL ratio was 0.5. Cytohistological correlation revealed a total of ten cases with significant discrepancy. The majority of these were carcinomas that were misdiagnosed as atypical glandular cells. These cytology smears and the subsequent biopsies were reviewed to elucidate the reasons for the discrepancies. Conclusions: The cervical cytology service at our centre is well within the accepted standards. An increased awareness of cytological features, especially of glandular lesions, a good clinician-laboratory communication and a regular cytohistological review would further improve the diagnostic standards.

  7. An audit of cervicovaginal cytology in a teaching hospital: Are atypical glandular cells under-recognised on cytological screening?

    Science.gov (United States)

    Crasta, Julian A; Chaitra, V; Simi, Cm; Correa, Marjorie

    2009-04-01

    Cervical cytology screening for carcinoma of the cervix in India is mainly opportunistic in nature and is practiced mainly in urban centres. The effectiveness of cervical cytology screening depends on various factors. The quality of cervicovaginal cytology service is assessed by various quality indices and by cyto-histology correlation, which is the most important quality assurance measure. To describe the cervical cytology diagnoses, estimate the quality indices, and evaluate the discrepant cases on cytohistological correlation. Retrospective observational study from a tertiary care centre in South India. Using a database search, all the cervicovaginal cytology reported during the period of 2002-2006 was retrieved and various diagnoses were described. The data was analysed to assess the quality indices. The cytohistologically discrepant cases were reviewed. A total of 10,787 cases were retrieved, of which 98.14% were labeled negative and 1.36% were unsatisfactory for evaluation. A few (0.81%) of the cases were labeled as squamous intraepithelial lesions and 0.38% as atypical squamous cells. The ASCUS: SIL ratio was 0.5. Cytohistological correlation revealed a total of ten cases with significant discrepancy. The majority of these were carcinomas that were misdiagnosed as atypical glandular cells. These cytology smears and the subsequent biopsies were reviewed to elucidate the reasons for the discrepancies. The cervical cytology service at our centre is well within the accepted standards. An increased awareness of cytological features, especially of glandular lesions, a good clinician-laboratory communication and a regular cytohistological review would further improve the diagnostic standards.

  8. Strategic and Operational Plan for Integrating Transcriptomics ...

    Science.gov (United States)

    Plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT; the details are in the attached slide presentation presentation on plans for incorporating high throughput transcriptomics into the current high throughput screening activities at NCCT, given at the OECD meeting on June 23, 2016

  9. Metastatic Urothelial Carcinoma with Glandular Differentiation That Confirmed the Response by Autopsy Specimen to Second-Line mFOLFOX6 (Fluorouracil, Oxaliplatin, and Leucovorin plus Bevacizumab Chemotherapy

    Directory of Open Access Journals (Sweden)

    Taku Naiki

    2017-11-01

    Full Text Available The prognostic significance of glandular differentiation in urothelial carcinoma (UC is controversial, and thus far there is no established treatment strategy against metastasis of glandular component. We describe here a case of metastatic UC with glandular differentiation that had histological disappearance of adenocarcinoma components at autopsy after sequential chemotherapy with S-1 and cisplatin (CDDP and with mFOLFOX6 (fluorouracil, oxaliplatin, and leucovorin plus bevacizumab (mFOLFOX6+Bev. A 62-year-old Asian male was diagnosed with invasive UC with glandular differentiation (T2N0M0 by radical cystectomy and ileal conduit, and careful follow-up observation was made. Eight years after radical operation, peritoneal metastases occurred, and a biopsy specimen using colon fiber revealed high-grade adenocarcinomas with an immunohistochemical profile that included positivity for cytokeratin 7 (CK7 and negativity for cytokeratin 20 (CK20 and uroplakin, which was identical to the radical cystectomy specimen. Thus, he received combination chemotherapy consisting of S-1 and CDDP; however, the peritoneal metastasis worsened after 2 cycles. Therefore, second-line mFOLFOX6+Bev chemotherapy was performed for a total of 5 courses. In spite of this, the patient died, and the final diagnosis by autopsy was multiple metastases of infiltrating pure UC to the lung, bone, and peritoneum. Interestingly, there were no pathological findings of adenocarcinoma, and the immunohistochemical profile of the metastatic lesions was identical to that of the previous specimens from the bladder and colon. This suggests that sequential chemotherapy of S-1 and CDDP and second-line mFOLFOX6+Bev might be a feasible option in metastatic UC with glandular differentiation.

  10. Monte Carlo evaluation of glandular dose in cone-beam X-ray computed tomography dedicated to the breast: Homogeneous and heterogeneous breast models.

    Science.gov (United States)

    Sarno, Antonio; Mettivier, Giovanni; Tucciariello, Raffaele M; Bliznakova, Kristina; Boone, John M; Sechopoulos, Ioannis; Di Lillo, Francesca; Russo, Paolo

    2018-06-07

    In cone-beam computed tomography dedicated to the breast (BCT), the mean glandular dose (MGD) is the dose metric of reference, evaluated from the measured air kerma by means of normalized glandular dose coefficients (DgN CT ). This work aimed at computing, for a simple breast model, a set of DgN CT values for monoenergetic and polyenergetic X-ray beams, and at validating the results vs. those for patient specific digital phantoms from BCT scans. We developed a Monte Carlo code for calculation of monoenergetic DgN CT coefficients (energy range 4.25-82.25 keV). The pendant breast was modelled as a cylinder of a homogeneous mixture of adipose and glandular tissue with glandular fractions by mass of 0.1%, 14.3%, 25%, 50% or 100%, enveloped by a 1.45 mm-thick skin layer. The breast diameter ranged between 8 cm and 18 cm. Then, polyenergetic DgN CT coefficients were analytically derived for 49-kVp W-anode spectra (half value layer 1.25-1.50 mm Al), as in a commercial BCT scanner. We compared the homogeneous models to 20 digital phantoms produced from classified 3D breast images. Polyenergetic DgN CT resulted 13% lower than most recent published data. The comparison vs. patient specific breast phantoms showed that the homogeneous cylindrical model leads to a DgN CT percentage difference between -15% and +27%, with an average overestimation of 8%. A dataset of monoenergetic and polyenergetic DgN CT coefficients for BCT was provided. Patient specific breast models showed a different volume distribution of glandular dose and determined a DgN CT 8% lower, on average, than homogeneous breast model. Copyright © 2018 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  11. Transcriptomic signatures in cartilage ageing

    Science.gov (United States)

    2013-01-01

    Introduction Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopically normal cartilage of the metacarpophalangeal joints of eight horses; four young donors (4 years old) and four old donors (>15 years old). RNA sequence libraries were prepared following ribosomal RNA depletion and sequencing was undertaken using the Illumina HiSeq 2000 platform. Differentially expressed genes were defined using Benjamini-Hochberg false discovery rate correction with a generalised linear model likelihood ratio test (P ageing cartilage. Conclusion There was an age-related dysregulation of matrix, anabolic and catabolic cartilage factors. This study has increased our knowledge of transcriptional networks in cartilage ageing by providing a global view of the transcriptome. PMID:23971731

  12. Developmental transcriptome of Aplysia californica'

    KAUST Repository

    Heyland, Andreas

    2010-12-06

    Genome-wide transcriptional changes in development provide important insight into mechanisms underlying growth, differentiation, and patterning. However, such large-scale developmental studies have been limited to a few representatives of Ecdysozoans and Chordates. Here, we characterize transcriptomes of embryonic, larval, and metamorphic development in the marine mollusc Aplysia californica and reveal novel molecular components associated with life history transitions. Specifically, we identify more than 20 signal peptides, putative hormones, and transcription factors in association with early development and metamorphic stages-many of which seem to be evolutionarily conserved elements of signal transduction pathways. We also characterize genes related to biomineralization-a critical process of molluscan development. In summary, our experiment provides the first large-scale survey of gene expression in mollusc development, and complements previous studies on the regulatory mechanisms underlying body plan patterning and the formation of larval and juvenile structures. This study serves as a resource for further functional annotation of transcripts and genes in Aplysia, specifically and molluscs in general. A comparison of the Aplysia developmental transcriptome with similar studies in the zebra fish Danio rerio, the fruit fly Drosophila melanogaster, the nematode Caenorhabditis elegans, and other studies on molluscs suggests an overall highly divergent pattern of gene regulatory mechanisms that are likely a consequence of the different developmental modes of these organisms. © 2010 Wiley-Liss, Inc., A Wiley Company.

  13. Glandular dose and image quality control in mammography facilities with computerized radiography systems; Dose glandular e controle de qualidade da imagem em servicos de mamografia com sistema de radiografia computadorizada

    Energy Technology Data Exchange (ETDEWEB)

    Dantas, Marcelino Vicente de Almeida

    2010-07-01

    Breast cancer is the most common cancer among women, and early detection is critical to its diagnosis and treatment. To date, the most effective method for early detection of breast cancer has been x-ray mammography for which the screen/film (SF) technique has been the gold standard. However, even though SF combinations have been improved and optimized over the years for breast imaging, there are some critical limitations, including a narrow exposure range, image artifacts, film processing problems, and inflexibility in image processing and film management. In recent years, digital mammography has been introduced in cancer screening programmes with the screen/film techniques gradually being phased out. Computed radiography (CR), also commonly known as photostimulable phosphor (PSP) imaging or storage phosphor, employs reusable imaging plates and associated hardware and software to acquire and to display digital projection radiographs. In this work, a protocol model was tested for performing image quality control and average glandular dose (AGD) evaluation in 19 institutions with computed radiography systems for mammography. The protocol was validated through tests at the Laboratorio de Radioprotecao Aplicada a Mamografia (LARAM) from the Centro de Desenvolvimento da Tecnologia Nuclear (CDTN). The image quality visual evaluation of CDMAM phantom showed that 53% of the facilities were able to produce images of excellent quality. Furthermore, the automated evaluation of image quality, using the analyze software cdcom.exe, showed that 57% of the images were considered to be of good quality. The detector linearity test showed that the CR response is very linear, where 95% of facilities evaluated were considered to be compliant. For the image noise was found that only 20% of facilities are in agreement with the parameters established for this test. The average glandular doses, which patients may be getting to perform an examination, were below the action levels

  14. A cohort of new adhesive proteins identified from transcriptomic analysis of mussel foot glands.

    Science.gov (United States)

    DeMartini, Daniel G; Errico, John M; Sjoestroem, Sebastian; Fenster, April; Waite, J Herbert

    2017-06-01

    The adaptive attachment of marine mussels to a wide range of substrates in a high-energy, saline environment has been explored for decades and is a significant driver of bioinspired wet adhesion research. Mussel attachment relies on a fibrous holdfast known as the byssus, which is made by a specialized appendage called the foot. Multiple adhesive and structural proteins are rapidly synthesized, secreted and moulded by the foot into holdfast threads. About 10 well-characterized proteins, namely the mussel foot proteins (Mfps), the preCols and the thread matrix proteins, are reported as representing the bulk of these structures. To explore how robust this proposition is, we sequenced the transcriptome of the glandular tissues that produce and secrete the various holdfast components using next-generation sequencing methods. Surprisingly, we found around 15 highly expressed genes that have not previously been characterized, but bear key similarities to the previously defined mussel foot proteins, suggesting additional contribution to byssal function. We verified the validity of these transcripts by polymerase chain reaction, cloning and Sanger sequencing as well as confirming their presence as proteins in the byssus. These newly identified proteins greatly expand the palette of mussel holdfast biochemistry and provide new targets for investigation into bioinspired wet adhesion. © 2017 The Author(s).

  15. Comparative transcriptomics in the Triticeae

    Directory of Open Access Journals (Sweden)

    Waugh Robbie

    2009-06-01

    Full Text Available Abstract Background Barley and particularly wheat are two grass species of immense agricultural importance. In spite of polyploidization events within the latter, studies have shown that genotypically and phenotypically these species are very closely related and, indeed, fertile hybrids can be created by interbreeding. The advent of two genome-scale Affymetrix GeneChips now allows studies of the comparison of their transcriptomes. Results We have used the Wheat GeneChip to create a "gene expression atlas" for the wheat transcriptome (cv. Chinese Spring. For this, we chose mRNA from a range of tissues and developmental stages closely mirroring a comparable study carried out for barley (cv. Morex using the Barley1 GeneChip. This, together with large-scale clustering of the probesets from the two GeneChips into "homologous groups", has allowed us to perform a genomic-scale comparative study of expression patterns in these two species. We explore the influence of the polyploidy of wheat on the results obtained with the Wheat GeneChip and quantify the correlation between conservation in gene sequence and gene expression in wheat and barley. In addition, we show how the conservation of expression patterns can be used to elucidate, probeset by probeset, the reliability of the Wheat GeneChip. Conclusion While there are many differences in expression on the level of individual genes and tissues, we demonstrate that the wheat and barley transcriptomes appear highly correlated. This finding is significant not only because given small evolutionary distance between the two species it is widely expected, but also because it demonstrates that it is possible to use the two GeneChips for comparative studies. This is the case even though their probeset composition reflects rather different design principles as well as, of course, the present incomplete knowledge of the gene content of the two species. We also show that, in general, the Wheat GeneChip is not able

  16. Evaluation of the influence of parameters that determine the mean glandular dose in mammography using different detectors; Evaluacion de la influencia de los parametros que determinan la dosis glandular media en Mamografia utilizando diferentes detectores

    Energy Technology Data Exchange (ETDEWEB)

    Costa, K.; Nogueira, M. S., E-mail: katicostabh@gmail.com [Centro de Desenvolvimento da Tecnologia Nuclear, Pos-graduacao em Ciencias e Tecnologia das Radiacoes, Minerais e Materiais / CNEN, Av. Pte. Antonio Carlos 6627, 31270-901 Belo Horizonte, Minas Gerais (Brazil)

    2015-10-15

    Full text: Mammography is a test used for early detection of breast cancer. The mean glandular dose (MGD) is dosimetric greatness accepted as indicative of carcinogenic risk induced by ionizing radiation in the breasts of women undergoing mammography exams. MGD value is estimated from the incident air kerma (k i), associated with conversion factors which depend on the half-value layer (HVL), the breast composition and thickness compressed breast. This study aims to evaluate the influence of the parameters used to determine the MGD using different measurement detectors. Measurements were performed on a Siemens Mammomat Model 300 Nova mammography equipment; this has the combinations Anode/Filter of Mo/Mo, Mo/Rh and W/Rh. Detectors used were the ionization chamber Model 10X6-6M manufactured by Radcal Co., two solid-state detectors, one Model AGMS-M manufactured by Radcal Co. and other Model Xi Mammo manufactured by UNFORS. The detectors measures were compared and the MGD value was estimated; differences between measurements and the reference values were higher in HVL and k i parameters. The results are displayed according to other published works. (Author)

  17. Characterizing the transcriptome and molecular markers information ...

    Indian Academy of Sciences (India)

    2008). Analyses of the genetic structure .... The annotations and classifications for the transcriptome ... Based on the Pfam classification, the predic- ..... J. Lipid. Res. 33, 251–262. Eckert C. G., Samis K. E. and Lougheed S. C. 2008 Genetic vari-.

  18. The floral transcriptome of Eucalyptus grandis

    CSIR Research Space (South Africa)

    Vining, KJ

    2015-10-01

    Full Text Available As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages...

  19. Evaluation of the influence of parameters that determine the mean glandular dose in mammography using different detectors

    International Nuclear Information System (INIS)

    Costa, K.; Nogueira, M. S.

    2015-10-01

    Full text: Mammography is a test used for early detection of breast cancer. The mean glandular dose (MGD) is dosimetric greatness accepted as indicative of carcinogenic risk induced by ionizing radiation in the breasts of women undergoing mammography exams. MGD value is estimated from the incident air kerma (k i), associated with conversion factors which depend on the half-value layer (HVL), the breast composition and thickness compressed breast. This study aims to evaluate the influence of the parameters used to determine the MGD using different measurement detectors. Measurements were performed on a Siemens Mammomat Model 300 Nova mammography equipment; this has the combinations Anode/Filter of Mo/Mo, Mo/Rh and W/Rh. Detectors used were the ionization chamber Model 10X6-6M manufactured by Radcal Co., two solid-state detectors, one Model AGMS-M manufactured by Radcal Co. and other Model Xi Mammo manufactured by UNFORS. The detectors measures were compared and the MGD value was estimated; differences between measurements and the reference values were higher in HVL and k i parameters. The results are displayed according to other published works. (Author)

  20. 3rd International Conference on Transcriptomics

    OpenAIRE

    John A Daniel

    2017-01-01

    Conference Series has been instrumental in conducting international Biochemistry meetings for seven years, and very excited to expand Europe, America and Asia Pacific continents. Previous meetings were held in major cities like Philadelphia, Orlando with success the meetings again scheduled in three continents. 3rd International Conference on Transcriptomics to be held during October 30 - November 01, 2017 at Bangkok, Thailand The Global Transcriptomics business sector to develop at a C...

  1. Integrative investigation of metabolic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    Önsan Z İlsen

    2006-04-01

    Full Text Available Abstract Background New analysis methods are being developed to integrate data from transcriptome, proteome, interactome, metabolome, and other investigative approaches. At the same time, existing methods are being modified to serve the objectives of systems biology and permit the interpretation of the huge datasets currently being generated by high-throughput methods. Results Transcriptomic and metabolic data from chemostat fermentors were collected with the aim of investigating the relationship between these two data sets. The variation in transcriptome data in response to three physiological or genetic perturbations (medium composition, growth rate, and specific gene deletions was investigated using linear modelling, and open reading-frames (ORFs whose expression changed significantly in response to these perturbations were identified. Assuming that the metabolic profile is a function of the transcriptome profile, expression levels of the different ORFs were used to model the metabolic variables via Partial Least Squares (Projection to Latent Structures – PLS using PLS toolbox in Matlab. Conclusion The experimental design allowed the analyses to discriminate between the effects which the growth medium, dilution rate, and the deletion of specific genes had on the transcriptome and metabolite profiles. Metabolite data were modelled as a function of the transcriptome to determine their congruence. The genes that are involved in central carbon metabolism of yeast cells were found to be the ORFs with the most significant contribution to the model.

  2. Entomology contribution in animal immunity: Determination of the crude thoraxial glandular protein extract of Stomoxys calcitrans as an antibody production enhancer in young horses

    Directory of Open Access Journals (Sweden)

    L. Rumokoy

    2017-12-01

    Full Text Available This experiment was conducted to evaluate the level of antigens protein contained in the crude thoraxial glandular protein (TGP extract of Stomoxys calcitrans which function as immunity enhancer in young horses. The detection of protein content of the thoraxial glandular samples was performed by using a spectrophotometer Nano Drop-1000. This result showed that the lowest level of antigen protein was 0.54 mg/mL, the highest was 72 mg/mL, and the average was 0.675 mg/mL. Six foals were used and divided into two groups. The first group was treated with a solution of 100 μg of TGP by subcutaneous injection, the other group acted as control. The TGP extract was injected on the first day of the experiment. Three ml of blood were sampled from the jugular vein on the 14th day after TGP injection. The blood sampled was centrifuged and its serum placed in micro-tubes to observe the IgG level. The injection of TGP had a significant effect on the IgG level of the experiment animals (P<0.05. This experiment emphasized an important relation between entomology and animal husbandry; health improvement in the young animals was observed after the injection of the insect antigen, so it can be concluded that crude thoraxial glandular proteins of S. calcitrans can be used to improve the immunoglobulin-G circulation in foals.

  3. Guideline for determining the mean glandular dose according to DIN 6868-162 and threshold contrast visibility according to the quality assurance guideline for digital mammography systems.

    Science.gov (United States)

    Sommer, A; Schopphoven, S; Land, I; Blaser, D; Sobczak, T

    2014-05-01

    As part of the physico-technical quality assurance of the German breast cancer screening program, the threshold contrast visibility and the average glandular dose of every digital mammography system have to fulfill the requirements of the "European guidelines for quality assurance in breast cancer screening and diagnosis" (4th Edition). To accomplish uniform measurements in all federal states of Germany, the physical board of the reference centers developed a special guideline in 2009. Due to recent changes in the guidelines and standards, a second version of the guideline was developed by the reference centers. This guideline describes the determination of the average glandular dose as well as the CDMAM image acquisition and the CDMAM image evaluation. The determination of the threshold contrast visibility can be performed visually or automatically. The determination of the average glandular dose is based on DIN 6868 - 162 and the threshold contrast visibility test is based on the German "Quality Assurance Guideline". © Georg Thieme Verlag KG Stuttgart · New York.

  4. Promoting helix pitch and trichome length to improve biomass harvesting efficiency and carbon dioxide fixation rate by Spirulina sp. in 660 m2 raceway ponds under purified carbon dioxide from a coal chemical flue gas.

    Science.gov (United States)

    Cheng, Jun; Guo, Wangbiao; Ameer Ali, Kubar; Ye, Qing; Jin, Guiyong; Qiao, Zhanshan

    2018-08-01

    The helix pitch and trichome length of Spirulina sp. were promoted to improve the biomass harvesting efficiency and CO 2 fixation rate in 660 m 2 raceway ponds aerated with food-grade CO 2 purified from a coal chemical flue gas. The CO 2 fixation rate was improved with increased trichome length of the Spirulina sp. in a raceway pond with double paddlewheels, baffles, and CO 2 aerators (DBA raceway pond). The trichome length has increased by 33.3 μm, and CO 2 fixation rate has increased by 42.3% and peaked to 51.3 g/m 2 /d in a DBA raceway pond. Biomass harvesting efficiency was increased with increased helix pitch. When the day-average greenhouse temperature was 33 °C and day-average sunlight intensity was 72,100 lu×, the helix pitch of Spirulina sp. was increased to 56.2 μm. Hence the biomass harvesting efficiency was maximized to 75.6% and biomass actual yield was increased to 35.9 kg in a DBA raceway pond. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. The Cellient automated cell block system is useful in the differential diagnosis of atypical glandular cells in Papanicolaou tests.

    Science.gov (United States)

    Xing, Wei; Hou, April Y; Fischer, Andrew; Owens, Christopher L; Jiang, Zhong

    2014-01-01

    Atypical glandular cells (AGC) is a very important diagnosis in gynecological cytology. In the current study, the authors investigated the usefulness of Cellient cell blocks (CB) for characterizing AGC on Papanicolaou (Pap) tests. A total of 148 patients with an AGC diagnosis based on Pap tests by cytotechnologists and referred to cytopathologists were studied. Among these patients, there were 68 patients with CB preparations and 80 patients with Pap tests only (TP-AGC group). Follow-up results by Pap tests or biopsies were obtained in 117 of 148 patients. The median follow-up was 13 months (range, 1 month-36 months). Of the 68 patients with CBs, 31 (46%) were reclassified as negative for dysplasia or low-grade intraepithelial lesion; 30 patients (44%) retained a diagnosis of AGC (CB-AGC group); and 7 patients (10%) were given specific diagnoses of high-grade intraepithelial lesion (3 patients), endocervical adenocarcinoma in situ (1 patient), and invasive adenocarcinoma (3 patients). On follow-up, the CB-AGC group was found to have a significantly lower rate of negative/low-grade squamous intraepithelial lesion diagnoses compared with the TP-AGC group (55% vs 85%; P= .006). The CB-AGC group had a significantly higher rate of endocervical or endometrial adenocarcinoma compared with the TP-AGC group (36% vs 8%; P= .003) at the time of follow-up. The rates of high-grade squamous intraepithelial lesion were not found to be statistically different between these 2 groups (9% vs 7%; P= .66). The Cellient CB is a useful technique to further categorize a diagnosis of AGC on Pap tests. Using the Cellient CB system, the pathologist has the ability to improve the diagnostic accuracy of AGC so that unnecessary colposcopic evaluation or biopsies can be avoided. © 2013 American Cancer Society.

  6. Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides.

    Science.gov (United States)

    Gagne, Steve J; Stout, Jake M; Liu, Enwu; Boubakir, Zakia; Clark, Shawn M; Page, Jonathan E

    2012-07-31

    Δ(9)-Tetrahydrocannabinol (THC) and other cannabinoids are responsible for the psychoactive and medicinal properties of Cannabis sativa L. (marijuana). The first intermediate in the cannabinoid biosynthetic pathway is proposed to be olivetolic acid (OA), an alkylresorcinolic acid that forms the polyketide nucleus of the cannabinoids. OA has been postulated to be synthesized by a type III polyketide synthase (PKS) enzyme, but so far type III PKSs from cannabis have been shown to produce catalytic byproducts instead of OA. We analyzed the transcriptome of glandular trichomes from female cannabis flowers, which are the primary site of cannabinoid biosynthesis, and searched for polyketide cyclase-like enzymes that could assist in OA cyclization. Here, we show that a type III PKS (tetraketide synthase) from cannabis trichomes requires the presence of a polyketide cyclase enzyme, olivetolic acid cyclase (OAC), which catalyzes a C2-C7 intramolecular aldol condensation with carboxylate retention to form OA. OAC is a dimeric α+β barrel (DABB) protein that is structurally similar to polyketide cyclases from Streptomyces species. OAC transcript is present at high levels in glandular trichomes, an expression profile that parallels other cannabinoid pathway enzymes. Our identification of OAC both clarifies the cannabinoid pathway and demonstrates unexpected evolutionary parallels between polyketide biosynthesis in plants and bacteria. In addition, the widespread occurrence of DABB proteins in plants suggests that polyketide cyclases may play an overlooked role in generating plant chemical diversity.

  7. Plant transcriptomics and responses to environmental stress: an ...

    Indian Academy of Sciences (India)

    3Centre for Environmental Research, Near East University, 33010, Lefkosha, Turkish Republic of the Northern Cyprus. 4Department of ...... Transcriptomic analysis of sense and antisense strands of .... 2008 Stem cell transcriptome profiling via.

  8. Blood transcriptomics: applications in toxicology

    Science.gov (United States)

    Joseph, Pius; Umbright, Christina; Sellamuthu, Rajendran

    2015-01-01

    The number of new chemicals that are being synthesized each year has been steadily increasing. While chemicals are of immense benefit to mankind, many of them have a significant negative impact, primarily owing to their inherent chemistry and toxicity, on the environment as well as human health. In addition to chemical exposures, human exposures to numerous non-chemical toxic agents take place in the environment and workplace. Given that human exposure to toxic agents is often unavoidable and many of these agents are found to have detrimental human health effects, it is important to develop strategies to prevent the adverse health effects associated with toxic exposures. Early detection of adverse health effects as well as a clear understanding of the mechanisms, especially at the molecular level, underlying these effects are key elements in preventing the adverse health effects associated with human exposure to toxic agents. Recent developments in genomics, especially transcriptomics, have prompted investigations into this important area of toxicology. Previous studies conducted in our laboratory and elsewhere have demonstrated the potential application of blood gene expression profiling as a sensitive, mechanistically relevant and practical surrogate approach for the early detection of adverse health effects associated with exposure to toxic agents. The advantages of blood gene expression profiling as a surrogate approach to detect early target organ toxicity and the molecular mechanisms underlying the toxicity are illustrated and discussed using recent studies on hepatotoxicity and pulmonary toxicity. Furthermore, the important challenges this emerging field in toxicology faces are presented in this review article. PMID:23456664

  9. The utility of transcriptomics in fish conservation.

    Science.gov (United States)

    Connon, Richard E; Jeffries, Ken M; Komoroske, Lisa M; Todgham, Anne E; Fangue, Nann A

    2018-01-29

    There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers. © 2018. Published by The Company of Biologists Ltd.

  10. Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis

    OpenAIRE

    Jones, Beryl M.; Wcislo, William T.; Robinson, Gene E.

    2015-01-01

    Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome fo...

  11. Morfologia dos tricomas das pétalas de espécies de Pseudobombax Dugand (Malvaceae, Bombacoideae e seu significado taxonômico Morphology of trichomes in petals of Pseudobombax Dugand (Malvaceae, Bombacoideae species and its taxonomic significance

    Directory of Open Access Journals (Sweden)

    Jefferson Guedes de Carvalho-Sobrinho

    2009-12-01

    Full Text Available O gênero Pseudobombax Dugand apresenta cerca de 30 espécies, é restrito à região Neotropical e apresenta taxonomia complexa, com muitas de suas espécies mal circunscritas. Parte de seus problemas taxonômicos é conseqüência do fato de que suas espécies perdem as folhas na floração e, portanto, a maioria delas é representada apenas por flores nas coleções de herbário. Neste trabalho, investigou-se a morfologia dos tricomas presentes nas pétalas de oito espécies de Pseudobombax. O estudo utilizou microscopia óptica e eletrônica de varredura a partir de amostras obtidas de material de herbário e flores fixadas em etanol a 70%. Em todas as espécies de Pseudobombax analisadas, foram encontrados dois tipos principais de tricomas: (a tricomas 2-4-armados, sésseis, longos, flexíveis e com paredes finas, situados na face adaxial de todas as espécies; (b tricomas tufosos, sésseis, curtos, rígidos, com paredes espessas e lignificadas, situados na face abaxial. Os dados qualitativos e quantitativos obtidos mostraram-se de valor taxonômico para a resolução de problemas de identificação específica em Pseudobombax.Trichome morphology of the petals of Pseudobombax Dugand species was investigated. The eight species selected of Pseudobombax were analyzed using optical microscopy and scanning electron microscopy. The study detected the existence of variation, both qualitative and quantitative, in morphology of trichomes in petals of species analyzed. In Pseudobombax petals, two kinds of trichomes were found: (a trichomes 2-4-armed, sessile, long, flexible and with thin walls, situated on the adaxial surface; (b tufted trichomes, sessile, short, rigid, with thick, lignified walls, on the abaxial surface of the petals. The qualitative and quantitative data were of taxonomic value for the resolution of problems of specific identification in the genus.

  12. Ectopic expression of Capsicum-specific cell wall protein Capsicum annuum senescence-delaying 1 (CaSD1) delays senescence and induces trichome formation in Nicotiana benthamiana.

    Science.gov (United States)

    Seo, Eunyoung; Yeom, Seon-In; Jo, Sunghwan; Jeong, Heejin; Kang, Byoung-Cheorl; Choi, Doil

    2012-04-01

    Secreted proteins are known to have multiple roles in plant development, metabolism, and stress response. In a previous study to understand the roles of secreted proteins, Capsicum annuum secreted proteins (CaS) were isolated by yeast secretion trap. Among the secreted proteins, we further characterized Capsicum annuum senescence-delaying 1 (CaSD1), a gene encoding a novel secreted protein that is present only in the genus Capsicum. The deduced CaSD1 contains multiple repeats of the amino acid sequence KPPIHNHKPTDYDRS. Interestingly, the number of repeats varied among cultivars and species in the Capsicum genus. CaSD1 is constitutively expressed in roots, and Agrobacterium-mediated transient overexpression of CaSD1 in Nicotiana benthamiana leaves resulted in delayed senescence with a dramatically increased number of trichomes and enlarged epidermal cells. Furthermore, senescence- and cell division-related genes were differentially regulated by CaSD1-overexpressing plants. These observations imply that the pepper-specific cell wall protein CaSD1 plays roles in plant growth and development by regulating cell division and differentiation.

  13. Blood transcriptomics and metabolomics for personalized medicine.

    Science.gov (United States)

    Li, Shuzhao; Todor, Andrei; Luo, Ruiyan

    2016-01-01

    Molecular analysis of blood samples is pivotal to clinical diagnosis and has been intensively investigated since the rise of systems biology. Recent developments have opened new opportunities to utilize transcriptomics and metabolomics for personalized and precision medicine. Efforts from human immunology have infused into this area exquisite characterizations of subpopulations of blood cells. It is now possible to infer from blood transcriptomics, with fine accuracy, the contribution of immune activation and of cell subpopulations. In parallel, high-resolution mass spectrometry has brought revolutionary analytical capability, detecting > 10,000 metabolites, together with environmental exposure, dietary intake, microbial activity, and pharmaceutical drugs. Thus, the re-examination of blood chemicals by metabolomics is in order. Transcriptomics and metabolomics can be integrated to provide a more comprehensive understanding of the human biological states. We will review these new data and methods and discuss how they can contribute to personalized medicine.

  14. The Human Transcriptome: An Unfinished Story

    Directory of Open Access Journals (Sweden)

    Mihaela Pertea

    2012-06-01

    Full Text Available Despite recent technological advances, the study of the human transcriptome is still in its early stages. Here we provide an overview of the complex human transcriptomic landscape, present the bioinformatics challenges posed by the vast quantities of transcriptomic data, and discuss some of the studies that have tried to determine how much of the human genome is transcribed. Recent evidence has suggested that more than 90% of the human genome is transcribed into RNA. However, this view has been strongly contested by groups of scientists who argued that many of the observed transcripts are simply the result of transcriptional noise. In this review, we conclude that the full extent of transcription remains an open question that will not be fully addressed until we decipher the complete range and biological diversity of the transcribed genomic sequences.

  15. Antibodies against Escherichia coli O24 and O56 O-Specific Polysaccharides Recognize Epitopes in Human Glandular Epithelium and Nervous Tissue

    Science.gov (United States)

    Korzeniowska-Kowal, Agnieszka; Kochman, Agata; Gamian, Elżbieta; Lis-Nawara, Anna; Lipiński, Tomasz; Seweryn, Ewa; Ziółkowski, Piotr; Gamian, Andrzej

    2015-01-01

    Lipopolysaccharide (LPS), the major component of the outer membrane of Gram-negative bacteria, contains the O-polysaccharide, which is important to classify bacteria into different O-serological types within species. The O-polysaccharides of serotypes O24 and O56 of E. coli contain sialic acid in their structures, already established in our previous studies. Here, we report the isolation of specific antibodies with affinity chromatography using immobilized lipopolysaccharides. Next, we evaluated the reactivity of anti-O24 and anti-O56 antibody on human tissues histologically. The study was conducted under the assumption that the sialic acid based molecular identity of bacterial and tissue structures provides not only an understanding of the mimicry-based bacterial pathogenicity. Cross-reacting antibodies could be used to recognize specific human tissues depending on their histogenesis and differentiation, which might be useful for diagnostic purposes. The results indicate that various human tissues are recognized by anti-O24 and anti-O56 antibodies. Interestingly, only a single specific reactivity could be found in the anti-O56 antibody preparation. Several tissues studied were not reactive with either antibody, thus proving that the presence of cross-reactive antigens was tissue specific. In general, O56 antibody performed better than O24 in staining epithelial and nervous tissues. Positive staining was observed for both normal (ganglia) and tumor tissue (ganglioneuroma). Epithelial tissue showed positive staining, but an epitope recognized by O56 antibody should be considered as a marker of glandular epithelium. The reason is that malignant glandular tumor and its metastasis are stained, and also epithelium of renal tubules and glandular structures of the thyroid gland are stained. Stratified epithelium such as that of skin is definitely not stained. Therefore, the most relevant observation is that the epitope recognized by anti-O56 antibodies is a new marker

  16. Morfoanatomia, tricomas glandulares e fitoquímica de Lomatozona artemisiifolia Baker (ASTERACEAE - EUPATORIEAE) - uma planta endêmica do Cerrado de Goiás

    OpenAIRE

    Trindade, Luma Mota Palmeira

    2013-01-01

    Morfoanatomia, tricomas glandulares e fitoquímica de Lomatozona artemisiifolia Baker (Asteraceae - Eupatorieae) – Uma planta endêmica do cerrado de Goiás - A família Asteraceae é amplamente distribuída, possuindo 24.000 espécies e 1.600 a 1700 gêneros, constituindo uma das maiores famílias de fanerógamas. No Cerrado, dentre as fanerógamas, é a segunda maior família em quantidade de espécies. Dentre as inúmeras espécies de Asteraceae está presente Lomatozona artemisiifolia Baker, pertence à tr...

  17. The transcriptome of Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Roos David S

    2005-12-01

    Full Text Available Abstract Background Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown. Results We have used serial analysis of gene expression (SAGE to define the Toxoplasma gondii transcriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (~300,000 SAGE tags representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity. Conclusion This study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1–5% of the tags in each developmental stage. We have also found that Toxoplasma mRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across all Toxoplasma chromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and

  18. Scrimer: designing primers from transcriptome data

    Czech Academy of Sciences Publication Activity Database

    Mořkovský, Libor; Pačes, Jan; Rídl, Jakub; Reifová, R.

    2015-01-01

    Roč. 15, č. 6 (2015), s. 1415-1420 ISSN 1755-098X R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 ; RVO:68378050 Keywords : next-generation sequencing * primer design * SNaPshot * SNP genotyping * transcriptome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.298, year: 2015

  19. Global daily dynamics of the pineal transcriptome

    DEFF Research Database (Denmark)

    Bustos, Diego M; Bailey, Michael J; Sugden, David

    2011-01-01

    Transcriptome profiling of the pineal gland has revealed night/day differences in the expression of a major fraction of the genes active in this tissue, with two-thirds of these being nocturnal increases. A set of over 600 transcripts exhibit two-fold to >100-fold daily differences in abundance...

  20. The transcriptome landscape of early maize meiosis

    Science.gov (United States)

    Meiosis, particularly meiotic recombination, is a major factor affecting yield and breeding of plants. To gain insight into the transcriptome landscape during early initiation steps of meiotic recombination, we profiled early prophase I meiocytes from maize using RNA-seq. Our analyses of genes prefe...

  1. The renal transcriptome in experimental hypertension

    NARCIS (Netherlands)

    Wesseling, S.

    2007-01-01

    The renal transcriptome in experimental hypertension The kidneys importantly determine blood pressure. Kidney dysfunction can result in hypertension, which in turn leads to renal damage. In primary hypertension the cause is unknown. The condition is polygenic, however, which genetic defects cause

  2. Transcriptome analysis of Anopheles stephensi embryo using ...

    Indian Academy of Sciences (India)

    Germ band retraction (GBR) stage is one of the important stages during insect development. It is associated with an extensive epithelial morphogenesis and may also be pivotal in generation of morphological diversity in insects. Despite its importance, only a handful of studies report the transcriptome repertoire of this stage ...

  3. Brain transcriptome atlases : A computational perspective

    NARCIS (Netherlands)

    Mahfouz, A.M.E.T.A.; Huisman, S.M.H.; Lelieveldt, B.P.F.; Reinders, M.J.T.

    2017-01-01

    The immense complexity of the mammalian brain is largely reflected in the underlying molecular signatures of its billions of cells. Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development. Such atlases

  4. A unique case of a huge mixed squamous cell and glandular papilloma of non-endobronchial origin with a peripheral growth

    Directory of Open Access Journals (Sweden)

    Kei Yabuki

    Full Text Available We report a case of a huge solitary non-endobronchial pulmonary tumor in a 76-year-old male smoker. The tumor measured 11 × 10 × 8 cm. It was ill-defined, and it was located periphery of the right lower lobe with the subpleural cystic spaces. He underwent right lower lobectomy with mediastinal lymph node dissection and is free from tumor 30 months after surgery. Microscopically, it was composed of a proliferation of squamous and ciliated columnar epithelial cells with a few mucous cells. These cells were arranged in a papillary growth fashion extending along the fibrously thickened alveolar septa together with metaplastic bronchiolar and squamous epithelia displaying an usual interstitial pneumonia-pattern. Although the histologic features of the tumor were that of a mixed squamous cell and glandular papilloma (MSCGP, it was peripherally located and showed a lepidic growth, and it was much larger than previously reported MSCGPs. It is possible that the tumor developed in association with bronchial metaplasia in the periphery of the lung, and then extended along the surface of the reconstructed air spaces, which resulted in its unique histologic appearance. Further investigations of respiratory papilloma are needed to clarify the pathogenesis of these lesions. Keywords: Mixed squamous cell and glandular papilloma, Non-endobronchial, Cytology, Interstitial pneumonia, Pulmonary tumor

  5. Reptilian Transcriptomes v2.0: An Extensive Resource for Sauropsida Genomics and Transcriptomics.

    Science.gov (United States)

    Tzika, Athanasia C; Ullate-Agote, Asier; Grbic, Djordje; Milinkovitch, Michel C

    2015-07-01

    Despite the availability of deep-sequencing techniques, genomic and transcriptomic data remain unevenly distributed across phylogenetic groups. For example, reptiles are poorly represented in sequence databases, hindering functional evolutionary and developmental studies in these lineages substantially more diverse than mammals. In addition, different studies use different assembly and annotation protocols, inhibiting meaningful comparisons. Here, we present the "Reptilian Transcriptomes Database 2.0," which provides extensive annotation of transcriptomes and genomes from species covering the major reptilian lineages. To this end, we sequenced normalized complementary DNA libraries of multiple adult tissues and various embryonic stages of the leopard gecko and the corn snake and gathered published reptilian sequence data sets from representatives of the four extant orders of reptiles: Squamata (snakes and lizards), the tuatara, crocodiles, and turtles. The LANE runner 2.0 software was implemented to annotate all assemblies within a single integrated pipeline. We show that this approach increases the annotation completeness of the assembled transcriptomes/genomes. We then built large concatenated protein alignments of single-copy genes and inferred phylogenetic trees that support the positions of turtles and the tuatara as sister groups of Archosauria and Squamata, respectively. The Reptilian Transcriptomes Database 2.0 resource will be updated to include selected new data sets as they become available, thus making it a reference for differential expression studies, comparative genomics and transcriptomics, linkage mapping, molecular ecology, and phylogenomic analyses involving reptiles. The database is available at www.reptilian-transcriptomes.org and can be enquired using a wwwblast server installed at the University of Geneva. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  6. Global meta-analysis of transcriptomics studies.

    Directory of Open Access Journals (Sweden)

    José Caldas

    Full Text Available Transcriptomics meta-analysis aims at re-using existing data to derive novel biological hypotheses, and is motivated by the public availability of a large number of independent studies. Current methods are based on breaking down studies into multiple comparisons between phenotypes (e.g. disease vs. healthy, based on the studies' experimental designs, followed by computing the overlap between the resulting differential expression signatures. While useful, in this methodology each study yields multiple independent phenotype comparisons, and connections are established not between studies, but rather between subsets of the studies corresponding to phenotype comparisons. We propose a rank-based statistical meta-analysis framework that establishes global connections between transcriptomics studies without breaking down studies into sets of phenotype comparisons. By using a rank product method, our framework extracts global features from each study, corresponding to genes that are consistently among the most expressed or differentially expressed genes in that study. Those features are then statistically modelled via a term-frequency inverse-document frequency (TF-IDF model, which is then used for connecting studies. Our framework is fast and parameter-free; when applied to large collections of Homo sapiens and Streptococcus pneumoniae transcriptomics studies, it performs better than similarity-based approaches in retrieving related studies, using a Medical Subject Headings gold standard. Finally, we highlight via case studies how the framework can be used to derive novel biological hypotheses regarding related studies and the genes that drive those connections. Our proposed statistical framework shows that it is possible to perform a meta-analysis of transcriptomics studies with arbitrary experimental designs by deriving global expression features rather than decomposing studies into multiple phenotype comparisons.

  7. Transcriptome architecture across tissues in the pig

    Directory of Open Access Journals (Sweden)

    Folch Josep M

    2008-04-01

    Full Text Available Abstract Background Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask: How relevant is tissue in terms of total transcriptome variability? Which are the genes most distinctly expressed between tissues? Does breed or sex equally affect the transcriptome across tissues? Results In order to gain insight on these issues, we conducted microarray expression profiling of 16 different tissues from four animals of two extreme pig breeds, Large White and Iberian, two males and two females. Mixed model analysis and neighbor – joining trees showed that tissues with similar developmental origin clustered closer than those with different embryonic origins. Often a sound biological interpretation was possible for overrepresented gene ontology categories within differentially expressed genes between groups of tissues. For instance, an excess of nervous system or muscle development genes were found among tissues of ectoderm or mesoderm origins, respectively. Tissue accounted for ~11 times more variability than sex or breed. Nevertheless, we were able to confidently identify genes with differential expression across tissues between breeds (33 genes and between sexes (19 genes. The genes primarily affected by sex were overall different than those affected by breed or tissue. Interaction with tissue can be important for differentially expressed genes between breeds but not so much for genes whose expression differ between sexes. Conclusion Embryonic development leaves an enduring footprint on the transcriptome. The interaction in gene × tissue for differentially expressed genes between breeds suggests that animal breeding has targeted differentially each tissue's transcriptome.

  8. Comparative Analysis of the Arabidopsis Pollen Transcriptome

    Czech Academy of Sciences Publication Activity Database

    Honys, David; Twell, D.

    2003-01-01

    Roč. 132, - (2003), s. 640ů652 ISSN 0032-0889 R&D Projects: GA AV ČR IAA5038207 Grant - others:Royal Society(GB) NATO Postdoctoral Fellowship (to D.H.) Institutional research plan: CEZ:AV0Z5038910; CEZ:MSM 113100003 Keywords : transcriptome profiling * Arabidopsis pollen * male gametophyte Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.634, year: 2003

  9. Transcriptome Dynamics during Maize Endosperm Development.

    Directory of Open Access Journals (Sweden)

    Jianzhou Qu

    Full Text Available The endosperm is a major organ of the seed that plays vital roles in determining seed weight and quality. However, genome-wide transcriptome patterns throughout maize endosperm development have not been comprehensively investigated to date. Accordingly, we performed a high-throughput RNA sequencing (RNA-seq analysis of the maize endosperm transcriptome at 5, 10, 15 and 20 days after pollination (DAP. We found that more than 11,000 protein-coding genes underwent alternative splicing (AS events during the four developmental stages studied. These genes were mainly involved in intracellular protein transport, signal transmission, cellular carbohydrate metabolism, cellular lipid metabolism, lipid biosynthesis, protein modification, histone modification, cellular amino acid metabolism, and DNA repair. Additionally, 7,633 genes, including 473 transcription factors (TFs, were differentially expressed among the four developmental stages. The differentially expressed TFs were from 50 families, including the bZIP, WRKY, GeBP and ARF families. Further analysis of the stage-specific TFs showed that binding, nucleus and ligand-dependent nuclear receptor activities might be important at 5 DAP, that immune responses, signalling, binding and lumen development are involved at 10 DAP, that protein metabolic processes and the cytoplasm might be important at 15 DAP, and that the responses to various stimuli are different at 20 DAP compared with the other developmental stages. This RNA-seq analysis provides novel, comprehensive insights into the transcriptome dynamics during early endosperm development in maize.

  10. Transposable elements in the Anopheles funestus transcriptome.

    Science.gov (United States)

    Fernández-Medina, Rita D; Carareto, Claudia M A; Struchiner, Cláudio J; Ribeiro, José M C

    2017-06-01

    Transposable elements (TEs) are present in most of the eukaryotic genomes and their impact on genome evolution is increasingly recognized. Although there is extensive information on the TEs present in several eukaryotic genomes, less is known about the expression of these elements at the transcriptome level. Here we present a detailed analysis regarding the expression of TEs in Anopheles funestus, the second most important vector of human malaria in Africa. Several transcriptionally active TE families belonging both to Class I and II were identified and characterized. Interestingly, we have identified a full-length putative active element (including the presence of full length TIRs in the genomic sequence) belonging to the hAT superfamily, which presents active members in other insect genomes. This work contributes to a comprehensive understanding of the landscape of transposable elements in A. funestus transcriptome. Our results reveal that TEs are abundant and diverse in the mosquito and that most of the TE families found in the genome are represented in the mosquito transcriptome, a fact that could indicate activity of these elements.The vast diversity of TEs expressed in A. funestus suggests that there is ongoing amplification of several families in this organism.

  11. Excess antibody immunoassays for rat glandular kallikreins. Measurement of kallikrein from different organs in the presence of cross-reacting antigens

    International Nuclear Information System (INIS)

    Johansen, L.; Oerstavik, T.B.; Holck, M.; Nustad, K.

    1983-01-01

    An immunoradiometric assay has previously been developed for measurement of rat glandular kallikrein. In the present paper, further studies on the specificity and sensitivity of the method are described. Problems of interference of immunologically cross-reacting antigens were overcome by proper preabsorption of the antibody. A method was thus established in which enzymatic activity of the immunoreactive kallikrein could be measured even in the presence of enzymes sharing immunological determinants and substrate specificity with kallikrein. Two variants of the immunoradiometric assay have been evaluated. A simplified version with simultaneous addition of all reagents gave results equal to those obtained in the original assay. A further modification with delayed addition of the solid-phase antibody, gave considerable improvement in assay sensitivity. (Auth.)

  12. Distinct Ezrin Truncations Differentiate Metastases in Sentinel Lymph Nodes from Unaffected Lymph Node Tissues, from Primary Breast Tumors, and from Healthy Glandular Breast Tissues

    Directory of Open Access Journals (Sweden)

    Claudia Röwer

    2018-02-01

    Full Text Available BACKGROUND: Lymph node metastasis status is a prognostic factor for further lymph node involvement and for patient survival in breast cancer patients. Frozen section analysis of lymph nodes is a reliable method for detection of macro-metastases. However, this method is far less effective in detecting micro-metastases, requesting improved diagnostic procedures. METHODS: We investigated expression and truncation of ezrin in (i sentinel lymph node metastases, (ii unaffected axillary lymph nodes, (iii primary breast tumors, and (iv healthy glandular breast tissues using 2D gel electrophoresis, SDS-PAGE, and mass spectrometry in addition to Western blotting. RESULTS: Full-length ezrin (E1; amino acids 1–586 is present in all four investigated tissues. Two truncated ezrin forms, one missing about the first hundred amino acids (E2a and the other lacking about 150 C-terminal amino acids (E2b were detectable in primary tumor tissues and in sentinel lymph node metastases but not in glandular tissues. Strikingly, an ezrin truncation (E3 which consists approximately of amino acids 238–586 was found strongly expressed in all sentinel lymph node metastases. Moreover, an N-terminal ezrin fragment (E4 that consists approximately of amino acids 1–273 was identified in sentinel lymph node metastases as well. CONCLUSIONS: We show for the first time the existence of tissue-dependent specific ezrin truncations. The distinguished strong Western blot staining of ezrin E3 in sentinel lymph node metastases underlines its capability to substantiate the occurrence of lymph node (micrometastases in breast cancer patients.

  13. Usefulness of p16ink4a, ProEX C, and Ki-67 for the diagnosis of glandular dysplasia and adenocarcinoma of the cervix uteri.

    Science.gov (United States)

    Negri, Giovanni; Bellisano, Giulia; Carico, Elisabetta; Faa, Gavino; Kasal, Armin; Antoniazzi, Sonia; Egarter-Vigl, Eduard; Piccin, Andrea; Dalla Palma, Paolo; Vittadello, Fabio

    2011-07-01

    Although the diagnostic criteria of in-situ and invasive adenocarcinomas of the cervix uteri are well established, the differentiation from benign mimics may be difficult and the morphologic features of the precursors of endocervical adenocarcinoma are still debated. In this study, we evaluated the usefulness of p16ink4a (p16), ProEX C, and Ki-67 for the diagnosis of endocervical adenocarcinoma and its precursors. Immunohistochemistry with p16, ProEX C, and Ki-67 was performed in 82 glandular lesions including 15 invasive adenocarcinomas, 29 adenocarcinomas in situ (AIS), 22 non-neoplastic samples, and 16 cases of glandular dysplasia (GD), which showed significant nuclear abnormalities but did not meet the diagnostic criteria for AIS. The immunohistochemical expression pattern was scored according to the percentage of the stained cells (0, 1+, 2+, and 3+ when 0% to 5%, 6% to 25%, 26% to 50%, and more than 50% of the cells were stained, respectively) and was evaluated for each antibody. p16 was at least focally expressed (1+ or more) in 14 of 15 invasive adenocarcinomas, in all AIS and in 7 negative samples. ProEX C and Ki-67 both scored 1+ or more in all adenocarcinomas and AIS and in 8 and 6 negative samples, respectively. Of the GD 15, 14, and 15 expressed p16, ProEX C, and Ki-67, respectively. The score differences between neoplastic and non-neoplastic samples were highly significant for each marker (Pcervix uteri and may also improve the diagnostic accuracy of endocervical GD. In particularly problematic cases, the combination of p16 and a proliferation marker can provide additional help for the interpretation of these lesions.

  14. Plasminogen-independent initiation of the pro-urokinase activation cascade in vivo. Activation of pro-urokinase by glandular kallikrein (mGK-6) in plasminogen-deficient mice

    DEFF Research Database (Denmark)

    List, K; Jensen, Ole Nørregaard; Bugge, T H

    2000-01-01

    )-antitrypsin. We suggest that mouse glandular kallikrein mGK-6 is an activator of pro-uPA in the mouse urinary tract in vivo. Since this kallikrein is expressed in a number of tissues and also occurs in plasma, it can also be considered a candidate for a physiological pro-uPA activator in other locations....

  15. MO-F-CAMPUS-I-02: Accuracy in Converting the Average Breast Dose Into the Mean Glandular Dose (MGD) Using the F-Factor in Cone Beam Breast CT- a Monte Carlo Study Using Homogeneous and Quasi-Homogeneous Phantoms

    Energy Technology Data Exchange (ETDEWEB)

    Lai, C; Zhong, Y; Wang, T; Shaw, C [UT MD Anderson Cancer Center, Houston, TX (United States)

    2015-06-15

    Purpose: To investigate the accuracy in estimating the mean glandular dose (MGD) for homogeneous breast phantoms by converting from the average breast dose using the F-factor in cone beam breast CT. Methods: EGSnrc-based Monte Carlo codes were used to estimate the MGDs. 13-cm in diameter, 10-cm high hemi-ellipsoids were used to simulate pendant-geometry breasts. Two different types of hemi-ellipsoidal models were employed: voxels in quasi-homogeneous phantoms were designed as either adipose or glandular tissue while voxels in homogeneous phantoms were designed as the mixture of adipose and glandular tissues. Breast compositions of 25% and 50% volume glandular fractions (VGFs), defined as the ratio of glandular tissue voxels to entire breast voxels in the quasi-homogeneous phantoms, were studied. These VGFs were converted into glandular fractions by weight and used to construct the corresponding homogeneous phantoms. 80 kVp x-rays with a mean energy of 47 keV was used in the simulation. A total of 109 photons were used to image the phantoms and the energies deposited in the phantom voxels were tallied. Breast doses in homogeneous phantoms were averaged over all voxels and then used to calculate the MGDs using the F-factors evaluated at the mean energy of the x-rays. The MGDs for quasi-homogeneous phantoms were computed directly by averaging the doses over all glandular tissue voxels. The MGDs estimated for the two types of phantoms were normalized to the free-in-air dose at the iso-center and compared. Results: The normalized MGDs were 0.756 and 0.732 mGy/mGy for the 25% and 50% VGF homogeneous breasts and 0.761 and 0.733 mGy/mGy for the corresponding quasi-homogeneous breasts, respectively. The MGDs estimated for the two types of phantoms were similar within 1% in this study. Conclusion: MGDs for homogeneous breast models may be adequately estimated by converting from the average breast dose using the F-factor.

  16. MO-F-CAMPUS-I-02: Accuracy in Converting the Average Breast Dose Into the Mean Glandular Dose (MGD) Using the F-Factor in Cone Beam Breast CT- a Monte Carlo Study Using Homogeneous and Quasi-Homogeneous Phantoms

    International Nuclear Information System (INIS)

    Lai, C; Zhong, Y; Wang, T; Shaw, C

    2015-01-01

    Purpose: To investigate the accuracy in estimating the mean glandular dose (MGD) for homogeneous breast phantoms by converting from the average breast dose using the F-factor in cone beam breast CT. Methods: EGSnrc-based Monte Carlo codes were used to estimate the MGDs. 13-cm in diameter, 10-cm high hemi-ellipsoids were used to simulate pendant-geometry breasts. Two different types of hemi-ellipsoidal models were employed: voxels in quasi-homogeneous phantoms were designed as either adipose or glandular tissue while voxels in homogeneous phantoms were designed as the mixture of adipose and glandular tissues. Breast compositions of 25% and 50% volume glandular fractions (VGFs), defined as the ratio of glandular tissue voxels to entire breast voxels in the quasi-homogeneous phantoms, were studied. These VGFs were converted into glandular fractions by weight and used to construct the corresponding homogeneous phantoms. 80 kVp x-rays with a mean energy of 47 keV was used in the simulation. A total of 109 photons were used to image the phantoms and the energies deposited in the phantom voxels were tallied. Breast doses in homogeneous phantoms were averaged over all voxels and then used to calculate the MGDs using the F-factors evaluated at the mean energy of the x-rays. The MGDs for quasi-homogeneous phantoms were computed directly by averaging the doses over all glandular tissue voxels. The MGDs estimated for the two types of phantoms were normalized to the free-in-air dose at the iso-center and compared. Results: The normalized MGDs were 0.756 and 0.732 mGy/mGy for the 25% and 50% VGF homogeneous breasts and 0.761 and 0.733 mGy/mGy for the corresponding quasi-homogeneous breasts, respectively. The MGDs estimated for the two types of phantoms were similar within 1% in this study. Conclusion: MGDs for homogeneous breast models may be adequately estimated by converting from the average breast dose using the F-factor

  17. Transcriptome complexity in a genome-reduced bacterium

    DEFF Research Database (Denmark)

    Güell, Marc; van Noort, Vera; Yus, Eva

    2009-01-01

    To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previousl...

  18. The Escherichia coli transcriptome linked to growth fitness

    Directory of Open Access Journals (Sweden)

    Bei-Wen Ying

    2016-03-01

    Full Text Available A series of Escherichia coli strains with varied genomic sequences were subjected to high-density microarray analyses to elucidate the fitness-correlated transcriptomes. Fitness, which is commonly evaluated by the growth rate during the exponential phase, is not only determined by the genome but is also linked to growth conditions, e.g., temperature. We previously reported genetic and environmental contributions to E. coli transcriptomes and evolutionary transcriptome changes in thermal adaptation. Here, we describe experimental details on how to prepare microarray samples that truly represent the growth fitness of the E. coli cells. A step-by-step record of sample preparation procedures that correspond to growing cells and transcriptome data sets that are deposited at the GEO database (GSE33212, GSE52770, GSE61739 are also provided for reference. Keywords: Transcriptome, Growth fitness, Escherichia coli, Microarray

  19. Transcriptome sequencing and comparative transcriptome analysis of the scleroglucan producer Sclerotium rolfsii

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    Stahl Ulf

    2010-05-01

    Full Text Available Abstract Background The plant pathogenic basidiomycete Sclerotium rolfsii produces the industrially exploited exopolysaccharide scleroglucan, a polymer that consists of (1 → 3-β-linked glucose with a (1 → 6-β-glycosyl branch on every third unit. Although the physicochemical properties of scleroglucan are well understood, almost nothing is known about the genetics of scleroglucan biosynthesis. Similarly, the biosynthetic pathway of oxalate, the main by-product during scleroglucan production, has not been elucidated yet. In order to provide a basis for genetic and metabolic engineering approaches, we studied scleroglucan and oxalate biosynthesis in S. rolfsii using different transcriptomic approaches. Results Two S. rolfsii transcriptomes obtained from scleroglucan-producing and scleroglucan-nonproducing conditions were pooled and sequenced using the 454 pyrosequencing technique yielding ~350,000 reads. These could be assembled into 21,937 contigs and 171,833 singletons, for which 6,951 had significant matches in public protein data bases. Sequence data were used to obtain first insights into the genomics of scleroglucan and oxalate production and to predict putative proteins involved in the synthesis of both metabolites. Using comparative transcriptomics, namely Agilent microarray hybridization and suppression subtractive hybridization, we identified ~800 unigenes which are differently expressed under scleroglucan-producing and non-producing conditions. From these, candidate genes were identified which could represent potential leads for targeted modification of the S. rolfsii metabolism for increased scleroglucan yields. Conclusions The results presented in this paper provide for the first time genomic and transcriptomic data about S. rolfsii and demonstrate the power and usefulness of combined transcriptome sequencing and comparative microarray analysis. The data obtained allowed us to predict the biosynthetic pathways of scleroglucan and

  20. Transcriptomic dissection of tongue squamous cell carcinoma

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    Schwartz Joel L

    2008-02-01

    Full Text Available Abstract Background The head and neck/oral squamous cell carcinoma (HNOSCC is a diverse group of cancers, which develop from many different anatomic sites and are associated with different risk factors and genetic characteristics. The oral tongue squamous cell carcinoma (OTSCC is one of the most common types of HNOSCC. It is significantly more aggressive than other forms of HNOSCC, in terms of local invasion and spread. In this study, we aim to identify specific transcriptomic signatures that associated with OTSCC. Results Genome-wide transcriptomic profiles were obtained for 53 primary OTSCCs and 22 matching normal tissues. Genes that exhibit statistically significant differences in expression between OTSCCs and normal were identified. These include up-regulated genes (MMP1, MMP10, MMP3, MMP12, PTHLH, INHBA, LAMC2, IL8, KRT17, COL1A2, IFI6, ISG15, PLAU, GREM1, MMP9, IFI44, CXCL1, and down-regulated genes (KRT4, MAL, CRNN, SCEL, CRISP3, SPINK5, CLCA4, ADH1B, P11, TGM3, RHCG, PPP1R3C, CEACAM7, HPGD, CFD, ABCA8, CLU, CYP3A5. The expressional difference of IL8 and MMP9 were further validated by real-time quantitative RT-PCR and immunohistochemistry. The Gene Ontology analysis suggested a number of altered biological processes in OTSCCs, including enhancements in phosphate transport, collagen catabolism, I-kappaB kinase/NF-kappaB signaling cascade, extracellular matrix organization and biogenesis, chemotaxis, as well as suppressions of superoxide release, hydrogen peroxide metabolism, cellular response to hydrogen peroxide, keratinization, and keratinocyte differentiation in OTSCCs. Conclusion In summary, our study provided a transcriptomic signature for OTSCC that may lead to a diagnosis or screen tool and provide the foundation for further functional validation of these specific candidate genes for OTSCC.

  1. The Characterization of the Phlebotomus papatasi Transcriptome

    Science.gov (United States)

    2013-04-01

    Le. infantum (Li: CAM68214.1), Le. major (Lm: XP_001683430.1), Homo sapiens (Hs: AAD17527.1) and Bo. mori (Bm: NP_001108470.1). The WAG substitution...blood meals in Ph. langeroni (Dillon, El Kordy 1997). Here we have identified 23 unique Ph. papatasi sequences with high identity (BLASTP, əe-50) to...Perkin SAH, Caler E, Bonaldo MF, Soares MB, El -Sayeed N, Aksoy S. Analysis of fat body transcriptome from the adult tsetse fly, Glossina morsitans

  2. The Human Blood Metabolome-Transcriptome Interface

    Science.gov (United States)

    Schramm, Katharina; Adamski, Jerzy; Gieger, Christian; Herder, Christian; Carstensen, Maren; Peters, Annette; Rathmann, Wolfgang; Roden, Michael; Strauch, Konstantin; Suhre, Karsten; Kastenmüller, Gabi; Prokisch, Holger; Theis, Fabian J.

    2015-01-01

    Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the ‘human blood metabolome-transcriptome interface’ (BMTI). Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease. PMID:26086077

  3. The Human Blood Metabolome-Transcriptome Interface.

    Directory of Open Access Journals (Sweden)

    Jörg Bartel

    2015-06-01

    Full Text Available Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system. Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mechanisms on a physiological scale. In this study, we systematically analyzed the relationship between fasting serum metabolomics and whole blood transcriptomics data from 712 individuals of the German KORA F4 cohort. Correlation-based analysis identified 1,109 significant associations between 522 transcripts and 114 metabolites summarized in an integrated network, the 'human blood metabolome-transcriptome interface' (BMTI. Bidirectional causality analysis using Mendelian randomization did not yield any statistically significant causal associations between transcripts and metabolites. A knowledge-based interpretation and integration with a genome-scale human metabolic reconstruction revealed systematic signatures of signaling, transport and metabolic processes, i.e. metabolic reactions mainly belonging to lipid, energy and amino acid metabolism. Moreover, the construction of a network based on functional categories illustrated the cross-talk between the biological layers at a pathway level. Using a transcription factor binding site enrichment analysis, this pathway cross-talk was further confirmed at a regulatory level. Finally, we demonstrated how the constructed networks can be used to gain novel insights into molecular mechanisms associated to intermediate clinical traits. Overall, our results demonstrate the utility of a multi-omics integrative approach to understand the molecular mechanisms underlying both normal physiology and disease.

  4. Comparative Transcriptomics Among Four White Pine Species

    Directory of Open Access Journals (Sweden)

    Ethan A. G. Baker

    2018-05-01

    Full Text Available Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus. The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola, limber pine (Pinus flexilis, whitebark pine (Pinus albicaulis, and sugar pine (Pinus lambertiana was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.

  5. Analysis of a human brain transcriptome map

    Directory of Open Access Journals (Sweden)

    Greene Jonathan R

    2002-04-01

    Full Text Available Abstract Background Genome wide transcriptome maps can provide tools to identify candidate genes that are over-expressed or silenced in certain disease tissue and increase our understanding of the structure and organization of the genome. Expressed Sequence Tags (ESTs from the public dbEST and proprietary Incyte LifeSeq databases were used to derive a transcript map in conjunction with the working draft assembly of the human genome sequence. Results Examination of ESTs derived from brain tissues (excluding brain tumor tissues suggests that these genes are distributed on chromosomes in a non-random fashion. Some regions on the genome are dense with brain-enriched genes while some regions lack brain-enriched genes, suggesting a significant correlation between distribution of genes along the chromosome and tissue type. ESTs from brain tumor tissues have also been mapped to the human genome working draft. We reveal that some regions enriched in brain genes show a significant decrease in gene expression in brain tumors, and, conversely that some regions lacking in brain genes show an increased level of gene expression in brain tumors. Conclusions This report demonstrates a novel approach for tissue specific transcriptome mapping using EST-based quantitative assessment.

  6. Crx broadly modulates the pineal transcriptome

    DEFF Research Database (Denmark)

    Rovsing, Louise; Clokie, Samuel; Bustos, Diego M

    2011-01-01

    Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use of micro......Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use......-type animals; only eight of these were also day/night expressed in the Crx-/- pineal gland. However, in the Crx-/- pineal gland 41 genes exhibited differential night/day expression that was not seen in wild-type animals. These findings indicate that Crx broadly modulates the pineal transcriptome and also...... influences differential night/day gene expression in this tissue. Some effects of Crx deletion on the pineal transcriptome might be mediated by Hoxc4 up-regulation....

  7. TRAM (Transcriptome Mapper: database-driven creation and analysis of transcriptome maps from multiple sources

    Directory of Open Access Journals (Sweden)

    Danieli Gian

    2011-02-01

    Full Text Available Abstract Background Several tools have been developed to perform global gene expression profile data analysis, to search for specific chromosomal regions whose features meet defined criteria as well as to study neighbouring gene expression. However, most of these tools are tailored for a specific use in a particular context (e.g. they are species-specific, or limited to a particular data format and they typically accept only gene lists as input. Results TRAM (Transcriptome Mapper is a new general tool that allows the simple generation and analysis of quantitative transcriptome maps, starting from any source listing gene expression values for a given gene set (e.g. expression microarrays, implemented as a relational database. It includes a parser able to assign univocal and updated gene symbols to gene identifiers from different data sources. Moreover, TRAM is able to perform intra-sample and inter-sample data normalization, including an original variant of quantile normalization (scaled quantile, useful to normalize data from platforms with highly different numbers of investigated genes. When in 'Map' mode, the software generates a quantitative representation of the transcriptome of a sample (or of a pool of samples and identifies if segments of defined lengths are over/under-expressed compared to the desired threshold. When in 'Cluster' mode, the software searches for a set of over/under-expressed consecutive genes. Statistical significance for all results is calculated with respect to genes localized on the same chromosome or to all genome genes. Transcriptome maps, showing differential expression between two sample groups, relative to two different biological conditions, may be easily generated. We present the results of a biological model test, based on a meta-analysis comparison between a sample pool of human CD34+ hematopoietic progenitor cells and a sample pool of megakaryocytic cells. Biologically relevant chromosomal segments and gene

  8. The developmental transcriptome of Drosophila melanogaster

    Energy Technology Data Exchange (ETDEWEB)

    University of Connecticut; Graveley, Brenton R.; Brooks, Angela N.; Carlson, Joseph W.; Duff, Michael O.; Landolin, Jane M.; Yang, Li; Artieri, Carlo G.; van Baren, Marijke J.; Boley, Nathan; Booth, Benjamin W.; Brown, James B.; Cherbas, Lucy; Davis, Carrie A.; Dobin, Alex; Li, Renhua; Lin, Wei; Malone, John H.; Mattiuzzo, Nicolas R.; Miller, David; Sturgill, David; Tuch, Brian B.; Zaleski, Chris; Zhang, Dayu; Blanchette, Marco; Dudoit, Sandrine; Eads, Brian; Green, Richard E.; Hammonds, Ann; Jiang, Lichun; Kapranov, Phil; Langton, Laura; Perrimon, Norbert; Sandler, Jeremy E.; Wan, Kenneth H.; Willingham, Aarron; Zhang, Yu; Zou, Yi; Andrews, Justen; Bicke, Peter J.; Brenner, Steven E.; Brent, Michael R.; Cherbas, Peter; Gingeras, Thomas R.; Hoskins, Roger A.; Kaufman, Thomas C.; Oliver, Brian; Celniker, Susan E.

    2010-12-02

    Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development. Drosophila melanogaster is an important non-mammalian model system that has had a critical role in basic biological discoveries, such as identifying chromosomes as the carriers of genetic information and uncovering the role of genes in development. Because it shares a substantial genic content with humans, Drosophila is increasingly used as a translational model for human development, homeostasis and disease. High-quality maps are needed for all functional genomic elements. Previous studies demonstrated that a rich collection of genes is deployed during the life cycle of the fly. Although expression profiling using microarrays has revealed the expression of, 13,000 annotated genes, it is difficult to map splice junctions and individual base modifications generated by RNA editing using such approaches. Single-base resolution is essential to define precisely the elements that comprise the Drosophila transcriptome. Estimates of the number of transcript isoforms are less accurate than estimates of the number of genes

  9. Sequencing and analysis of the Mediterranean amphioxus (Branchiostoma lanceolatum transcriptome.

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    Silvan Oulion

    Full Text Available BACKGROUND: The basally divergent phylogenetic position of amphioxus (Cephalochordata, as well as its conserved morphology, development and genetics, make it the best proxy for the chordate ancestor. Particularly, studies using the amphioxus model help our understanding of vertebrate evolution and development. Thus, interest for the amphioxus model led to the characterization of both the transcriptome and complete genome sequence of the American species, Branchiostoma floridae. However, recent technical improvements allowing induction of spawning in the laboratory during the breeding season on a daily basis with the Mediterranean species Branchiostoma lanceolatum have encouraged European Evo-Devo researchers to adopt this species as a model even though no genomic or transcriptomic data have been available. To fill this need we used the pyrosequencing method to characterize the B. lanceolatum transcriptome and then compared our results with the published transcriptome of B. floridae. RESULTS: Starting with total RNA from nine different developmental stages of B. lanceolatum, a normalized cDNA library was constructed and sequenced on Roche GS FLX (Titanium mode. Around 1.4 million of reads were produced and assembled into 70,530 contigs (average length of 490 bp. Overall 37% of the assembled sequences were annotated by BlastX and their Gene Ontology terms were determined. These results were then compared to genomic and transcriptomic data of B. floridae to assess similarities and specificities of each species. CONCLUSION: We obtained a high-quality amphioxus (B. lanceolatum reference transcriptome using a high throughput sequencing approach. We found that 83% of the predicted genes in the B. floridae complete genome sequence are also found in the B. lanceolatum transcriptome, while only 41% were found in the B. floridae transcriptome obtained with traditional Sanger based sequencing. Therefore, given the high degree of sequence conservation

  10. Average glandular dose in paired digital mammography and digital breast tomosynthesis acquisitions in a population based screening program: effects of measuring breast density, air kerma and beam quality

    Science.gov (United States)

    Helge Østerås, Bjørn; Skaane, Per; Gullien, Randi; Catrine Trægde Martinsen, Anne

    2018-02-01

    The main purpose was to compare average glandular dose (AGD) for same-compression digital mammography (DM) and digital breast tomosynthesis (DBT) acquisitions in a population based screening program, with and without breast density stratification, as determined by automatically calculated breast density (Quantra™). Secondary, to compare AGD estimates based on measured breast density, air kerma and half value layer (HVL) to DICOM metadata based estimates. AGD was estimated for 3819 women participating in the screening trial. All received craniocaudal and mediolateral oblique views of each breasts with paired DM and DBT acquisitions. Exposure parameters were extracted from DICOM metadata. Air kerma and HVL were measured for all beam qualities used to acquire the mammograms. Volumetric breast density was estimated using Quantra™. AGD was estimated using the Dance model. AGD reported directly from the DICOM metadata was also assessed. Mean AGD was 1.74 and 2.10 mGy for DM and DBT, respectively. Mean DBT/DM AGD ratio was 1.24. For fatty breasts: mean AGD was 1.74 and 2.27 mGy for DM and DBT, respectively. For dense breasts: mean AGD was 1.73 and 1.79 mGy, for DM and DBT, respectively. For breasts of similar thickness, dense breasts had higher AGD for DM and similar AGD for DBT. The DBT/DM dose ratio was substantially lower for dense compared to fatty breasts (1.08 versus 1.33). The average c-factor was 1.16. Using previously published polynomials to estimate glandularity from thickness underestimated the c-factor by 5.9% on average. Mean AGD error between estimates based on measurements (air kerma and HVL) versus DICOM header data was 3.8%, but for one mammography unit as high as 7.9%. Mean error of using the AGD value reported in the DICOM header was 10.7 and 13.3%, respectively. Thus, measurement of breast density, radiation dose and beam quality can substantially affect AGD estimates.

  11. Terpene synthases from Cannabis sativa.

    Directory of Open Access Journals (Sweden)

    Judith K Booth

    Full Text Available Cannabis (Cannabis sativa plants produce and accumulate a terpene-rich resin in glandular trichomes, which are abundant on the surface of the female inflorescence. Bouquets of different monoterpenes and sesquiterpenes are important components of cannabis resin as they define some of the unique organoleptic properties and may also influence medicinal qualities of different cannabis strains and varieties. Transcriptome analysis of trichomes of the cannabis hemp variety 'Finola' revealed sequences of all stages of terpene biosynthesis. Nine cannabis terpene synthases (CsTPS were identified in subfamilies TPS-a and TPS-b. Functional characterization identified mono- and sesqui-TPS, whose products collectively comprise most of the terpenes of 'Finola' resin, including major compounds such as β-myrcene, (E-β-ocimene, (--limonene, (+-α-pinene, β-caryophyllene, and α-humulene. Transcripts associated with terpene biosynthesis are highly expressed in trichomes compared to non-resin producing tissues. Knowledge of the CsTPS gene family may offer opportunities for selection and improvement of terpene profiles of interest in different cannabis strains and varieties.

  12. Terpene synthases from Cannabis sativa.

    Science.gov (United States)

    Booth, Judith K; Page, Jonathan E; Bohlmann, Jörg

    2017-01-01

    Cannabis (Cannabis sativa) plants produce and accumulate a terpene-rich resin in glandular trichomes, which are abundant on the surface of the female inflorescence. Bouquets of different monoterpenes and sesquiterpenes are important components of cannabis resin as they define some of the unique organoleptic properties and may also influence medicinal qualities of different cannabis strains and varieties. Transcriptome analysis of trichomes of the cannabis hemp variety 'Finola' revealed sequences of all stages of terpene biosynthesis. Nine cannabis terpene synthases (CsTPS) were identified in subfamilies TPS-a and TPS-b. Functional characterization identified mono- and sesqui-TPS, whose products collectively comprise most of the terpenes of 'Finola' resin, including major compounds such as β-myrcene, (E)-β-ocimene, (-)-limonene, (+)-α-pinene, β-caryophyllene, and α-humulene. Transcripts associated with terpene biosynthesis are highly expressed in trichomes compared to non-resin producing tissues. Knowledge of the CsTPS gene family may offer opportunities for selection and improvement of terpene profiles of interest in different cannabis strains and varieties.

  13. Relative Composition of Fibrous Connective and Fatty/Glandular Tissue in Connective Tissue Grafts Depends on the Harvesting Technique but not the Donor Site of the Hard Palate.

    Science.gov (United States)

    Bertl, Kristina; Pifl, Markus; Hirtler, Lena; Rendl, Barbara; Nürnberger, Sylvia; Stavropoulos, Andreas; Ulm, Christian

    2015-12-01

    Whether the composition of palatal connective tissue grafts (CTGs) varies depending on donor site or harvesting technique in terms of relative amounts of fibrous connective tissue (CT) and fatty/glandular tissue (FGT) is currently unknown and is histologically assessed in the present study. In 10 fresh human cadavers, tissue samples were harvested in the anterior and posterior palate and in areas close to (marginal) and distant from (apical) the mucosal margin. Mucosal thickness, lamina propria thickness (defined as the extent of subepithelial portion of the biopsy containing ≤25% or ≤50% FGT), and proportions of CT and FGT were semi-automatically estimated for the entire mucosa and for CTGs virtually harvested by split-flap (SF) preparation minimum 1 mm deep or after deepithelialization (DE). Palatal mucosal thickness, ranging from 2.35 to 6.89 mm, and histologic composition showed high interindividual variability. Lamina propria thickness (P >0.21) and proportions of CT (P = 0.48) and FGT (P = 0.15) did not differ significantly among the donor sites (anterior, posterior, marginal, apical). However, thicker palatal tissue was associated with higher FGT content (P tissue composition in the hard palate, DE-harvested CTG contains much larger amounts of CT and much lower amounts of FGT than SF-harvested CTG, irrespective of the harvesting site.

  14. A Survey On Mean Glandular Dose From Full-Field Digital Mammography Systems, Operate Using Mo/ Mo And W/Rh Target/ Filter Combinations

    International Nuclear Information System (INIS)

    Noriah Jamal; Siti Selina Abdul Hamid; Humairah Samad Cheung; Siti Kamariah Che Mohamed; Ellyda Muhammed Nordin; Radhiana Hassan; Rehir Dahalan

    2013-01-01

    We had conducted a survey on Mean Glandular Dose (MGD) from Full-Field Digital Mammography systems (FFDM) operate using Molybdenum/ Molybdenum (Mo/ Mo) and Tungsten/ Rhodium (W/ Rh) target/ filter combinations. A survey was carried out at two randomly selected mammography centres in Malaysia, namely National Cancer Society and International Islamic University of Malaysia. The first centre operates using a W/ Rh, while the second centre operates using an Mo/ Mo target/ filter combinations. On the basis of recorded information, data on mammographic views, MGD, age and Compressed Breast Thickness (CBT) were recorded for 100 patients, for each mammographic centre respectively. The MGD data were analyzed for variation with age group, with 5 years increment. The MGD data were also analyzed for variation with CBT, with 5 mm increment. We found that for both CC and MLO views, FFDM systems operated using Mo/ Mo and W/ Rh target/ filter combinations present the same trend on MGD. The average MGD decreases as age increases. While average MGD increases with the increasing of CBT. However, FFDM system operates using Mo/ Mo gives higher MGD as compared with FFDM system operates using W/ Rh. (author)

  15. Expression of podoplanin and TGF-beta in glandular odontogenic cyst and its comparison with developmental and inflammatory odontogenic cystic lesions.

    Science.gov (United States)

    Alaeddini, Mojgan; Eshghyar, Nosratollah; Etemad-Moghadam, Shahroo

    2017-01-01

    The number of studies investigating the immunohistochemical characteristics of glandular odontogenic cysts (GOCs) is limited, due to its rarity. TGF-beta has been suggested to induce podoplanin expression in some lesions. We aimed to evaluate and compare podoplanin and TGF-beta expression in GOC and other odontogenic cystic lesions. A total of 43 samples including five GOCs, 10 dentigerous cysts (DCs), eight unicystic ameloblastoma (UAs), and 20 radicular cysts (RCs) were selected and subjected to immunohistochemical staining using monoclonal antibodies against podoplanin and TGF-beta. Kruskal-Wallis test and Mann-Whitney U-test were used for statistical analysis along with Bonferroni for adjusting P-values (P < 0.05). Podoplanin immunoreactivity was observed in 80%, 70%, and 100% of DCs, RCs, and UAs, respectively, while none of the GOCs were positive for this marker (P = 0.004). Significant differences were only found in the GOC specimens. TGF-beta positivity occurred in the capsule and epithelium of all GOCs and DCs, while RCs and UAs demonstrated different expression percentages in the capsular and epithelial tissues. Epithelial TGF-beta showed significant differences among the studied lesions (P = 0.007) with the main difference found between DCs with RCs and DCs with UAs. Lack of podoplanin expression might be involved in the characteristic histologic and behavioral features of GOC, which seems to be unrelated to TGF-beta expression. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Development of an Expert System as a Diagnostic Support of Cervical Cancer in Atypical Glandular Cells, Based on Fuzzy Logics and Image Interpretation

    Directory of Open Access Journals (Sweden)

    Karem R. Domínguez Hernández

    2013-01-01

    Full Text Available Cervical cancer is the second largest cause of death among women worldwide. Nowadays, this disease is preventable and curable at low cost and low risk when an accurate diagnosis is done in due time, since it is the neoplasm with the highest prevention potential. This work describes the development of an expert system able to provide a diagnosis to cervical neoplasia (CN precursor injuries through the integration of fuzzy logics and image interpretation techniques. The key contribution of this research focuses on atypical cases, specifically on atypical glandular cells (AGC. The expert system consists of 3 phases: (1 risk diagnosis which consists of the interpretation of a patient’s clinical background and the risks for contracting CN according to specialists; (2 cytology images detection which consists of image interpretation (IM and the Bethesda system for cytology interpretation, and (3 determination of cancer precursor injuries which consists of in retrieving the information from the prior phases and integrating the expert system by means of a fuzzy logics (FL model. During the validation stage of the system, 21 already diagnosed cases were tested with a positive correlation in which 100% effectiveness was obtained. The main contribution of this work relies on the reduction of false positives and false negatives by providing a more accurate diagnosis for CN.

  17. A comparison of mean glandular dose diagnostic reference levels within the all-digital irish national breast screening programme and the Irish symptomatic breast services

    International Nuclear Information System (INIS)

    O'Leary, D.; Rainford, L.

    2013-01-01

    Data on image quality, compression and radiation dose were collected from symptomatic breast units within the Republic of Ireland. Quantitative and qualitative data were analysed using SPSS. Recommendations of mean glandular dose (MGD) diagnostic reference levels were made at various levels for film-screen and full field digital mammography units to match levels published worldwide. MGDs received by symptomatic breast patients within Ireland are higher than those received in the all-digital Irish Breast Screening service; 55-65 mm breast: 1.75 mGy (screening) vs. 2.4 mGy (symptomatic) at the 95. percentile; various reasons are proposed for the differences. MGDs achieved in the screening service may be lower because of the exacting requirements for radiographer training, characteristics of the patients and equipment quality assurance levels. More precise imaging guidelines, standards and training of symptomatic radiographers performing mammography are suggested to remediate MGDs delivered to the breasts of Irish women attending the symptomatic breast services. (authors)

  18. Peroxidase gene discovery from the horseradish transcriptome.

    Science.gov (United States)

    Näätsaari, Laura; Krainer, Florian W; Schubert, Michael; Glieder, Anton; Thallinger, Gerhard G

    2014-03-24

    Horseradish peroxidases (HRPs) from Armoracia rusticana have long been utilized as reporters in various diagnostic assays and histochemical stainings. Regardless of their increasing importance in the field of life sciences and suggested uses in medical applications, chemical synthesis and other industrial applications, the HRP isoenzymes, their substrate specificities and enzymatic properties are poorly characterized. Due to lacking sequence information of natural isoenzymes and the low levels of HRP expression in heterologous hosts, commercially available HRP is still extracted as a mixture of isoenzymes from the roots of A. rusticana. In this study, a normalized, size-selected A. rusticana transcriptome library was sequenced using 454 Titanium technology. The resulting reads were assembled into 14871 isotigs with an average length of 1133 bp. Sequence databases, ORF finding and ORF characterization were utilized to identify peroxidase genes from the 14871 isotigs generated by de novo assembly. The sequences were manually reviewed and verified with Sanger sequencing of PCR amplified genomic fragments, resulting in the discovery of 28 secretory peroxidases, 23 of them previously unknown. A total of 22 isoenzymes including allelic variants were successfully expressed in Pichia pastoris and showed peroxidase activity with at least one of the substrates tested, thus enabling their development into commercial pure isoenzymes. This study demonstrates that transcriptome sequencing combined with sequence motif search is a powerful concept for the discovery and quick supply of new enzymes and isoenzymes from any plant or other eukaryotic organisms. Identification and manual verification of the sequences of 28 HRP isoenzymes do not only contribute a set of peroxidases for industrial, biological and biomedical applications, but also provide valuable information on the reliability of the approach in identifying and characterizing a large group of isoenzymes.

  19. The human airway epithelial basal cell transcriptome.

    Directory of Open Access Journals (Sweden)

    Neil R Hackett

    2011-05-01

    Full Text Available The human airway epithelium consists of 4 major cell types: ciliated, secretory, columnar and basal cells. During natural turnover and in response to injury, the airway basal cells function as stem/progenitor cells for the other airway cell types. The objective of this study is to better understand human airway epithelial basal cell biology by defining the gene expression signature of this cell population.Bronchial brushing was used to obtain airway epithelium from healthy nonsmokers. Microarrays were used to assess the transcriptome of basal cells purified from the airway epithelium in comparison to the transcriptome of the differentiated airway epithelium. This analysis identified the "human airway basal cell signature" as 1,161 unique genes with >5-fold higher expression level in basal cells compared to differentiated epithelium. The basal cell signature was suppressed when the basal cells differentiated into a ciliated airway epithelium in vitro. The basal cell signature displayed overlap with genes expressed in basal-like cells from other human tissues and with that of murine airway basal cells. Consistent with self-modulation as well as signaling to other airway cell types, the human airway basal cell signature was characterized by genes encoding extracellular matrix components, growth factors and growth factor receptors, including genes related to the EGF and VEGF pathways. Interestingly, while the basal cell signature overlaps that of basal-like cells of other organs, the human airway basal cell signature has features not previously associated with this cell type, including a unique pattern of genes encoding extracellular matrix components, G protein-coupled receptors, neuroactive ligands and receptors, and ion channels.The human airway epithelial basal cell signature identified in the present study provides novel insights into the molecular phenotype and biology of the stem/progenitor cells of the human airway epithelium.

  20. A transcriptome anatomy of human colorectal cancers

    International Nuclear Information System (INIS)

    Lü, Bingjian; Xu, Jing; Lai, Maode; Zhang, Hao; Chen, Jian

    2006-01-01

    Accumulating databases in human genome research have enabled integrated genome-wide study on complicated diseases such as cancers. A practical approach is to mine a global transcriptome profile of disease from public database. New concepts of these diseases might emerge by landscaping this profile. In this study, we clustered human colorectal normal mucosa (N), inflammatory bowel disease (IBD), adenoma (A) and cancer (T) related expression sequence tags (EST) into UniGenes via an in-house GetUni software package and analyzed the transcriptome overview of these libraries by GOTree Machine (GOTM). Additionally, we downloaded UniGene based cDNA libraries of colon and analyzed them by Xprofiler to cross validate the efficiency of GetUni. Semi-quantitative RT-PCR was used to validate the expression of β-catenin and. 7 novel genes in colorectal cancers. The efficiency of GetUni was successfully validated by Xprofiler and RT-PCR. Genes in library N, IBD and A were all found in library T. A total of 14,879 genes were identified with 2,355 of them having at least 2 transcripts. Differences in gene enrichment among these libraries were statistically significant in 50 signal transduction pathways and Pfam protein domains by GOTM analysis P < 0.01 Hypergeometric Test). Genes in two metabolic pathways, ribosome and glycolysis, were more enriched in the expression profiles of A and IBD than in N and T. Seven transmembrane receptor superfamily genes were typically abundant in cancers. Colorectal cancers are genetically heterogeneous. Transcription variants are common in them. Aberrations of ribosome and glycolysis pathway might be early indicators of precursor lesions in colon cancers. The electronic gene expression profile could be used to highlight the integral molecular events in colorectal cancers

  1. Transcriptome sequences resolve deep relationships of the grape family.

    Science.gov (United States)

    Wen, Jun; Xiong, Zhiqiang; Nie, Ze-Long; Mao, Likai; Zhu, Yabing; Kan, Xian-Zhao; Ickert-Bond, Stefanie M; Gerrath, Jean; Zimmer, Elizabeth A; Fang, Xiao-Dong

    2013-01-01

    Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

  2. Transcriptome sequences resolve deep relationships of the grape family.

    Directory of Open Access Journals (Sweden)

    Jun Wen

    Full Text Available Previous phylogenetic studies of the grape family (Vitaceae yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated.

  3. Illumina–based de novo transcriptome sequencing and analysis of ...

    Indian Academy of Sciences (India)

    Administrator

    2017-10-25

    Oct 25, 2017 ... (Shanghai, China) following manufacturer's protocols (Illumina, San .... suggests that pathways involved in musk production are expressed at a ..... Strickler S. R., Aureliano B. and Mueller L. A. 2012 Designing a transcriptome.

  4. Alternative Approach to Traumatic Stensen’s Duct Injuries Accompanied by Glandular Involvement: Botulinum Toxin Injection to the Gland in Conjunction with Microsurgical Repair of the Duct in an Acute Setting

    OpenAIRE

    Mert Çalış; Zeynep Öz; Hakan Uzun; Burçe Özgen; Alp Çetin3; Ali Emre Aksu

    2017-01-01

    Objective: The aim of this study was to evaluate the long-term results of a simultaneous application of botulinum toxin to the parotid gland in conjunction with the microsurgical repair of the duct in an acute setting and to encourage using botulinum toxin as a first-line option to prevent future complications associated with glandular involvement. Material and Methods: Three patients who were referred to the Plastic Surgery Clinic by the emergency room of the Hacettepe University Hospita...

  5. Genome Annotation and Transcriptomics of Oil-Producing Algae

    Science.gov (United States)

    2015-03-16

    AFRL-OSR-VA-TR-2015-0103 GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE Sabeeha Merchant UNIVERSITY OF CALIFORNIA LOS ANGELES Final...2010 To 12-31-2014 4. TITLE AND SUBTITLE GENOME ANNOTATION AND TRANSCRIPTOMICS OF OIL-PRODUCING ALGAE 5a. CONTRACT NUMBER FA9550-10-1-0095 5b...NOTES 14. ABSTRACT Most algae accumulate triacylglycerols (TAGs) when they are starved for essential nutrients like N, S, P (or Si in the case of some

  6. ALTERATIONS IN THE DEVELOPING TESTIS TRANSCRIPTOME FOLLOWING EMBRYONIC VINCLOZOLIN EXPOSURE

    OpenAIRE

    Clement, Tracy M.; Savenkova, Marina I.; Settles, Matthew; Anway, Matthew D.; Skinner, Michael K.

    2010-01-01

    The current study investigates the direct effects of in utero vinclozolin exposure on the developing F1 generation rat testis transcriptome. Previous studies have demonstrated that exposure to vinclozolin during embryonic gonadal sex determination induces epigenetic modifications of the germ line and transgenerational adult onset disease states. Microarray analyses were performed to compare control and vinclozolin treated testis transcriptomes at embryonic day 13, 14 and 16. A total of 576 di...

  7. Correlação dos aspectos laparoscópicos com as alterações histológicas glandulares das lesões endometrióticas peritoneais Correlation between laparoscopic aspects and glandular hystological findings of peritoneal endometriotic lesions

    Directory of Open Access Journals (Sweden)

    Francesco Antonio Viscomi

    2004-09-01

    Full Text Available OBJETIVOS: Correlacionar os aspectos laparoscópicos com os achados histológicos na endometriose peritoneal para facilitar a compreensão da teoria evolutiva da endometriose. MÉTODOS: Foram selecionadas aleatoriamente para o presente estudo prospectivo 67 pacientes submetidas a laparoscopia, com diagnóstico de endometriose peritoneal. A avaliação laparoscópica foi baseada no aspecto visual do implante suspeito de endometriose peritoneal, submetido a estudo anatomopatológico. De acordo com o aspecto laparoscópico, as lesões foram agrupadas em: grupo V - vermelhas, grupo N - negras, grupo B - brancas. A avaliação histológica foi realizada observando-se as características funcionais do epitélio glandular, a presença de debris intraluminais, o número de mitoses e a relação estroma/glândula. RESULTADOS: As características funcionais do epitélio glandular mostraram associação estatisticamente significante entre os grupos, sendo o epitélio com carcterística secretora encontrado em 68,4% das lesões do grupo V, 15,8% do grupo N e B, enquanto que o epitélio incaracterístico foi encontrado em 19,4% das lesões vermelhas, 38,7% das lesões negras e 41,9% das brancas e o epitélio proliferativo foi observado em 50% das pacientes do grupo B e em 25% dos grupos V e N (p=0,011. Em relação à presença de debris intraluminais, também houve diferença significante entre os grupos, estando presentes em 58,4% das lesões negras, 33,3% das lesões brancas e 8,3% das lesões vermelhas (p=0,016. Quanto ao número de mitoses, não houve diferença significante nos três grupos de estudo (p=0,428. O mesmo foi observado na relação estroma/glândula, não havendo diferença significante nos grupos de estudo (p=0,159. CONCLUSÃO: A associação entre atividade funcional nas lesões vermelhas e baixa atividade funcional nas lesões negras e brancas, bem como a presença de debris intraluminais nos diferentes grupos, reforçam a teoria

  8. Principle considerations for the use of transcriptomics in doping research.

    Science.gov (United States)

    Neuberger, Elmo W I; Moser, Dirk A; Simon, Perikles

    2011-10-01

    Over the course of the past decade, technical progress has enabled scientists to investigate genome-wide RNA expression using microarray platforms. This transcriptomic approach represents a promising tool for the discovery of basic gene expression patterns and for identification of cellular signalling pathways under various conditions. Since doping substances have been shown to influence mRNA expression, it has been suggested that these changes can be detected by screening the blood transcriptome. In this review, we critically discuss the potential but also the pitfalls of this application as a tool in doping research. Transcriptomic approaches were considered to potentially provide researchers with a unique gene expression signature or with a specific biomarker for various physiological and pathophysiological conditions. Since transcriptomic approaches are considerably prone to biological and technical confounding factors that act on study subjects or samples, very strict guidelines for the use of transcriptomics in human study subjects have been developed. Typical field conditions associated with doping controls limit the feasibility of following these strict guidelines as there are too many variables counteracting a standardized procedure. After almost a decade of research using transcriptomic tools, it still remains a matter of future technological progress to identify the ultimate biomarker using technologies and/or methodologies that are sufficiently robust against typical biological and technical bias and that are valid in a court of law. Copyright © 2011 John Wiley & Sons, Ltd.

  9. PIVOT: platform for interactive analysis and visualization of transcriptomics data.

    Science.gov (United States)

    Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

    2018-01-05

    Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

  10. Sequencing and characterization of the guppy (Poecilia reticulata transcriptome

    Directory of Open Access Journals (Sweden)

    Rodd F Helen

    2011-04-01

    Full Text Available Abstract Background Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history. Results We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs, and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA-sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in

  11. Establishment of a long-term three-dimensional primary culture of mouse glandular stomach epithelial cells within the stem cell niche

    International Nuclear Information System (INIS)

    Katano, Takahito; Ootani, Akifumi; Mizoshita, Tsutomu; Tanida, Satoshi; Tsukamoto, Hironobu; Ozeki, Keiji; Ebi, Masahide; Mori, Yoshinori; Kataoka, Hiromi; Kamiya, Takeshi; Toda, Shuji; Joh, Takashi

    2013-01-01

    Highlights: ► We established a 3D culture system to allow long-term culture of stomach cells. ► In this culture system, gastric epithelial cells grew for about 3 months. ► The cultured cells differentiated into multi-units of the stomach. ► This culture method should be useful for elucidating the cause of gastric diseases. -- Abstract: Compared to the small intestine and colon, little is known about stem cells in the stomach because of a lack of specific stem cell markers and an in vitro system that allows long-term culture. Here we describe a long-term three-dimensional (3D) primary gastric culture system within the stem cell niche. Glandular stomach cells from neonatal mice cultured in collagen gel yielded expanding sphere-like structures for 3 months. The wall of the gastrospheres consisted of a highly polarized epithelial monolayer with an outer lining of myofibroblasts. The epithelial cells showed a tall columnar cell shape, basal round nuclei, and mucus-filled cytoplasm as well as expression of MUC5AC, indicating differentiation into gastric surface mucous cells. These cells demonstrated the features of fully differentiated gastric surface mucous cells such as microvilli, junctional complexes, and glycogen and secretory granules. Fewer than 1% of cultured epithelial cells differentiated into enteroendocrine cells. Active proliferation of the epithelial cells and many apoptotic cells in the inner lumen revealed the rapid cell turnover in gastrospheres in vitro. This method enables us to investigate the role of signaling between cell–cell and epithelial–mesenchymal interactions in an environment that is extremely similar to the in vivo environment

  12. Establishment of a long-term three-dimensional primary culture of mouse glandular stomach epithelial cells within the stem cell niche

    Energy Technology Data Exchange (ETDEWEB)

    Katano, Takahito [Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Ootani, Akifumi [Department of Gastroenterology and GI Endoscopy Center, Shin-Kokura Hospital, Federation of National Public Service Personnel Mutual Aid Associations, 1-3-1 Kanada, Kokurakita-ku, Kitakyushu 803-0816 (Japan); Department of Internal Medicine, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501 (Japan); Mizoshita, Tsutomu, E-mail: tmizoshi@med.nagoya-cu.ac.jp [Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Tanida, Satoshi; Tsukamoto, Hironobu; Ozeki, Keiji; Ebi, Masahide; Mori, Yoshinori; Kataoka, Hiromi; Kamiya, Takeshi [Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan); Toda, Shuji [Department of Pathology and Microbiology, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501 (Japan); Joh, Takashi [Department of Gastroenterology and Metabolism, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601 (Japan)

    2013-03-22

    Highlights: ► We established a 3D culture system to allow long-term culture of stomach cells. ► In this culture system, gastric epithelial cells grew for about 3 months. ► The cultured cells differentiated into multi-units of the stomach. ► This culture method should be useful for elucidating the cause of gastric diseases. -- Abstract: Compared to the small intestine and colon, little is known about stem cells in the stomach because of a lack of specific stem cell markers and an in vitro system that allows long-term culture. Here we describe a long-term three-dimensional (3D) primary gastric culture system within the stem cell niche. Glandular stomach cells from neonatal mice cultured in collagen gel yielded expanding sphere-like structures for 3 months. The wall of the gastrospheres consisted of a highly polarized epithelial monolayer with an outer lining of myofibroblasts. The epithelial cells showed a tall columnar cell shape, basal round nuclei, and mucus-filled cytoplasm as well as expression of MUC5AC, indicating differentiation into gastric surface mucous cells. These cells demonstrated the features of fully differentiated gastric surface mucous cells such as microvilli, junctional complexes, and glycogen and secretory granules. Fewer than 1% of cultured epithelial cells differentiated into enteroendocrine cells. Active proliferation of the epithelial cells and many apoptotic cells in the inner lumen revealed the rapid cell turnover in gastrospheres in vitro. This method enables us to investigate the role of signaling between cell–cell and epithelial–mesenchymal interactions in an environment that is extremely similar to the in vivo environment.

  13. Leaf morphology and anatomy of varieties of Turnera diffusa var ...

    African Journals Online (AJOL)

    Results: The leaves of diffusa variety were twice as large as those of the aphrodisiaca variety, whereas papillose glandular trichomes were observed with greater density in the aphrodisiaca variety than those on diffusa leaves where unicellular trichomes were the ones observed in greater density. The leaves of both ...

  14. Network Analysis of Rodent Transcriptomes in Spaceflight

    Science.gov (United States)

    Ramachandran, Maya; Fogle, Homer; Costes, Sylvain

    2017-01-01

    Network analysis methods leverage prior knowledge of cellular systems and the statistical and conceptual relationships between analyte measurements to determine gene connectivity. Correlation and conditional metrics are used to infer a network topology and provide a systems-level context for cellular responses. Integration across multiple experimental conditions and omics domains can reveal the regulatory mechanisms that underlie gene expression. GeneLab has assembled rich multi-omic (transcriptomics, proteomics, epigenomics, and epitranscriptomics) datasets for multiple murine tissues from the Rodent Research 1 (RR-1) experiment. RR-1 assesses the impact of 37 days of spaceflight on gene expression across a variety of tissue types, such as adrenal glands, quadriceps, gastrocnemius, tibalius anterior, extensor digitorum longus, soleus, eye, and kidney. Network analysis is particularly useful for RR-1 -omics datasets because it reinforces subtle relationships that may be overlooked in isolated analyses and subdues confounding factors. Our objective is to use network analysis to determine potential target nodes for therapeutic intervention and identify similarities with existing disease models. Multiple network algorithms are used for a higher confidence consensus.

  15. Transcriptomic analysis of Salmonella desiccation resistance.

    Science.gov (United States)

    Li, Haiping; Bhaskara, Anuhya; Megalis, Christina; Tortorello, Mary Lou

    2012-12-01

    The survival of Salmonella in low moisture foods and processing environments remains a great challenge for the food industry and public health. To explore the mechanisms of Salmonella desiccation resistance, we studied the transcriptomic responses in Salmonella Tennessee (Tennessee), using Salmonella Typhimurium LT2 (LT2), a strain weakly resistant to desiccation, as a reference strain. In response to 2 h of air-drying at 11% equilibrated relative humidity, approximately one-fourth of the open reading frames (ORFs) in the Tennessee genome and one-fifth in LT2 were differentially expressed (>2-fold). Among all differentially expressed functional groups (>5-fold) in both strains, the expression fold change associated with fatty acid metabolism was the highest, and constituted 51% and 35% of the total expression fold change in Tennessee and LT2, respectively. Tennessee showed greater changes in expression of genes associated with stress response and envelope modification than LT2, while showing lesser changes in protein biosynthesis expression. Expression of flagella genes was significantly more inhibited in stationary phase cells of Tennessee than LT2 both before and after desiccation. The accumulation of the osmolyte trehalose was significantly induced by desiccation in Tennessee, but no increase was detectable in LT2, which is consistent with the expression patterns of the entire trehalose biosynthesis and degradation pathways in both strains. Results from this study present a global view of the dynamic desiccation responses in Salmonella, which will guide future research efforts to control Salmonella in low moisture environments.

  16. Transcriptome States Reflect Imaging of Aging States.

    Science.gov (United States)

    Eckley, D Mark; Coletta, Christopher E; Orlov, Nikita V; Wilson, Mark A; Iser, Wendy; Bastian, Paul; Lehrmann, Elin; Zhang, Yonqing; Becker, Kevin G; Goldberg, Ilya G

    2018-06-14

    In this study, we describe a morphological biomarker that detects multiple discrete subpopulations (or "age-states") at several chronological ages in a population of nematodes (Caenorhabditis elegans). We determined the frequencies of three healthy adult states and the timing of the transitions between them across the lifespan. We used short-lived and long-lived strains to confirm the general applicability of the state classifier and to monitor state progression. This exploration revealed healthy and unhealthy states, the former being favored in long-lived strains and the latter showing delayed onset. Short-lived strains rapidly transitioned through the putative healthy state. We previously found that age-matched animals in different age-states have distinct transcriptome profiles. We isolated animals at the beginning and end of each identified state and performed microarray analysis (principal component analysis, relative sample to sample distance measurements, and gene set enrichment analysis). In some comparisons, chronologically identical individuals were farther apart than morphologically identical individuals isolated on different days. The age-state biomarker allowed assessment of aging in a novel manner, complementary to chronological age progression. We found hsp70 and some small heat shock protein genes are expressed later in adulthood, consistent with the proteostasis collapse model.

  17. A transcriptome approach to ecdysozoan phylogeny.

    Science.gov (United States)

    Borner, Janus; Rehm, Peter; Schill, Ralph O; Ebersberger, Ingo; Burmester, Thorsten

    2014-11-01

    The monophyly of Ecdysozoa, which comprise molting phyla, has received strong support from several lines of evidence. However, the internal relationships of Ecdysozoa are still contended. We generated expressed sequence tags from a priapulid (penis worm), a kinorhynch (mud dragon), a tardigrade (water bear) and five chelicerate taxa by 454 transcriptome sequencing. A multigene alignment was assembled from 63 taxa, which comprised after matrix optimization 24,249 amino acid positions with high data density (2.6% gaps, 19.1% missing data). Phylogenetic analyses employing various models support the monophyly of Ecdysozoa. A clade combining Priapulida and Kinorhyncha (i.e. Scalidophora) was recovered as the earliest branch among Ecdysozoa. We conclude that Cycloneuralia, a taxon erected to combine Priapulida, Kinorhyncha and Nematoda (and others), are paraphyletic. Rather Arthropoda (including Onychophora) are allied with Nematoda and Tardigrada. Within Arthropoda, we found strong support for most clades, including monophyletic Mandibulata and Pancrustacea. The phylogeny within the Euchelicerata remained largely unresolved. There is conflicting evidence on the position of tardigrades: While Bayesian and maximum likelihood analyses of only slowly evolving genes recovered Tardigrada as a sister group to Arthropoda, analyses of the full data set, and of subsets containing genes evolving at fast and intermediate rates identified a clade of Tardigrada and Nematoda. Notably, the latter topology is also supported by the analyses of indel patterns. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Gingival tissue transcriptomes in experimental gingivitis

    Science.gov (United States)

    Jönsson, Daniel; Ramberg, Per; Demmer, Ryan T.; Kebschull, Moritz; Dahlén, Gunnar; Papapanou, Panos N.

    2012-01-01

    Aims We investigated the sequential gene expression in the gingiva during the induction and resolution of experimental gingivitis. Methods Twenty periodontally and systemically healthy non-smoking volunteers participated in a 3-week experimental gingivitis protocol, followed by debridement and 2-week regular plaque control. We recorded clinical indices and harvested gingival tissue samples from 4 interproximal palatal sites in half of the participants at baseline, Day 7, 14 and 21 (‘induction phase’), and at day 21, 25, 30 and 35 in the other half (‘resolution phase’). RNA was extracted, amplified, reversed transcribed, amplified, labeled and hybridized with Affymetrix Human Genome U133Plus2.0 microarrays. Paired t-tests compared gene expression changes between consecutive time points. Gene ontology analyses summarized the expression patterns into biologically relevant categories. Results The median gingival index was 0 at baseline, 2 at Day 21 and 1 at Day 35. Differential gene regulation peaked during the third week of induction and the first four days of resolution. Leukocyte transmigration, cell adhesion and antigen processing/presentation were the top differentially regulated pathways. Conclusions Transcriptomic studies enhance our understanding of the pathobiology of the reversible inflammatory gingival lesion and provide a detailed account of the dynamic tissue responses during induction and resolution of experimental gingivitis. PMID:21501207

  19. Transcriptome analysis of zebrafish embryogenesis using microarrays.

    Directory of Open Access Journals (Sweden)

    Sinnakaruppan Mathavan

    2005-08-01

    Full Text Available Zebrafish (Danio rerio is a well-recognized model for the study of vertebrate developmental genetics, yet at the same time little is known about the transcriptional events that underlie zebrafish embryogenesis. Here we have employed microarray analysis to study the temporal activity of developmentally regulated genes during zebrafish embryogenesis. Transcriptome analysis at 12 different embryonic time points covering five different developmental stages (maternal, blastula, gastrula, segmentation, and pharyngula revealed a highly dynamic transcriptional profile. Hierarchical clustering, stage-specific clustering, and algorithms to detect onset and peak of gene expression revealed clearly demarcated transcript clusters with maximum gene activity at distinct developmental stages as well as co-regulated expression of gene groups involved in dedicated functions such as organogenesis. Our study also revealed a previously unidentified cohort of genes that are transcribed prior to the mid-blastula transition, a time point earlier than when the zygotic genome was traditionally thought to become active. Here we provide, for the first time to our knowledge, a comprehensive list of developmentally regulated zebrafish genes and their expression profiles during embryogenesis, including novel information on the temporal expression of several thousand previously uncharacterized genes. The expression data generated from this study are accessible to all interested scientists from our institute resource database (http://giscompute.gis.a-star.edu.sg/~govind/zebrafish/data_download.html.

  20. EFEITO DE TRICOMAS, ALELOQUÍMICOS E NUTRIENTES NA RESISTÊNCIA DE LYCOPERSICON HIRSUTUM À TRAÇA-DO-TOMATEIRO EFFECT OF TRICHOMES, ALELLOCHEMICALS AND MINERALS ON THE RESISTANCE OF LYCOPERSICON HIRSUTUM TO TOMATO LEAF MINER

    Directory of Open Access Journals (Sweden)

    GERMANO LEÃO DEMOLIN LEITE

    1999-11-01

    Full Text Available Estudos foram conduzidos com o objetivo de verificar o efeito de tricomas, aleloquímicos e nutrientes nas folhas de partes do dossel das plantas na resistência de Lycopersicon hirsutum à traça- do-tomateiro, Tuta absoluta (Lepidoptera: Gelechiidae. Foram quantificados os teores de 2-tridecanona (2-TD, 2-undecanona (2-UD, N, P, K, Ca e Mg, densidade e tipos de tricomas e tamanho das folhas nos terços apical, mediano e basal do dossel de plantas de L. hirsutum e de L. esculentum e estudaram- se os efeitos destes fatores sobre características biológicas de T. absoluta. Observou-se elevação no teor de 2-TD da base para o ápice do dossel. Não se detectou diferença significativa quanto ao número de ovos de T. absoluta ao longo do dossel de L. hirsutum, constatando-se em L. esculentum maior oviposição nos terços apical e mediano do que no basal. As folhas do terço apical de L. hirsutum apresentaram maior efeito deletério sobre as larvas de traça.The objective of this work was to study the effect of trichomes, alellochemicals and minerals in the leaves of different canopy heights on the resistance of Lycopersicon hirsutum to tomato leaf miner, Tuta absoluta (Lepidoptera: Gelechiidae. Effects of 2-tridecanone (2-TD, 2-undecanone (2-UD, N, P, K, Ca and Mg levels, density and types of trichomes and leaf area on apical, medium and basal parts of plant dossel of L. hirsutum and L. esculentum on the oviposition and mines number of T. absoluta was studied. Production of 2-TD increased from the bottom to the top of the canopy. The apical part of plants of L. hirsutum showed more antibiotic effect on the caterpillar. T. absoluta oviposited more on leaves of the apical and medium portion of the plants than in the basal parts of L. esculentum.

  1. Transcriptome profiling of Elettaria cardamomum (L. Maton (small cardamom

    Directory of Open Access Journals (Sweden)

    F. Nadiya

    2017-03-01

    Full Text Available Elettaria cardamomum (L. Maton, known as ‘queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base and 24,889,197 (75 base raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild and SRX1141276 (cultivars. The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

  2. Analysis of the Citrullus colocynthis transcriptome during water deficit stress.

    Directory of Open Access Journals (Sweden)

    Zhuoyu Wang

    Full Text Available Citrullus colocynthis is a very drought tolerant species, closely related to watermelon (C. lanatus var. lanatus, an economically important cucurbit crop. Drought is a threat to plant growth and development, and the discovery of drought inducible genes with various functions is of great importance. We used high throughput mRNA Illumina sequencing technology and bioinformatic strategies to analyze the C. colocynthis leaf transcriptome under drought treatment. Leaf samples at four different time points (0, 24, 36, or 48 hours of withholding water were used for RNA extraction and Illumina sequencing. qRT-PCR of several drought responsive genes was performed to confirm the accuracy of RNA sequencing. Leaf transcriptome analysis provided the first glimpse of the drought responsive transcriptome of this unique cucurbit species. A total of 5038 full-length cDNAs were detected, with 2545 genes showing significant changes during drought stress. Principle component analysis indicated that drought was the major contributing factor regulating transcriptome changes. Up regulation of many transcription factors, stress signaling factors, detoxification genes, and genes involved in phytohormone signaling and citrulline metabolism occurred under the water deficit conditions. The C. colocynthis transcriptome data highlight the activation of a large set of drought related genes in this species, thus providing a valuable resource for future functional analysis of candidate genes in defense of drought stress.

  3. Developmental Transcriptome for a Facultatively Eusocial Bee, Megalopta genalis.

    Science.gov (United States)

    Jones, Beryl M; Wcislo, William T; Robinson, Gene E

    2015-08-14

    Transcriptomes provide excellent foundational resources for mechanistic and evolutionary analyses of complex traits. We present a developmental transcriptome for the facultatively eusocial bee Megalopta genalis, which represents a potential transition point in the evolution of eusociality. A de novo transcriptome assembly of Megalopta genalis was generated using paired-end Illumina sequencing and the Trinity assembler. Males and females of all life stages were aligned to this transcriptome for analysis of gene expression profiles throughout development. Gene Ontology analysis indicates that stage-specific genes are involved in ion transport, cell-cell signaling, and metabolism. A number of distinct biological processes are upregulated in each life stage, and transitions between life stages involve shifts in dominant functional processes, including shifts from transcriptional regulation in embryos to metabolism in larvae, and increased lipid metabolism in adults. We expect that this transcriptome will provide a useful resource for future analyses to better understand the molecular basis of the evolution of eusociality and, more generally, phenotypic plasticity. Copyright © 2015 Jones et al.

  4. Evaluating de Bruijn graph assemblers on 454 transcriptomic data.

    Directory of Open Access Journals (Sweden)

    Xianwen Ren

    Full Text Available Next generation sequencing (NGS technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets. Because of the huge amount of data generated by NGS technologies for each run, many assemblers, e.g., ABySS, Velvet and Trinity, are developed based on a de Bruijn graph due to its time- and space-efficiency. However, most of these assemblers were developed initially for the Illumina/Solexa platform. The performance of these assemblers on 454 transcriptomic data is unknown. In this study, we evaluated and compared the relative performance of these de Bruijn graph based assemblers on both simulated and real 454 transcriptomic data. The results suggest that Trinity, the Illumina/Solexa-specialized transcriptomic assembler, performs the best among the multiple de Bruijn graph assemblers, comparable to or even outperforming the standard 454 assembler Newbler which is based on the overlap-layout-consensus algorithm. Our evaluation is expected to provide helpful guidance for researchers to choose assemblers when analyzing 454 transcriptomic data.

  5. The testes transcriptome derived from the New World Screwworm, Cochliomyia hominivorax TSA

    Science.gov (United States)

    In a collaboration with National Center for Genome Resources researchers, we sequenced and assembled the testes transcriptome derived from the Pacora, Panama, production plant strain of the New World Screwworm, Cochliomyia hominivorax. This transcriptome contains 4,149 unigenes and the Transcriptome...

  6. Major differences between human atopic dermatitis and murine models as determined by global transcriptomic profiling

    DEFF Research Database (Denmark)

    Ewald, David Adrian; Noda, Shinji; Oliva, Margeaux

    2017-01-01

    , and a comparison of these models with the human AD transcriptomic fingerprint is lacking. We sought to evaluate the transcriptomic profiles of six common murine models and determine how they relate to human AD skin. Transcriptomic profiling was performed using microarrays and qRT-PCR on biopsies from NC/Nga, flaky...

  7. De novo transcriptome assembly of shrimp Palaemon serratus

    Directory of Open Access Journals (Sweden)

    Alejandra Perina

    2017-03-01

    Full Text Available The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000 to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769. The obtained data were subjected to de novo transcriptome assembly using Trinity software, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s to annotate the identified proteins. The transcriptome data could provide some insight into the understanding of genes involved in the larval development and metamorphosis.

  8. Transcriptomic signatures of ash (Fraxinus spp. phloem.

    Directory of Open Access Journals (Sweden)

    Xiaodong Bai

    2011-01-01

    Full Text Available Ash (Fraxinus spp. is a dominant tree species throughout urban and forested landscapes of North America (NA. The rapid invasion of NA by emerald ash borer (Agrilus planipennis, a wood-boring beetle endemic to Eastern Asia, has resulted in the death of millions of ash trees and threatens billions more. Larvae feed primarily on phloem tissue, which girdles and kills the tree. While NA ash species including black (F. nigra, green (F. pennsylvannica and white (F. americana are highly susceptible, the Asian species Manchurian ash (F. mandshurica is resistant to A. planipennis perhaps due to their co-evolutionary history. Little is known about the molecular genetics of ash. Hence, we undertook a functional genomics approach to identify the repertoire of genes expressed in ash phloem.Using 454 pyrosequencing we obtained 58,673 high quality ash sequences from pooled phloem samples of green, white, black, blue and Manchurian ash. Intriguingly, 45% of the deduced proteins were not significantly similar to any sequences in the GenBank non-redundant database. KEGG analysis of the ash sequences revealed a high occurrence of defense related genes. Expression analysis of early regulators potentially involved in plant defense (i.e. transcription factors, calcium dependent protein kinases and a lipoxygenase 3 revealed higher mRNA levels in resistant ash compared to susceptible ash species. Lastly, we predicted a total of 1,272 single nucleotide polymorphisms and 980 microsatellite loci, among which seven microsatellite loci showed polymorphism between different ash species.The current transcriptomic data provide an invaluable resource for understanding the genetic make-up of ash phloem, the target tissue of A. planipennis. These data along with future functional studies could lead to the identification/characterization of defense genes involved in resistance of ash to A. planipennis, and in future ash breeding programs for marker development.

  9. Atypical endometrial cells and atypical glandular cells favor endometrial origin in Papanicolaou cervicovaginal tests: Correlation with histologic follow-up and abnormal clinical presentations

    Directory of Open Access Journals (Sweden)

    Longwen Chen

    2014-01-01

    Full Text Available The 2001 Bethesda system recommends further classifying atypical glandular cells (AGCs as either endocervical or endometrial origin. Numerous studies have investigated the clinical significance of AGC. In this study, we investigated the incidence of clinically significant lesions among women with liquid-based Papanicolaou cervicovaginal (Pap interpretations of atypical endometrial cells (AEMs or AGC favor endometrial origin (AGC-EM. More importantly, we correlated patients of AEM or AGC-EM with their clinical presentations to determine if AEM/AGC-EM combined with abnormal vaginal bleeding is associated with a higher incidence of significant endometrial pathology. All liquid-based Pap tests with an interpretation of AEM and AGC-EM from July, 2004 through June, 2009 were retrieved from the database. Women with an interpretation of atypical endocervical cells, AGC, favor endocervical origin or AGC, favor neoplastic were not included in the study. The most severe subsequent histologic diagnoses were recorded for each patient. During this 5-year period, we accessioned 332,470 Pap tests of which 169 (0.05% were interpreted as either AEM or AGC-EM. Of the 169 patients, 133 had histologic follow-up within the health care system. The patients ranged in age from 21 to 71 years old (mean 49.7. On follow-up histology, 27 (20.3% had neoplastic/preneoplastic uterine lesions. Among them, 20 patients were diagnosed with adenocarcinoma (18 endometrial, 1 endocervical, and 1 metastatic colorectal, 3 with atypical endometrial hyperplasia, and 4 with endometrial hyperplasia without atypia. All patients with significant endometrial pathology, except one, were over 40 years old, and 22 of 25 patients reported abnormal vaginal bleeding at the time of endometrial biopsy or curettage. This study represents a large series of women with liquid-based Pap test interpretations of AEM and AGC-EM with clinical follow-up. Significant preneoplastic or neoplastic endometrial

  10. Transcriptomics resources of human tissues and organs

    DEFF Research Database (Denmark)

    Uhlén, Mathias; Hallström, Björn M.; Lindskog, Cecilia

    2016-01-01

    a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome......Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide...

  11. Response of sunflower (Helianthus annuus L.) leaf surface defenses to exogenous methyl jasmonate.

    Science.gov (United States)

    Rowe, Heather C; Ro, Dae-kyun; Rieseberg, Loren H

    2012-01-01

    Helianthus annuus, the common sunflower, produces a complex array of secondary compounds that are secreted into glandular trichomes, specialized structures found on leaf surfaces and anther appendages of flowers. The primary components of these trichome secretions are sesquiterpene lactones (STL), a diverse class of compounds produced abundantly by the plant family Compositae and believed to contribute to plant defense against herbivory. We treated wild and cultivated H. annuus accessions with exogenous methyl jasmonate, a plant hormone that mediates plant defense against insect herbivores and certain classes of fungal pathogens. The wild sunflower produced a higher density of glandular trichomes on its leaves than the cultivar. Comparison of the profiles of glandular trichome extracts obtained by liquid chromatography-mass spectroscopy (LC-MS) showed that wild and cultivated H. annuus were qualitatively similar in surface chemistry, although differing in the relative size and proportion of various compounds detected. Despite observing consistent transcriptional responses to methyl jasmonate treatment, we detected no significant effect on glandular trichome density or LC-MS profile in cultivated or wild sunflower, with wild sunflower exhibiting a declining trend in overall STL production and foliar glandular trichome density of jasmonate-treated plants. These results suggest that glandular trichomes and associated compounds may act as constitutive defenses or require greater levels of stimulus for induction than the observed transcriptional responses to exogenous jasmonate. Reduced defense investment in domesticated lines is consistent with predicted tradeoffs caused by selection for increased yield; future research will focus on the development of genetic resources to explicitly test the ecological roles of glandular trichomes and associated effects on plant growth and fitness.

  12. Caracterización de gneises glandulares del alto valle del Lozoya (Sistema Central Español) en base al quimismo de las biotitas y estado estructural del feldespato potásico

    OpenAIRE

    Tornos Arroyo, Fernando; Casquet, César

    1982-01-01

    En el presente trabajo se estudian las litologías gneísicas glandulares que afloran en la ladera este del Macizo de Peñalara (Sistema Central Español), en base a la interpretación del quimismo de las biotitas de glándulas y mesostasia y del estado estructural del feldespato potásico que forma la mayoría de estas glándulas. Se deduce a partir del estudio de las biotitas, que las glándulas se comportan como sistema cerrado para el Ti y abierto para el Al durante el metamorf...

  13. Transcriptome analysis of adiposity in domestic ducks by transcriptomic comparison with their wild counterparts.

    Science.gov (United States)

    Chen, L; Luo, J; Li, J X; Li, J J; Wang, D Q; Tian, Y; Lu, L Z

    2015-06-01

    Excessive adiposity is a major problem in the duck industry, but its molecular mechanisms remain unknown. Genetic comparisons between domestic and wild animals have contributed to the exploration of genetic mechanisms responsible for many phenotypic traits. Significant differences in body fat mass have been detected between domestic and wild ducks. In this study, we used the Peking duck and Anas platyrhynchos as the domestic breed and wild counterpart respectively and performed a transcriptomic comparison of abdominal fat between the two breeds to comprehensively analyze the transcriptome basis of adiposity in ducks. We obtained approximately 350 million clean reads; assembled 61 250 transcripts, including 23 699 novel ones; and identified alternative 5' splice sites, alternative 3' splice sites, skipped exons and retained intron as the main alternative splicing events. A differential expression analysis between the two breeds showed that 753 genes exhibited differential expression. In Peking ducks, some lipid metabolism-related genes (IGF2, FABP5, BMP7, etc.) and oncogenes (RRM2, AURKA, CYR61, etc.) were upregulated, whereas genes related to tumor suppression and immunity (TNFRSF19, TNFAIP6, IGSF21, NCF1, etc.) were downregulated, suggesting adiposity might closely associate with tumorigenesis in ducks. Furthermore, 280 576 single-nucleotide variations were found differentiated between the two breeds, including 8641 non-synonymous ones, and some of the non-synonymous ones were found enriched in genes involved in lipid-associated and immune-associated pathways, suggesting abdominal fat of the duck undertakes both a metabolic function and immune-related function. These datasets enlarge our genetic information of ducks and provide valuable resources for analyzing mechanisms underlying adiposity in ducks. © 2015 Stichting International Foundation for Animal Genetics.

  14. Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants.

    Science.gov (United States)

    Li, Xinguo; Wu, Harry X; Southerton, Simon G

    2010-06-21

    Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.

  15. 20180311 - High Throughput Transcriptomics: From screening to pathways (SOT 2018)

    Science.gov (United States)

    The EPA ToxCast effort has screened thousands of chemicals across hundreds of high-throughput in vitro screening assays. The project is now leveraging high-throughput transcriptomic (HTTr) technologies to substantially expand its coverage of biological pathways. The first HTTr sc...

  16. Transcriptome Profiling in Human Diseases: New Advances and Perspectives

    Directory of Open Access Journals (Sweden)

    Amelia Casamassimi

    2017-07-01

    Full Text Available In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements and TCGA (The Cancer Genome Atlas, to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.

  17. A pathology atlas of the human cancer transcriptome

    DEFF Research Database (Denmark)

    Uhlén, Mathias; Zhang, Xi-Cheng; Lee, Sunjae

    2017-01-01

    Cancer is one of the leading causes of death, and there is great interest in understanding the underlying molecular mechanisms involved in the pathogenesis and progression of individual tumors. We used systems-level approaches to analyze the genome-wide transcriptome of the protein-coding genes o...

  18. Transcriptome and genome size analysis of the venus flytrap

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Vogt, Josef Korbinian; Bressendorff, Simon

    2015-01-01

    . muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified...

  19. Minor class splicing shapes the zebrafish transcriptome during development

    DEFF Research Database (Denmark)

    Markmiller, Sebastian; Cloonan, Nicole; Lardelli, Rea M

    2014-01-01

    known as Taybi-Linder syndrome or microcephalic osteodysplastic primordial dwarfism 1, and a hereditary intestinal polyposis condition, Peutz-Jeghers syndrome. Although a key mechanism for regulating gene expression, the impact of impaired U12-type splicing on the transcriptome is unknown. Here, we...

  20. Transcriptomes of the desiccation- tolerant resurrection plant Craterostigma plantagineum

    DEFF Research Database (Denmark)

    Rodriguez, M. C.; Edsgard, Stefan Daniel; Hussain, S. S.

    2010-01-01

    the transcriptomes of C. plantagineum leaves at four stages of dehydration and rehydration. This reveals that genes involved in several pathways, such as those required for vitamin K and thiamin biosynthesis, are tightly regulated at the level of gene expression. Our analysis also provides a comprehensive picture...

  1. Single cell transcriptome profiling of developing chick retinal cells.

    Science.gov (United States)

    Laboissonniere, Lauren A; Martin, Gregory M; Goetz, Jillian J; Bi, Ran; Pope, Brock; Weinand, Kallie; Ellson, Laura; Fru, Diane; Lee, Miranda; Wester, Andrea K; Liu, Peng; Trimarchi, Jeffrey M

    2017-08-15

    The vertebrate retina is a specialized photosensitive tissue comprised of six neuronal and one glial cell types, each of which develops in prescribed proportions at overlapping timepoints from a common progenitor pool. While each of these cells has a specific function contributing to proper vision in the mature animal, their differential representation in the retina as well as the presence of distinctive cellular subtypes makes identifying the transcriptomic signatures that lead to each retinal cell's fate determination and development challenging. We have analyzed transcriptomes from individual cells isolated from the chick retina throughout retinogenesis. While we focused our efforts on the retinal ganglion cells, our transcriptomes of developing chick cells also contained representation from multiple retinal cell types, including photoreceptors and interneurons at different stages of development. Most interesting was the identification of transcriptomes from individual mixed lineage progenitor cells in the chick as these cells offer a window into the cell fate decision-making process. Taken together, these data sets will enable us to uncover the most critical genes acting in the steps of cell fate determination and early differentiation of various retinal cell types. © 2017 Wiley Periodicals, Inc.

  2. Illumina-based de novo transcriptome sequencing and analysis

    Indian Academy of Sciences (India)

    In the present study, we used Illumina HiSeq technology to perform de novo assembly of heart and musk gland transcriptomes from the Chinese forest musk deer. A total of 239,383 transcripts and 176,450 unigenes were obtained, of which 37,329 unigenes were matched to known sequences in the NCBI nonredundant ...

  3. Transcriptome of the Antarctic brooding gastropod mollusc Margarella antarctica.

    Science.gov (United States)

    Clark, Melody S; Thorne, Michael A S

    2015-12-01

    454 RNA-Seq transcriptome data were generated from foot tissue of the Antarctic brooding gastropod mollusc Margarella antarctica. A total of 6195 contigs were assembled de novo, providing a useful resource for researchers with an interest in Antarctic marine species, phylogenetics and mollusc biology, especially shell production. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Transcriptome dynamics-based operon prediction in prokaryotes.

    Science.gov (United States)

    Fortino, Vittorio; Smolander, Olli-Pekka; Auvinen, Petri; Tagliaferri, Roberto; Greco, Dario

    2014-05-16

    Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available.

  5. De novo transcriptome assembly of heavy metal tolerant Silene dioica

    Czech Academy of Sciences Publication Activity Database

    Čegan, R.; Hudzieczek, V.; Hobza, Roman

    2017-01-01

    Roč. 11, MAR (2017), s. 118-119 ISSN 2213-5960 Institutional support: RVO:61389030 Keywords : genome * Silene dioica * RNA-Seq * Transcriptome * Heavy metal tolerance * Sex chromosomes Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany

  6. Transcriptome of barley under three different heavy metal stress reaction

    Czech Academy of Sciences Publication Activity Database

    Kintlová, Martina; Blavet, Nicolas; Cegan, R.; Hobza, Roman

    2017-01-01

    Roč. 13, SEP (2017), s. 15-17 ISSN 2213-5960 R&D Projects: GA ČR GBP501/12/G090 Institutional support: RVO:61389030 Keywords : plants * Barley * RNA-Seq * Transcriptome * Heavy metal * Copper * Zinc * Cadmium Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Plant sciences, botany

  7. Transcriptome Profiling in Human Diseases: New Advances and Perspectives.

    Science.gov (United States)

    Casamassimi, Amelia; Federico, Antonio; Rienzo, Monica; Esposito, Sabrina; Ciccodicola, Alfredo

    2017-07-29

    In the last decades, transcriptome profiling has been one of the most utilized approaches to investigate human diseases at the molecular level. Through expression studies, many molecular biomarkers and therapeutic targets have been found for several human pathologies. This number is continuously increasing thanks to total RNA sequencing. Indeed, this new technology has completely revolutionized transcriptome analysis allowing the quantification of gene expression levels and allele-specific expression in a single experiment, as well as to identify novel genes, splice isoforms, fusion transcripts, and to investigate the world of non-coding RNA at an unprecedented level. RNA sequencing has also been employed in important projects, like ENCODE (Encyclopedia of the regulatory elements) and TCGA (The Cancer Genome Atlas), to provide a snapshot of the transcriptome of dozens of cell lines and thousands of primary tumor specimens. Moreover, these studies have also paved the way to the development of data integration approaches in order to facilitate management and analysis of data and to identify novel disease markers and molecular targets to use in the clinics. In this scenario, several ongoing clinical trials utilize transcriptome profiling through RNA sequencing strategies as an important instrument in the diagnosis of numerous human pathologies.

  8. Bacillus anthracis genome organization in light of whole transcriptome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

    2010-03-22

    Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

  9. Transcriptome profiling reveals regulatory mechanisms underlying Corolla Senescence in Petunia

    Science.gov (United States)

    Genetic regulatory mechanisms that govern petal natural senescence in petunia is complicated and unclear. To identify key genes and pathways that regulate the process, we initiated a transcriptome analysis in petunia petals at four developmental time points, including petal opening without anthesis ...

  10. Construction of an EST-SSR-based interspecific transcriptome ...

    Indian Academy of Sciences (India)

    Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. CHUANXIANG LIU, DAOJUN YUAN and ZHONGXU LIN. ∗. National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan),. Huazhong Agricultural University, Wuhan ...

  11. Asowata et al., Afr J Tradit Complement Altern Med. (2016) 13(2 ...

    African Journals Online (AJOL)

    acer

    According to Werker and Fahn (1981), glandular trichomes limit the transpiration rate and reduce leaf temperature. Withering and falling leaves with intact glandular hairs may .... Glycosidically-bound aroma volatiles in the skin and pulp of 'Kensington Pride' mango fruit at different stages of maturity. Postharvest Biology and ...

  12. Comparative leaf morpho-anatomical studies of two South American species of Cardiospermum (Sapindaceae) with special reference to adaxial domatia

    NARCIS (Netherlands)

    Solís, S.M.; Ferrucci, M.S.

    2006-01-01

    Morphological and anatomical studies of leaves of two closely related Cardiospermum species from South America, C. procumbens and C. pterocarpum, were assayed. Both species have amphistomatic leaves, anomocytic stomata, non-glandular and glandular trichomes, secretory cells present in the epidermis

  13. Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis

    Science.gov (United States)

    Vukmirovic, Milica; Kaminski, Naftali

    2018-01-01

    Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease characterized by aberrant remodeling of the lung parenchyma with extensive changes to the phenotypes of all lung resident cells. The introduction of transcriptomics, genome scale profiling of thousands of RNA transcripts, caused a significant inversion in IPF research. Instead of generating hypotheses based on animal models of disease, or biological plausibility, with limited validation in humans, investigators were able to generate hypotheses based on unbiased molecular analysis of human samples and then use animal models of disease to test their hypotheses. In this review, we describe the insights made from transcriptomic analysis of human IPF samples. We describe how transcriptomic studies led to identification of novel genes and pathways involved in the human IPF lung such as: matrix metalloproteinases, WNT pathway, epithelial genes, role of microRNAs among others, as well as conceptual insights such as the involvement of developmental pathways and deep shifts in epithelial and fibroblast phenotypes. The impact of lung and transcriptomic studies on disease classification, endotype discovery, and reproducible biomarkers is also described in detail. Despite these impressive achievements, the impact of transcriptomic studies has been limited because they analyzed bulk tissue and did not address the cellular and spatial heterogeneity of the IPF lung. We discuss new emerging technologies and applications, such as single-cell RNAseq and microenvironment analysis that may address cellular and spatial heterogeneity. We end by making the point that most current tissue collections and resources are not amenable to analysis using the novel technologies. To take advantage of the new opportunities, we need new efforts of sample collections, this time focused on access to all the microenvironments and cells in the IPF lung. PMID:29670881

  14. Transcriptome signature of the adult mouse choroid plexus

    Directory of Open Access Journals (Sweden)

    Marques Fernanda

    2011-01-01

    Full Text Available Abstract Background Although the gene expression profile of several tissues in humans and in rodent animal models has been explored, analysis of the complete choroid plexus (CP transcriptome is still lacking. A better characterization of the CP transcriptome can provide key insights into its functions as one of the barriers that separate the brain from the periphery and in the production of cerebrospinal fluid. Methods This work extends further what is known about the mouse CP transcriptome through a microarray analysis of CP tissue from normal mice under physiological conditions. Results We found that the genes most highly expressed are those implicated in energy metabolism (oxidative phosphorylation, glycolysis/gluconeogenesis and in ribosomal function, which is in agreement with the secretory nature of the CP. On the other hand, genes encoding for immune mediators are among those with lower expression in basal conditions. In addition, we found genes known to be relevant during brain development, and not previously identified to be expressed in the CP, including those encoding for various axonal guidance and angiogenesis molecules and for growth factors. Some of these are known to influence the neural stem cell niche in the subventricular zone, highlighting the involvement of the CP as a likely modulator of neurogenesis. Interestingly, our observations confirm that the CP transcriptome is unique, displaying low homology with that of other tissues. Of note, we describe here that the closest similarity is with the transcriptome of the endothelial cells of the blood-brain barrier. Conclusions Based on the data presented here, it will now be possible to further explore the function of particular proteins of the CP secretome in health and in disease.

  15. Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation

    Directory of Open Access Journals (Sweden)

    Hawdon John

    2010-05-01

    Full Text Available Abstract Background Hookworm infection is one of the most important neglected diseases in developing countries, with approximately 1 billion people infected worldwide. To better understand hookworm biology and nematode parasitism, the present study generated a near complete transcriptome of the canine hookworm Ancylostoma caninum to a very high coverage using high throughput technology, and compared it to those of the free-living nematode Caenorhabditis elegans and the parasite Brugia malayi. Results The generated transcripts from four developmental stages, infective L3, serum stimulated L3, adult male and adult female, covered 93% of the A. caninum transcriptome. The broad diversity among nematode transcriptomes was confirmed, and an impact of parasitic adaptation on transcriptome diversity was inferred. Intra-population analysis showed that A. caninum has higher coding sequence diversity than humans. Examining the developmental expression profiles of A. caninum revealed major transitions in gene expression from larval stages to adult. Adult males expressed the highest number of selectively expressed genes, but adult female expressed the highest number of selective parasitism-related genes. Genes related to parasitism adaptation and A. caninum specific genes exhibited more expression selectivity while those conserved in nematodes tend to be consistently expressed. Parasitism related genes were expressed more selectively in adult male and female worms. The comprehensive analysis of digital expression profiles along with transcriptome comparisons enabled identification of a set of parasitism genes encoding secretory proteins in animal parasitic nematode. Conclusions This study validated the usage of deep sequencing for gene expression profiling. Parasitic adaptation of the canine hookworm is related to its diversity and developmental dynamics. This comprehensive comparative genomic and expression study substantially improves our understanding of

  16. Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome.

    Science.gov (United States)

    Azim, M Kamran; Khan, Ishtaiq A; Zhang, Yong

    2014-05-01

    We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80% of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37%) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member.

  17. Optimization of technique factors for a silicon diode array full-field digital mammography system and comparison to screen-film mammography with matched average glandular dose

    International Nuclear Information System (INIS)

    Berns, Eric A.; Hendrick, R. Edward; Cutter, Gary R.

    2003-01-01

    Contrast-detail experiments were performed to optimize technique factors for the detection of low-contrast lesions using a silicon diode array full-field digital mammography (FFDM) system under the conditions of a matched average glandular dose (AGD) for different techniques. Optimization was performed for compressed breast thickness from 2 to 8 cm. FFDM results were compared to screen-film mammography (SFM) at each breast thickness. Four contrast-detail (CD) images were acquired on a SFM unit with optimal techniques at 2, 4, 6, and 8 cm breast thicknesses. The AGD for each breast thickness was calculated based on half-value layer (HVL) and entrance exposure measurements on the SFM unit. A computer algorithm was developed and used to determine FFDM beam current (mAs) that matched AGD between FFDM and SFM at each thickness, while varying target, filter, and peak kilovoltage (kVp) across the full range available for the FFDM unit. CD images were then acquired on FFDM for kVp values from 23-35 for a molybdenum-molybdenum (Mo-Mo), 23-40 for a molybdenum-rhodium (Mo-Rh), and 25-49 for a rhodium-rhodium (Rh-Rh) target-filter under the constraint of matching the AGD from screen-film for each breast thickness (2, 4, 6, and 8 cm). CD images were scored independently for SFM and each FFDM technique by six readers. CD scores were analyzed to assess trends as a function of target-filter and kVp and were compared to SFM at each breast thickness. For 2 cm thick breasts, optimal FFDM CD scores occurred at the lowest possible kVp setting for each target-filter, with significant decreases in FFDM CD scores as kVp was increased under the constraint of matched AGD. For 2 cm breasts, optimal FFDM CD scores were not significantly different from SFM CD scores. For 4-8 cm breasts, optimum FFDM CD scores were superior to SFM CD scores. For 4 cm breasts, FFDM CD scores decreased as kVp increased for each target-filter combination. For 6 cm breasts, CD scores decreased slightly as k

  18. Transcriptome analysis of monocyte-HIV interactions

    Directory of Open Access Journals (Sweden)

    Tran Huyen

    2010-06-01

    macrophages can contribute to sustained chronic immune activation during HIV infection, e.g. through the perturbation of cytokine and chemokine networks 141516. With the acknowledged notion of chronic immune activation as a paradoxical driving force of immune suppression 17, this pro-inflammatory macrophage phenotype during HIV infection may be a crucial parameter in disease progression. Yet other macrophage dysfunctions are associated with more peripheral HIV- or ART-associated disorders such as atherosclerosis 18, lipodystrophy 19, and metabolic syndrome during HIV infection and/or combination ART 2021. Monocytes, for their part, are much less permissive to infection with HIV, both in vitro 22 and in vivo, where estimates of infected circulating monocytes are consistently low 2324. Circulating monocytes represent the most accessible primary model for macrophage dysfunction during HIV infection, however, and are furthermore of sufficient importance to study in their own right. Infectious virus can be recovered from circulating monocytes, both in untreated patients 24 and in patients undergoing long-term successful combination ART 25. Additionally, the circulating monocyte pool as a whole does seem to be affected during HIV infection, despite the low frequency of actually infected monocytes. Transcriptome studies, in particular, show a form of hybrid phenotype exhibiting both increased and decreased pro-inflammatory features 2627. This modulation of the non-infected monocyte population could be due to the virus itself through mechanisms which do not require direct infection 28, or to other factors contributing to (aberrant immune activation occurring during HIV infection, such as perturbed cytokine networks 29 or other inflammatory stimulants 30. Several key factors in the described dysregulated processes have been identified 1831, but many molecular components remain elusive. Furthermore, other aspects of HIV and combination ART pathogenesis in which monocyte

  19. Human Transcriptome and Chromatin Modifications: An ENCODE Perspective

    Directory of Open Access Journals (Sweden)

    Li Shen

    2013-06-01

    Full Text Available A decade-long project, led by several international research groups, called the Encyclopedia of DNA Elements (ENCODE, recently released an unprecedented amount of data. The ambitious project covers transcriptome, cistrome, epigenome, and interactome data from more than 1,600 sets of experiments in human. To make use of this valuable resource, it is important to understand the information it represents and the techniques that were used to generate these data. In this review, we introduce the data that ENCODE generated, summarize the observations from the data analysis, and revisit a computational approach that ENCODE used to predict gene expression, with a focus on the human transcriptome and its association with chromatin modifications.

  20. Transcriptome dynamics of the microRNA inhibition response

    DEFF Research Database (Denmark)

    Wen, Jiayu; Leucci, Elenora; Vendramin, Roberto

    2015-01-01

    We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line-the first such dynamic study of the microRNA inhibition response-revealing both general and specific aspects of the physiological response. We show...... validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods...... of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies....

  1. Transcriptome profiling of Curcuma longa L. cv. Suvarna

    Directory of Open Access Journals (Sweden)

    Ambika Sahoo

    2016-12-01

    Full Text Available Turmeric is an economically valued crop, because of its utility in the food, pharmaceutical industries and Ayurvedic medicine, attracts the attention in many areas of research work. In the present study, we executed resequencing through transcriptome assembly of the turmeric cultivar Suvarna (CL_Suv_10. Resequencing of Suvarna variety has generated 5 Gbases raw data with 75 bp paired-end sequence. The raw data has been submitted to SRA database of NCBI with accession number SRR4042181. Reads were assembled using Cufflinks-2.2.1 tool which ended up with 42994 numbers of transcripts. The length of transcripts ranged from 83 to15565, with a N50 value 1216 and median transcript length 773. The transcripts were annotated through number of databases. For the first time transcriptome profiling of cultivar Suvarna has been done, which could help towards identification of single nucleotide polymorphisms (SNPs between Suvarna and other turmeric cultivars for its authentic identification.

  2. Alterations in the developing testis transcriptome following embryonic vinclozolin exposure.

    Science.gov (United States)

    Clement, Tracy M; Savenkova, Marina I; Settles, Matthew; Anway, Matthew D; Skinner, Michael K

    2010-11-01

    The current study investigates the direct effects of in utero vinclozolin exposure on the developing F1 generation rat testis transcriptome. Previous studies have demonstrated that exposure to vinclozolin during embryonic gonadal sex determination induces epigenetic modifications of the germ line and transgenerational adult onset disease states. Microarray analyses were performed to compare control and vinclozolin treated testis transcriptomes at embryonic days 13, 14 and 16. A total of 576 differentially expressed genes were identified and the major cellular functions and pathways associated with these altered transcripts were examined. The sets of regulated genes at the different development periods were found to be transiently altered and distinct. Categorization by major known functions of altered genes was performed. Specific cellular process and pathway analyses suggest the involvement of Wnt and calcium signaling, vascular development and epigenetic mechanisms as potential mediators of the direct F1 generation actions of vinclozolin. Copyright © 2010 Elsevier Inc. All rights reserved.

  3. Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

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    Sarah Lück

    2014-10-01

    Full Text Available The rich mammalian cellular circadian output affects thousands of genes in many cell types and has been the subject of genome-wide transcriptome and proteome studies. The results have been enigmatic because transcript peak abundances do not always follow the peaks of gene-expression activity in time. We posited that circadian degradation of mRNAs and proteins plays a pivotal role in setting their peak times. To establish guiding principles, we derived a theoretical framework that fully describes the amplitudes and phases of biomolecules with circadian half-lives. We were able to explain the circadian transcriptome and proteome studies with the same unifying theory, including cases in which transcripts or proteins appeared before the onset of increased production rates. Furthermore, we estimate that 30% of the circadian transcripts in mouse liver and Drosophila heads are affected by rhythmic posttranscriptional regulation.

  4. An Atlas of annotations of Hydra vulgaris transcriptome.

    Science.gov (United States)

    Evangelista, Daniela; Tripathi, Kumar Parijat; Guarracino, Mario Rosario

    2016-09-22

    RNA sequencing takes advantage of the Next Generation Sequencing (NGS) technologies for analyzing RNA transcript counts with an excellent accuracy. Trying to interpret this huge amount of data in biological information is still a key issue, reason for which the creation of web-resources useful for their analysis is highly desiderable. Starting from a previous work, Transcriptator, we present the Atlas of Hydra's vulgaris, an extensible web tool in which its complete transcriptome is annotated. In order to provide to the users an advantageous resource that include the whole functional annotated transcriptome of Hydra vulgaris water polyp, we implemented the Atlas web-tool contains 31.988 accesible and downloadable transcripts of this non-reference model organism. Atlas, as a freely available resource, can be considered a valuable tool to rapidly retrieve functional annotation for transcripts differentially expressed in Hydra vulgaris exposed to the distinct experimental treatments. WEB RESOURCE URL: http://www-labgtp.na.icar.cnr.it/Atlas .

  5. Transcriptome complexity in cardiac development and diseases--an expanding universe between genome and phenome.

    Science.gov (United States)

    Gao, Chen; Wang, Yibin

    2014-01-01

    With the advancement of transcriptome profiling by micro-arrays and high-throughput RNA-sequencing, transcriptome complexity and its dynamics are revealed at different levels in cardiovascular development and diseases. In this review, we will highlight the recent progress in our knowledge of cardiovascular transcriptome complexity contributed by RNA splicing, RNA editing and noncoding RNAs. The emerging importance of many of these previously under-explored aspects of gene regulation in cardiovascular development and pathology will be discussed.

  6. Analysis of the salivary gland transcriptome of Frankliniella occidentalis.

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    Candice A Stafford-Banks

    Full Text Available Saliva is known to play a crucial role in insect feeding behavior and virus transmission. Currently, little is known about the salivary glands and saliva of thrips, despite the fact that Frankliniella occidentalis (Pergande (the western flower thrips is a serious pest due to its destructive feeding, wide host range, and transmission of tospoviruses. As a first step towards characterizing thrips salivary gland functions, we sequenced the transcriptome of the primary salivary glands of F. occidentalis using short read sequencing (Illumina technology. A de novo-assembled transcriptome revealed 31,392 high quality contigs with an average size of 605 bp. A total of 12,166 contigs had significant BLASTx or tBLASTx hits (E≤1.0E-6 to known proteins, whereas a high percentage (61.24% of contigs had no apparent protein or nucleotide hits. Comparison of the F. occidentalis salivary gland transcriptome (sialotranscriptome against a published F. occidentalis full body transcriptome assembled from Roche-454 reads revealed several contigs with putative annotations associated with salivary gland functions. KEGG pathway analysis of the sialotranscriptome revealed that the majority (18 out of the top 20 predicted KEGG pathways of the salivary gland contig sequences match proteins involved in metabolism. We identified several genes likely to be involved in detoxification and inhibition of plant defense responses including aldehyde dehydrogenase, metalloprotease, glucose oxidase, glucose dehydrogenase, and regucalcin. We also identified several genes that may play a role in the extra-oral digestion of plant structural tissues including β-glucosidase and pectin lyase; and the extra-oral digestion of sugars, including α-amylase, maltase, sucrase, and α-glucosidase. This is the first analysis of a sialotranscriptome for any Thysanopteran species and it provides a foundational tool to further our understanding of how thrips interact with their plant hosts and the

  7. Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome.

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    Sumedha S Gunewardena

    Full Text Available During development, liver undergoes a rapid transition from a hematopoietic organ to a major organ for drug metabolism and nutrient homeostasis. However, little is known on a transcriptome level of the genes and RNA-splicing variants that are differentially regulated with age, and which up-stream regulators orchestrate age-specific biological functions in liver. We used RNA-Seq to interrogate the developmental dynamics of the liver transcriptome in mice at 12 ages from late embryonic stage (2-days before birth to maturity (60-days after birth. Among 21,889 unique NCBI RefSeq-annotated genes, 9,641 were significantly expressed in at least one age, 7,289 were differently regulated with age, and 859 had multiple (> = 2 RNA splicing-variants. Factor analysis showed that the dynamics of hepatic genes fall into six distinct groups based on their temporal expression. The average expression of cytokines, ion channels, kinases, phosphatases, transcription regulators and translation regulators decreased with age, whereas the average expression of peptidases, enzymes and transmembrane receptors increased with age. The average expression of growth factors peak between Day-3 and Day-10, and decrease thereafter. We identified critical biological functions, upstream regulators, and putative transcription modules that seem to govern age-specific gene expression. We also observed differential ontogenic expression of known splicing variants of certain genes, and 1,455 novel splicing isoform candidates. In conclusion, the hepatic ontogeny of the transcriptome ontogeny has unveiled critical networks and up-stream regulators that orchestrate age-specific biological functions in liver, and suggest that age contributes to the complexity of the alternative splicing landscape of the hepatic transcriptome.

  8. Establishment and analysis of a reference transcriptome for Spodoptera frugiperda.

    Science.gov (United States)

    Legeai, Fabrice; Gimenez, Sylvie; Duvic, Bernard; Escoubas, Jean-Michel; Gosselin Grenet, Anne-Sophie; Blanc, Florence; Cousserans, François; Séninet, Imène; Bretaudeau, Anthony; Mutuel, Doriane; Girard, Pierre-Alain; Monsempes, Christelle; Magdelenat, Ghislaine; Hilliou, Frédérique; Feyereisen, René; Ogliastro, Mylène; Volkoff, Anne-Nathalie; Jacquin-Joly, Emmanuelle; d'Alençon, Emmanuelle; Nègre, Nicolas; Fournier, Philippe

    2014-08-23

    Spodoptera frugiperda (Noctuidae) is a major agricultural pest throughout the American continent. The highly polyphagous larvae are frequently devastating crops of importance such as corn, sorghum, cotton and grass. In addition, the Sf9 cell line, widely used in biochemistry for in vitro protein production, is derived from S. frugiperda tissues. Many research groups are using S. frugiperda as a model organism to investigate questions such as plant adaptation, pest behavior or resistance to pesticides. In this study, we constructed a reference transcriptome assembly (Sf_TR2012b) of RNA sequences obtained from more than 35 S. frugiperda developmental time-points and tissue samples. We assessed the quality of this reference transcriptome by annotating a ubiquitous gene family--ribosomal proteins--as well as gene families that have a more constrained spatio-temporal expression and are involved in development, immunity and olfaction. We also provide a time-course of expression that we used to characterize the transcriptional regulation of the gene families studied. We conclude that the Sf_TR2012b transcriptome is a valid reference transcriptome. While its reliability decreases for the detection and annotation of genes under strong transcriptional constraint we still recover a fair percentage of tissue-specific transcripts. That allowed us to explore the spatial and temporal expression of genes and to observe that some olfactory receptors are expressed in antennae and palps but also in other non related tissues such as fat bodies. Similarly, we observed an interesting interplay of gene families involved in immunity between fat bodies and antennae.

  9. Transcriptome Analysis of the Response of Burmese Python to Digestion

    OpenAIRE

    Duan, Jinjie; Sanggaard, Kristian Wejse; Schauser, Leif; Lauridsen, Sanne Enok; Enghild, Jan J.; Schierup, Mikkel Heide; Wang, Tobias

    2017-01-01

    Abstract Exceptional and extreme feeding behaviour makes the Burmese python (Python bivittatus) an interesting model to study physiological remodelling and metabolic adaptation in response to refeeding after prolonged starvation. In this study, we used transcriptome sequencing of 5 visceral organs during fasting as well as 24 hours and 48 hours after ingestion of a large meal to unravel the postprandial changes in Burmese pythons. We first used the pooled data to perform a de novo assembly of...

  10. Detailed transcriptome description of the neglected cestode Taenia multiceps.

    Science.gov (United States)

    Wu, Xuhang; Fu, Yan; Yang, Deying; Zhang, Runhui; Zheng, Wanpeng; Nie, Huaming; Xie, Yue; Yan, Ning; Hao, Guiying; Gu, Xiaobin; Wang, Shuxian; Peng, Xuerong; Yang, Guangyou

    2012-01-01

    The larval stage of Taenia multiceps, a global cestode, encysts in the central nervous system (CNS) of sheep and other livestock. This frequently leads to their death and huge socioeconomic losses, especially in developing countries. This parasite can also cause zoonotic infections in humans, but has been largely neglected due to a lack of diagnostic techniques and studies. Recent developments in next-generation sequencing provide an opportunity to explore the transcriptome of T. multiceps. We obtained a total of 31,282 unigenes (mean length 920 bp) using Illumina paired-end sequencing technology and a new Trinity de novo assembler without a referenced genome. Individual transcription molecules were determined by sequence-based annotations and/or domain-based annotations against public databases (Nr, UniprotKB/Swiss-Prot, COG, KEGG, UniProtKB/TrEMBL, InterPro and Pfam). We identified 26,110 (83.47%) unigenes and inferred 20,896 (66.8%) coding sequences (CDS). Further comparative transcripts analysis with other cestodes (Taenia pisiformis, Taenia solium, Echincoccus granulosus and Echincoccus multilocularis) and intestinal parasites (Trichinella spiralis, Ancylostoma caninum and Ascaris suum) showed that 5,100 common genes were shared among three Taenia tapeworms, 261 conserved genes were detected among five Taeniidae cestodes, and 109 common genes were found in four zoonotic intestinal parasites. Some of the common genes were genes required for parasite survival, involved in parasite-host interactions. In addition, we amplified two full-length CDS of unigenes from the common genes using RT-PCR. This study provides an extensive transcriptome of the adult stage of T. multiceps, and demonstrates that comparative transcriptomic investigations deserve to be further studied. This transcriptome dataset forms a substantial public information platform to achieve a fundamental understanding of the biology of T. multiceps, and helps in the identification of drug targets and

  11. Transcriptome profiling of male gametophyte development in Nicotiana tabacum

    Czech Academy of Sciences Publication Activity Database

    Bokvaj, Pavel; Hafidh, Said; Honys, David

    2015-01-01

    Roč. 3, MAR (2015), s. 106-111 ISSN 2213-5960 R&D Projects: GA ČR(CZ) GAP501/11/1462; GA ČR(CZ) GAP305/12/2611; GA MŠk(CZ) LD14109; GA ČR(CZ) GA13-06943S; GA MŠk(CZ) LD13049 Institutional support: RVO:61389030 Keywords : Pollen development transcriptome * Tobacco * Reproduction Subject RIV: EB - Genetics ; Molecular Biology

  12. Detailed transcriptome description of the neglected cestode Taenia multiceps.

    Directory of Open Access Journals (Sweden)

    Xuhang Wu

    Full Text Available BACKGROUND: The larval stage of Taenia multiceps, a global cestode, encysts in the central nervous system (CNS of sheep and other livestock. This frequently leads to their death and huge socioeconomic losses, especially in developing countries. This parasite can also cause zoonotic infections in humans, but has been largely neglected due to a lack of diagnostic techniques and studies. Recent developments in next-generation sequencing provide an opportunity to explore the transcriptome of T. multiceps. METHODOLOGY/PRINCIPAL FINDINGS: We obtained a total of 31,282 unigenes (mean length 920 bp using Illumina paired-end sequencing technology and a new Trinity de novo assembler without a referenced genome. Individual transcription molecules were determined by sequence-based annotations and/or domain-based annotations against public databases (Nr, UniprotKB/Swiss-Prot, COG, KEGG, UniProtKB/TrEMBL, InterPro and Pfam. We identified 26,110 (83.47% unigenes and inferred 20,896 (66.8% coding sequences (CDS. Further comparative transcripts analysis with other cestodes (Taenia pisiformis, Taenia solium, Echincoccus granulosus and Echincoccus multilocularis and intestinal parasites (Trichinella spiralis, Ancylostoma caninum and Ascaris suum showed that 5,100 common genes were shared among three Taenia tapeworms, 261 conserved genes were detected among five Taeniidae cestodes, and 109 common genes were found in four zoonotic intestinal parasites. Some of the common genes were genes required for parasite survival, involved in parasite-host interactions. In addition, we amplified two full-length CDS of unigenes from the common genes using RT-PCR. CONCLUSIONS/SIGNIFICANCE: This study provides an extensive transcriptome of the adult stage of T. multiceps, and demonstrates that comparative transcriptomic investigations deserve to be further studied. This transcriptome dataset forms a substantial public information platform to achieve a fundamental understanding of

  13. Comparative Transcriptomics to Identify Novel Genes and Pathways in Dinoflagellates

    Science.gov (United States)

    Ryan, D.

    2016-02-01

    The unarmored dinoflagellate Karenia brevis is among the most prominent harmful, bloom-forming phytoplankton species in the Gulf of Mexico. During blooms, the polyketides PbTx-1 and PbTx-2 (brevetoxins) are produced by K. brevis. Brevetoxins negatively impact human health and the Gulf shellfish harvest. However, the genes underlying brevetoxin synthesis are currently unknown. Because the K. brevis genome is extremely large ( 1 × 1011 base pairs long), and with a high proportion of repetitive, non-coding DNA, it has not been sequenced. In fact, large, repetitive genomes are common among the dinoflagellate group. High-throughput RNA sequencing technology enabled us to assemble Karenia transcriptomes de novo and investigate potential genes in the brevetoxin pathway through comparative transcriptomics. The brevetoxin profile varies among K. brevis clonal cultures. For example, well-documented Wilson-CCFWC268 typically produces 8-10 pg PbTx per cell, whereas SP1 produces differences in gene expression. Of the 85,000 transcripts in the K. brevis transcriptome, 4,600 transcripts, including novel unannotated orthologs and putative polyketide synthases (PKSs), were only expressed by brevetoxin-producing K. brevis and K. papilionacea, not K. mikimotoi. Examination of gene expression between the typical- and low-toxin Wilson clones identified about 3,500 genes with significantly different expression levels, including 2 putative PKSs. One of the 2 PKSs was only found in the brevetoxin-producing Karenia species. These transcriptomes could not have been characterized without high-throughput RNA sequencing.

  14. Comparing de novo assemblers for 454 transcriptome data.

    Science.gov (United States)

    Kumar, Sujai; Blaxter, Mark L

    2010-10-16

    Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs however gave a more credible

  15. Comparing de novo assemblers for 454 transcriptome data

    Directory of Open Access Journals (Sweden)

    Blaxter Mark L

    2010-10-01

    Full Text Available Abstract Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects, which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies

  16. Transcriptome analysis of the Asian honey bee Apis cerana cerana.

    Directory of Open Access Journals (Sweden)

    Zi Long Wang

    Full Text Available BACKGROUND: The Eastern hive honey bee, Apis cerana cerana is a native and widely bred honey bee species in China. Molecular biology research about this honey bee species is scarce, and genomic information for A. c. cerana is not currently available. Transcriptome and expression profiling data for this species are therefore important resources needed to better understand the biological mechanisms of A. c. cerana. In this study, we obtained the transcriptome information of A. c. cerana by RNA-sequencing and compared gene expression differences between queens and workers of A. c. cerana by digital gene expression (DGE analysis. RESULTS: Using high-throughput Illumina RNA sequencing we obtained 51,581,510 clean reads corresponding to 4.64 Gb total nucleotides from a single run. These reads were assembled into 46,999 unigenes with a mean length of 676 bp. Based on a sequence similarity search against the five public databases (NR, Swissport, GO, COG, KEGG with a cut-off E-value of 10(-5 using BLASTX, a total of 24,630 unigenes were annotated with gene descriptions, gene ontology terms, or metabolic pathways. Using these transcriptome data as references we analyzed the gene expression differences between the queens and workers of A. c. cerana using a tag-based digital gene expression method. We obtained 5.96 and 5.66 million clean tags from the queen and worker samples, respectively. A total of 414 genes were differentially expressed between them, with 189 up-regulated and 225 down-regulated in queens. CONCLUSIONS: Our transcriptome data provide a comprehensive sequence resource for future A. c. cerana study, establishing an important public information platform for functional genomic studies in A. c. cerana. Furthermore, the DGE data provide comprehensive gene expression information for the queens and workers, which will facilitate our understanding of the molecular mechanisms of the different physiological aspects of the two castes.

  17. Transcriptome and proteomic analysis of mango (Mangifera indica Linn) fruits.

    Science.gov (United States)

    Wu, Hong-xia; Jia, Hui-min; Ma, Xiao-wei; Wang, Song-biao; Yao, Quan-sheng; Xu, Wen-tian; Zhou, Yi-gang; Gao, Zhong-shan; Zhan, Ru-lin

    2014-06-13

    Here we used Illumina RNA-seq technology for transcriptome sequencing of a mixed fruit sample from 'Zill' mango (Mangifera indica Linn) fruit pericarp and pulp during the development and ripening stages. RNA-seq generated 68,419,722 sequence reads that were assembled into 54,207 transcripts with a mean length of 858bp, including 26,413 clusters and 27,794 singletons. A total of 42,515(78.43%) transcripts were annotated using public protein databases, with a cut-off E-value above 10(-5), of which 35,198 and 14,619 transcripts were assigned to gene ontology terms and clusters of orthologous groups respectively. Functional annotation against the Kyoto Encyclopedia of Genes and Genomes database identified 23,741(43.79%) transcripts which were mapped to 128 pathways. These pathways revealed many previously unknown transcripts. We also applied mass spectrometry-based transcriptome data to characterize the proteome of ripe fruit. LC-MS/MS analysis of the mango fruit proteome was using tandem mass spectrometry (MS/MS) in an LTQ Orbitrap Velos (Thermo) coupled online to the HPLC. This approach enabled the identification of 7536 peptides that matched 2754 proteins. Our study provides a comprehensive sequence for a systemic view of transcriptome during mango fruit development and the most comprehensive fruit proteome to date, which are useful for further genomics research and proteomic studies. Our study provides a comprehensive sequence for a systemic view of both the transcriptome and proteome of mango fruit, and a valuable reference for further research on gene expression and protein identification. This article is part of a Special Issue entitled: Proteomics of non-model organisms. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. A comparative transcriptomic approach to understanding the formation of cork.

    Science.gov (United States)

    Boher, Pau; Soler, Marçal; Sánchez, Anna; Hoede, Claire; Noirot, Céline; Paiva, Jorge Almiro Pinto; Serra, Olga; Figueras, Mercè

    2018-01-01

    The transcriptome comparison of two oak species reveals possible candidates accounting for the exceptionally thick and pure cork oak phellem, such as those involved in secondary metabolism and phellogen activity. Cork oak, Quercus suber, differs from other Mediterranean oaks such as holm oak (Quercus ilex) by the thickness and organization of the external bark. While holm oak outer bark contains sequential periderms interspersed with dead secondary phloem (rhytidome), the cork oak outer bark only contains thick layers of phellem (cork rings) that accumulate until reaching a thickness that allows industrial uses. Here we compare the cork oak outer bark transcriptome with that of holm oak. Both transcriptomes present similitudes in their complexity, but whereas cork oak external bark is enriched with upregulated genes related to suberin, which is the main polymer responsible for the protective function of periderm, the upregulated categories of holm oak are enriched in abiotic stress and chromatin assembly. Concomitantly with the upregulation of suberin-related genes, there is also induction of regulatory and meristematic genes, whose predicted activities agree with the increased number of phellem layers found in the cork oak sample. Further transcript profiling among different cork oak tissues and conditions suggests that cork and wood share many regulatory mechanisms, probably reflecting similar ontogeny. Moreover, the analysis of transcripts accumulation during the cork growth season showed that most regulatory genes are upregulated early in the season when the cork cambium becomes active. Altogether our work provides the first transcriptome comparison between cork oak and holm oak outer bark, which unveils new regulatory candidate genes of phellem development.

  19. Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds.

    Science.gov (United States)

    Pradhan, Seema; Bandhiwal, Nitesh; Shah, Niraj; Kant, Chandra; Gaur, Rashmi; Bhatia, Sabhyata

    2014-01-01

    Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L.) seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilized to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analyzed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs), about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

  20. Global transcriptome analysis of developing chickpea (Cicer arietinum L. seeds

    Directory of Open Access Journals (Sweden)

    Seema ePradhan

    2014-12-01

    Full Text Available Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L. seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilised to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analysed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs, about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

  1. Transcriptome analysis of the response of Burmese python to digestion.

    Science.gov (United States)

    Duan, Jinjie; Sanggaard, Kristian Wejse; Schauser, Leif; Lauridsen, Sanne Enok; Enghild, Jan J; Schierup, Mikkel Heide; Wang, Tobias

    2017-08-01

    Exceptional and extreme feeding behaviour makes the Burmese python (Python bivittatus) an interesting model to study physiological remodelling and metabolic adaptation in response to refeeding after prolonged starvation. In this study, we used transcriptome sequencing of 5 visceral organs during fasting as well as 24 hours and 48 hours after ingestion of a large meal to unravel the postprandial changes in Burmese pythons. We first used the pooled data to perform a de novo assembly of the transcriptome and supplemented this with a proteomic survey of enzymes in the plasma and gastric fluid. We constructed a high-quality transcriptome with 34 423 transcripts, of which 19 713 (57%) were annotated. Among highly expressed genes (fragments per kilo base per million sequenced reads > 100 in 1 tissue), we found that the transition from fasting to digestion was associated with differential expression of 43 genes in the heart, 206 genes in the liver, 114 genes in the stomach, 89 genes in the pancreas, and 158 genes in the intestine. We interrogated the function of these genes to test previous hypotheses on the response to feeding. We also used the transcriptome to identify 314 secreted proteins in the gastric fluid of the python. Digestion was associated with an upregulation of genes related to metabolic processes, and translational changes therefore appear to support the postprandial rise in metabolism. We identify stomach-related proteins from a digesting individual and demonstrate that the sensitivity of modern liquid chromatography/tandem mass spectrometry equipment allows the identification of gastric juice proteins that are present during digestion. © The Authors 2017. Published by Oxford University Press.

  2. Massively parallel sequencing and analysis of the Necator americanus transcriptome.

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    Cinzia Cantacessi

    2010-05-01

    Full Text Available The blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide. In order to elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses.A total of 19,997 contigs were assembled from the sequence data; 6,771 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and most of them encoded proteins with WD40 repeats (10.6%, proteinase inhibitors (7.8% or calcium-binding EF-hand proteins (6.7%. Bioinformatic analyses inferred that the C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%, oxidative phosphorylation (63% and/or proteases (60%; most of these molecules were predicted to be involved in more than one biological pathway. Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. For instance, proteinase inhibitors were inferred to be highly represented in the former species, whereas SCP/Tpx-1/Ag5/PR-1/Sc7 proteins ( = SCP/TAPS or Ancylostoma-secreted proteins were predominant in the latter. In N. americanus, essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have homologues in the human host. These candidate targets were inferred to be linked to mitochondrial (e.g., processing proteins or amino acid metabolism (e.g., asparagine t-RNA synthetase.This study has provided detailed insights into the transcriptome of the adult stage of N. americanus and examines similarities and differences between this species and A. caninum. Future efforts should focus on comparative transcriptomic and proteomic investigations of the other predominant human

  3. Genetic Dissection of the Spaceflight Transcriptome Responses in Plants: are some responses unnecessary?

    Data.gov (United States)

    National Aeronautics and Space Administration — Experimentation on the International Space Station has reached the stage where repeated and nuanced transcriptome studies are beginning to illuminate the structural...

  4. Comparison of the spaceflight transcriptome of four commonly used Arabidopsis thaliana ecotypes

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    National Aeronautics and Space Administration — This experiment compared the spaceflight transcriptomes of four commonly used natural variants (ecotypes) of Arabidopsis thaliana using RNAseq. In nature Arabidopsis...

  5. Histological chorioamnionitis shapes the neonatal transcriptomic immune response.

    Science.gov (United States)

    Weitkamp, Jörn-Hendrik; Guthrie, Scott O; Wong, Hector R; Moldawer, Lyle L; Baker, Henry V; Wynn, James L

    2016-07-01

    Histologic chorioamnionitis (HCA) is commonly associated with preterm birth and deleterious post-natal outcomes including sepsis and necrotizing enterocolitis. Transcriptomic analysis has been used to uncover gene signatures that permit diagnosis and prognostication, show new therapeutic targets, and reveal mechanisms that underlie differential outcomes with other complex disease states in neonates such as sepsis. To define the transcriptomic and inflammatory protein response in peripheral blood among infants with exposure to histologic chorioamnionitis. Prospective, observational study. Uninfected preterm neonates retrospectively categorized based on placental pathology with no HCA exposure (n=18) or HCA exposure (n=15). We measured the transcriptomic and inflammatory mediator response in prospectively collected whole blood. We found 488 significant (p<0.001), differentially expressed genes in whole blood samples among uninfected neonates with HCA exposure that collectively represented activated innate and adaptive immune cellular pathways and revealed a potential regulatory role for the pleotropic microRNA molecule miR-155. Differentially secreted plasma cytokines in patients with HCA exposure compared to patients without HCA included MCP-1, MPO, and MMP-9 (p<0.05). Exposure to HCA distinctively activates the neonatal immune system in utero with potentially long-term health consequences. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  6. Current Knowledge and Recent Advances in Marine Dinoflagellate Transcriptomic Research

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    Muhamad Afiq Akbar

    2018-02-01

    Full Text Available Dinoflagellates are essential components in marine ecosystems, and they possess two dissimilar flagella to facilitate movement. Dinoflagellates are major components of marine food webs and of extreme importance in balancing the ecosystem energy flux in oceans. They have been reported to be the primary cause of harmful algae bloom (HABs events around the world, causing seafood poisoning and therefore having a direct impact on human health. Interestingly, dinoflagellates in the genus Symbiodinium are major components of coral reef foundations. Knowledge regarding their genes and genome organization is currently limited due to their large genome size and other genetic and cytological characteristics that hinder whole genome sequencing of dinoflagellates. Transcriptomic approaches and genetic analyses have been employed to unravel the physiological and metabolic characteristics of dinoflagellates and their complexity. In this review, we summarize the current knowledge and findings from transcriptomic studies to understand the cell growth, effects on environmental stress, toxin biosynthesis, dynamic of HABs, phylogeny and endosymbiosis of dinoflagellates. With the advancement of high throughput sequencing technologies and lower cost of sequencing, transcriptomic approaches will likely deepen our understanding in other aspects of dinoflagellates’ molecular biology such as gene functional analysis, systems biology and development of model organisms.

  7. De novo transcriptome assembly of mangosteen (Garcinia mangostana L. fruit

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    Deden Derajat Matra

    2016-12-01

    Full Text Available Garcinia mangostana L. (Mangosteen, of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.

  8. Quantitative developmental transcriptomes of the Mediterranean sea urchin Paracentrotus lividus.

    Science.gov (United States)

    Gildor, Tsvia; Malik, Assaf; Sher, Noa; Avraham, Linor; Ben-Tabou de-Leon, Smadar

    2016-02-01

    Embryonic development progresses through the timely activation of thousands of differentially activated genes. Quantitative developmental transcriptomes provide the means to relate global patterns of differentially expressed genes to the emerging body plans they generate. The sea urchin is one of the classic model systems for embryogenesis and the models of its developmental gene regulatory networks are of the most comprehensive of their kind. Thus, the sea urchin embryo is an excellent system for studies of its global developmental transcriptional profiles. Here we produced quantitative developmental transcriptomes of the sea urchin Paracentrotus lividus (P. lividus) at seven developmental stages from the fertilized egg to prism stage. We generated de-novo reference transcriptome and identified 29,817 genes that are expressed at this time period. We annotated and quantified gene expression at the different developmental stages and confirmed the reliability of the expression profiles by QPCR measurement of a subset of genes. The progression of embryo development is reflected in the observed global expression patterns and in our principle component analysis. Our study illuminates the rich patterns of gene expression that participate in sea urchin embryogenesis and provide an essential resource for further studies of the dynamic expression of P. lividus genes. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Histological and Transcriptomic Analysis during Bulbil Formation in Lilium lancifolium

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    Panpan Yang

    2017-08-01

    Full Text Available Aerial bulbils are an important propagative organ, playing an important role in population expansion. However, the detailed gene regulatory patterns and molecular mechanism underlying bulbil formation remain unclear. Triploid Lilium lancifolium, which develops many aerial bulbils on the leaf axils of middle-upper stem, is a useful species for investigating bulbil formation. To investigate the mechanism of bulbil formation in triploid L. lancifolium, we performed histological and transcriptomic analyses using samples of leaf axils located in the upper and lower stem of triploid L. lancifolium during bulbil formation. Histological results indicated that the bulbils of triploid L. lancifolium are derived from axillary meristems that initiate de novo from cells on the adaxial side of the petiole base. Transcriptomic analysis generated ~650 million high-quality reads and 11,871 differentially expressed genes (DEGs. Functional analysis showed that the DEGs were significantly enriched in starch and sucrose metabolism and plant hormone signal transduction. Starch synthesis and accumulation likely promoted the initiation of upper bulbils in triploid L. lancifolium. Hormone-associated pathways exhibited distinct patterns of change in each sample. Auxin likely promoted the initiation of bulbils and then inhibited further bulbil formation. High biosynthesis and low degradation of cytokinin might have led to bulbil formation in the upper leaf axil. The present study achieved a global transcriptomic analysis focused on gene expression changes and pathways' enrichment during upper bulbil formation in triploid L. lancifolium, laying a solid foundation for future molecular studies on bulbil formation.

  10. DOGMA: domain-based transcriptome and proteome quality assessment.

    Science.gov (United States)

    Dohmen, Elias; Kremer, Lukas P M; Bornberg-Bauer, Erich; Kemena, Carsten

    2016-09-01

    Genome studies have become cheaper and easier than ever before, due to the decreased costs of high-throughput sequencing and the free availability of analysis software. However, the quality of genome or transcriptome assemblies can vary a lot. Therefore, quality assessment of assemblies and annotations are crucial aspects of genome analysis pipelines. We developed DOGMA, a program for fast and easy quality assessment of transcriptome and proteome data based on conserved protein domains. DOGMA measures the completeness of a given transcriptome or proteome and provides information about domain content for further analysis. DOGMA provides a very fast way to do quality assessment within seconds. DOGMA is implemented in Python and published under GNU GPL v.3 license. The source code is available on https://ebbgit.uni-muenster.de/domainWorld/DOGMA/ CONTACTS: e.dohmen@wwu.de or c.kemena@wwu.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  11. De novo transcriptome assembly of two contrasting pumpkin cultivars

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    Aliki Xanthopoulou

    2016-03-01

    Full Text Available Cucurbita pepo (squash, pumpkin, gourd, a worldwide-cultivated vegetable of American origin, is extremely variable in fruit characteristics. However, the information associated with genes and genetic markers for pumpkin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis (RNA-Seq of two contrasting pumpkin cultivars. Leaves and female flowers of cultivars, ‘Big Moose’ with large round fruits and ‘Munchkin’ with small round fruits, were harvested for total RNA extraction. We obtained a total of 6 GB (Big Moose; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056882 and 5 GB (Munchkin; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056883 sequence data (NCBI SRA database SRX1502732 and SRX1502735, respectively, which correspond to 18,055,786 and 14,824,292 150-base reads. After quality assessment, the clean sequences where 17,995,932 and 14,774,486 respectively. The numbers of total transcripts for ‘Big Moose’ and ‘Munchkin’ were 84,727 and 68,051, respectively. TransDecoder identified possible coding regions in assembled transcripts. This study provides transcriptome data for two contrasting pumpkin cultivars, which might be useful for genetic marker development and comparative transcriptome analyses. Keywords: RNA-Seq, Pumpkin, Contrasting cultivars, Cucurbita pepo

  12. Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

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    Gyoungju Nah

    Full Text Available Prairie cordgrass (Spartina pectinata, a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY. The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation.

  13. [SSR loci information analysis in transcriptome of Andrographis paniculata].

    Science.gov (United States)

    Li, Jun-Ren; Chen, Xiu-Zhen; Tang, Xiao-Ting; He, Rui; Zhan, Ruo-Ting

    2018-06-01

    To study the SSR loci information and develop molecular markers, a total of 43 683 Unigenes in transcriptome of Andrographis paniculata were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MicroSAtellite software, SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 14 135 SSR loci were found in the transcriptome of A. paniculata, which distributed in 9 973 Unigenes with a distribution frequency of 32.36%. Di-nucleotide and Tri-nucleotide repeat were the main types, accounted for 75.54% of all SSRs. The repeat motifs of AT/AT and CCG/CGG were the predominant repeat types of Di-nucleotide and Tri-nucleotide, respectively. A total of 4 740 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. Ten pairs of primers in 20 pairs of randomly picked primers produced fragments with expected molecular size. The gene function of Unigenes containing SSR were mostly related to the basic metabolism function of A. paniculata. The SSR markers in transcriptome of A. paniculata show rich type, strong specificity and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. Copyright© by the Chinese Pharmaceutical Association.

  14. Annotation of nerve cord transcriptome in earthworm Eisenia fetida

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    Vasanthakumar Ponesakki

    2017-12-01

    Full Text Available In annelid worms, the nerve cord serves as a crucial organ to control the sensory and behavioral physiology. The inadequate genome resource of earthworms has prioritized the comprehensive analysis of their transcriptome dataset to monitor the genes express in the nerve cord and predict their role in the neurotransmission and sensory perception of the species. The present study focuses on identifying the potential transcripts and predicting their functional features by annotating the transcriptome dataset of nerve cord tissues prepared by Gong et al., 2010 from the earthworm Eisenia fetida. Totally 9762 transcripts were successfully annotated against the NCBI nr database using the BLASTX algorithm and among them 7680 transcripts were assigned to a total of 44,354 GO terms. The conserve domain analysis indicated the over representation of P-loop NTPase domain and calcium binding EF-hand domain. The COG functional annotation classified 5860 transcript sequences into 25 functional categories. Further, 4502 contig sequences were found to map with 124 KEGG pathways. The annotated contig dataset exhibited 22 crucial neuropeptides having considerable matches to the marine annelid Platynereis dumerilii, suggesting their possible role in neurotransmission and neuromodulation. In addition, 108 human stem cell marker homologs were identified including the crucial epigenetic regulators, transcriptional repressors and cell cycle regulators, which may contribute to the neuronal and segmental regeneration. The complete functional annotation of this nerve cord transcriptome can be further utilized to interpret genetic and molecular mechanisms associated with neuronal development, nervous system regeneration and nerve cord function.

  15. De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle

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    Yeonhwa Jo

    2015-12-01

    Full Text Available Sour cherry (Prunus cerasus in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170. De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing.

  16. The Transcriptomic Responses of Pinus massoniana to Drought Stress

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    Mingfeng Du

    2018-06-01

    Full Text Available Masson pine (Pinus massoniana is a major fast-growing timber species planted in southern China, a region of seasonal drought. Using a drought-tolerance genotype of Masson pine, we conducted large-scale transcriptome sequencing using Illumina technology. This work aimed to evaluate the transcriptomic responses of Masson pine to different levels of drought stress. First, 3397, 1695 and 1550 unigenes with differential expression were identified by comparing plants subjected to light, moderate or severe drought with control plants. Second, several gene ontology (GO categories (oxidation-reduction and metabolism and Kyoto Encyclopedia of Genes and Genomes (KEGG pathways (plant hormone signal transduction and metabolic pathways were enriched, indicating that the expression levels of some genes in these enriched GO terms and pathways were altered under drought stress. Third, several transcription factors (TFs associated with circadian rhythms (HY5 and LHY, signal transduction (ERF, and defense responses (WRKY were identified, and these TFs may play key roles in adapting to drought stress. Drought also caused significant changes in the expression of certain functional genes linked to osmotic adjustment (P5CS, abscisic acid (ABA responses (NCED, PYL, PP2C and SnRK, and reactive oxygen species (ROS scavenging (GPX, GST and GSR. These transcriptomic results provide insight into the molecular mechanisms of drought stress adaptation in Masson pine.

  17. Transcriptome profiling of ontogeny in the acridid grasshopper Chorthippus biguttulus.

    Science.gov (United States)

    Berdan, Emma L; Finck, Jonas; Johnston, Paul R; Waurick, Isabelle; Mazzoni, Camila J; Mayer, Frieder

    2017-01-01

    Acridid grasshoppers (Orthoptera:Acrididae) are widely used model organisms for developmental, evolutionary, and neurobiological research. Although there has been recent influx of orthopteran transcriptomic resources, many use pooled ontogenetic stages obscuring information about changes in gene expression during development. Here we developed a de novo transcriptome spanning 7 stages in the life cycle of the acridid grasshopper Chorthippus biguttulus. Samples from different stages encompassing embryonic development through adults were used for transcriptomic profiling, revealing patterns of differential gene expression that highlight processes in the different life stages. These patterns were validated with semi-quantitative RT-PCR. Embryonic development showed a strongly differentiated expression pattern compared to all of the other stages and genes upregulated in this stage were involved in signaling, cellular differentiation, and organ development. Our study is one of the first to examine gene expression during post-embryonic development in a hemimetabolous insect and we found that only the fourth and fifth instars had clusters of genes upregulated during these stages. These genes are involved in various processes ranging from synthesis of biogenic amines to chitin binding. These observations indicate that post-embryonic ontogeny is not a continuous process and that some instars are differentiated. Finally, genes upregulated in the imago were generally involved in aging and immunity. Our study highlights the importance of looking at ontogeny as a whole and indicates promising directions for future research in orthopteran development.

  18. Chromosomal clustering of a human transcriptome reveals regulatory background

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    Purmann Antje

    2005-09-01

    Full Text Available Abstract Background There has been much evidence recently for a link between transcriptional regulation and chromosomal gene order, but the relationship between genomic organization, regulation and gene function in higher eukaryotes remains to be precisely defined. Results Here, we present evidence for organization of a large proportion of a human transcriptome into gene clusters throughout the genome, which are partly regulated by the same transcription factors, share biological functions and are characterized by non-housekeeping genes. This analysis was based on the cardiac transcriptome identified by our genome-wide array analysis of 55 human heart samples. We found 37% of these genes to be arranged mainly in adjacent pairs or triplets. A significant number of pairs of adjacent genes are putatively regulated by common transcription factors (p = 0.02. Furthermore, these gene pairs share a significant number of GO functional classification terms. We show that the human cardiac transcriptome is organized into many small clusters across the whole genome, rather than being concentrated in a few larger clusters. Conclusion Our findings suggest that genes expressed in concert are organized in a linear arrangement for coordinated regulation. Determining the relationship between gene arrangement, regulation and nuclear organization as well as gene function will have broad biological implications.

  19. Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

    Directory of Open Access Journals (Sweden)

    Jennifer A Mitchell

    Full Text Available In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs.

  20. Whole transcriptome organisation in the dehydrated supraoptic nucleus

    Directory of Open Access Journals (Sweden)

    C.C.T. Hindmarch

    2013-12-01

    Full Text Available The supraoptic nucleus (SON is part of the central osmotic circuitry that synthesises the hormone vasopressin (Avp and transports it to terminals in the posterior lobe of the pituitary. Following osmotic stress such as dehydration, this tissue undergoes morphological, electrical and transcriptional changes to facilitate the appropriate regulation and release of Avp into the circulation where it conserves water at the level of the kidney. Here, the organisation of the whole transcriptome following dehydration is modelled to fit Zipf's law, a natural power law that holds true for all natural languages, that states if the frequency of word usage is plotted against its rank, then the log linear regression of this is -1. We have applied this model to our previously published euhydrated and dehydrated SON data to observe this trend and how it changes following dehydration. In accordance with other studies, our whole transcriptome data fit well with this model in the euhydrated SON microarrays, but interestingly, fit better in the dehydrated arrays. This trend was observed in a subset of differentially regulated genes and also following network reconstruction using a third-party database that mines public data. We make use of language as a metaphor that helps us philosophise about the role of the whole transcriptome in providing a suitable environment for the delivery of Avp following a survival threat like dehydration.

  1. Transgenerational epigenetic programming of the brain transcriptome and anxiety behavior.

    Directory of Open Access Journals (Sweden)

    Michael K Skinner

    Full Text Available Embryonic exposure to the endocrine disruptor vinclozolin during gonadal sex determination promotes an epigenetic reprogramming of the male germ-line that is associated with transgenerational adult onset disease states. Further analysis of this transgenerational phenotype on the brain demonstrated reproducible changes in the brain transcriptome three generations (F3 removed from the exposure. The transgenerational alterations in the male and female brain transcriptomes were distinct. In the males, the expression of 92 genes in the hippocampus and 276 genes in the amygdala were transgenerationally altered. In the females, the expression of 1,301 genes in the hippocampus and 172 genes in the amygdala were transgenerationally altered. Analysis of specific gene sets demonstrated that several brain signaling pathways were influenced including those involved in axon guidance and long-term potentiation. An investigation of behavior demonstrated that the vinclozolin F3 generation males had a decrease in anxiety-like behavior, while the females had an increase in anxiety-like behavior. These observations demonstrate that an embryonic exposure to an environmental compound appears to promote a reprogramming of brain development that correlates with transgenerational sex-specific alterations in the brain transcriptomes and behavior. Observations are discussed in regards to environmental and transgenerational influences on the etiology of brain disease.

  2. Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes

    Directory of Open Access Journals (Sweden)

    Rebecca M. Davidson

    2011-11-01

    Full Text Available Transcriptome sequencing is a powerful method for studying global expression patterns in large, complex genomes. Evaluation of sequence-based expression profiles during reproductive development would provide functional annotation to genes underlying agronomic traits. We generated transcriptome profiles for 12 diverse maize ( L. reproductive tissues representing male, female, developing seed, and leaf tissues using high throughput transcriptome sequencing. Overall, ∼80% of annotated genes were expressed. Comparative analysis between sequence and hybridization-based methods demonstrated the utility of ribonucleic acid sequencing (RNA-seq for expression determination and differentiation of paralagous genes (∼85% of maize genes. Analysis of 4975 gene families across reproductive tissues revealed expression divergence is proportional to family size. In all pairwise comparisons between tissues, 7 (pre- vs. postemergence cobs to 48% (pollen vs. ovule of genes were differentially expressed. Genes with expression restricted to a single tissue within this study were identified with the highest numbers observed in leaves, endosperm, and pollen. Coexpression network analysis identified 17 gene modules with complex and shared expression patterns containing many previously described maize genes. The data and analyses in this study provide valuable tools through improved gene annotation, gene family characterization, and a core set of candidate genes to further characterize maize reproductive development and improve grain yield potential.

  3. Coevolutionary genetic variation in the legume-rhizobium transcriptome.

    Science.gov (United States)

    Heath, Katy D; Burke, Patricia V; Stinchcombe, John R

    2012-10-01

    Coevolutionary change requires reciprocal selection between interacting species, where the partner genotypes that are favoured in one species depend on the genetic composition of the interacting species. Coevolutionary genetic variation is manifested as genotype × genotype (G × G) interactions for fitness in interspecific interactions. Although quantitative genetic approaches have revealed abundant evidence for G × G interactions in symbioses, the molecular basis of this variation remains unclear. Here we study the molecular basis of G × G interactions in a model legume-rhizobium mutualism using gene expression microarrays. We find that, like quantitative traits such as fitness, variation in the symbiotic transcriptome may be partitioned into additive and interactive genetic components. Our results suggest that plant genetic variation had the largest influence on nodule gene expression and that plant genotype and the plant genotype × rhizobium genotype interaction determine global shifts in rhizobium gene expression that in turn feedback to influence plant fitness benefits. Moreover, the transcriptomic variation we uncover implicates regulatory changes in both species as drivers of symbiotic gene expression variation. Our study is the first to partition genetic variation in a symbiotic transcriptome and illuminates potential molecular routes of coevolutionary change. © 2012 Blackwell Publishing Ltd.

  4. Alternative Approach to Traumatic Stensen’s Duct Injuries Accompanied by Glandular Involvement: Botulinum Toxin Injection to the Gland in Conjunction with Microsurgical Repair of the Duct in an Acute Setting

    Directory of Open Access Journals (Sweden)

    Mert Çalış

    2017-12-01

    Full Text Available Objective: The aim of this study was to evaluate the long-term results of a simultaneous application of botulinum toxin to the parotid gland in conjunction with the microsurgical repair of the duct in an acute setting and to encourage using botulinum toxin as a first-line option to prevent future complications associated with glandular involvement. Material and Methods: Three patients who were referred to the Plastic Surgery Clinic by the emergency room of the Hacettepe University Hospital after maxillofacial trauma are reviewed in this study. Exploration of the facial nerve and Stensen’s duct was planned for all patients within the first 72 hours after their injuries. After intraoral catheterization of the Stensen’s duct through the papilla using an epidural catheter, microsurgical end-to-end anastomosis was performed. Concurrently, 100 units of botulinum toxin A was injected at standardized eight points to the parotid gland. Results: Postoperative magnetic resonance (MR sialography revealed patency in all patients at the end of postoperative first year. The mean postoperative parotid volume of the injured and non-injured sides were 19.82±10.55 cm3 and 17.79±10.98 cm3, respectively, and the results were found to be comparable. Fibrillation potentials in the postoperative electromyography recordings and clinical examination demonstrated nerve regeneration. Conclusion: Botulinum toxin A appears to be effective in treating duct injuries accompanied by glandular involvement in an acute setting, as well as in preventing long-term complications.

  5. Integrated transcriptomic and proteomic evaluation of gentamicin nephrotoxicity in rats

    International Nuclear Information System (INIS)

    Com, Emmanuelle; Boitier, Eric; Marchandeau, Jean-Pierre; Brandenburg, Arnd; Schroeder, Susanne; Hoffmann, Dana; Mally, Angela; Gautier, Jean-Charles

    2012-01-01

    Gentamicin is an aminoglycoside antibiotic, which induces renal tubular necrosis in rats. In the context of the European InnoMed PredTox project, transcriptomic and proteomic studies were performed to provide new insights into the molecular mechanisms of gentamicin-induced nephrotoxicity. Male Wistar rats were treated with 25 and 75 mg/kg/day subcutaneously for 1, 3 and 14 days. Histopathology observations showed mild tubular degeneration/necrosis and regeneration and moderate mononuclear cell infiltrate after long-term treatment. Transcriptomic data indicated a strong treatment-related gene expression modulation in kidney and blood cells at the high dose after 14 days of treatment, with the regulation of 463 and 3241 genes, respectively. Of note, the induction of NF-kappa B pathway via the p38 MAPK cascade in the kidney, together with the activation of T-cell receptor signaling in blood cells were suggestive of inflammatory processes in relation with the recruitment of mononuclear cells in the kidney. Proteomic results showed a regulation of 163 proteins in kidney at the high dose after 14 days of treatment. These protein modulations were suggestive of a mitochondrial dysfunction with impairment of cellular energy production, induction of oxidative stress, an effect on protein biosynthesis and on cellular assembly and organization. Proteomic results also provided clues for potential nephrotoxicity biomarkers such as AGAT and PRBP4 which were strongly modulated in the kidney. Transcriptomic and proteomic data turned out to be complementary and their integration gave a more comprehensive insight into the putative mode of nephrotoxicity of gentamicin which was in accordance with histopathological findings. -- Highlights: ► Gentamicin induces renal tubular necrosis in rats. ► The mechanisms of gentamicin nephrotoxicity remain still elusive. ► Transcriptomic and proteomic analyses were performed to study this toxicity in rats. ► Transcriptomic and proteomic

  6. Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Arbeitman Michelle N

    2011-07-01

    Full Text Available Abstract Background Understanding animal development and physiology at a molecular-biological level has been advanced by the ability to determine at high resolution the repertoire of mRNA molecules by whole transcriptome resequencing. This includes the ability to detect and quantify rare abundance transcripts and isoform-specific mRNA variants produced from a gene. The sex hierarchy consists of a pre-mRNA splicing cascade that directs the production of sex-specific transcription factors that specify nearly all sexual dimorphism. We have used deep RNA sequencing to gain insight into how the Drosophila sex hierarchy generates somatic sex differences, by examining gene and transcript isoform expression differences between the sexes in adult head tissues. Results Here we find 1,381 genes that differ in overall expression levels and 1,370 isoform-specific transcripts that differ between males and females. Additionally, we find 512 genes not regulated downstream of transformer that are significantly more highly expressed in males than females. These 512 genes are enriched on the × chromosome and reside adjacent to dosage compensation complex entry sites, which taken together suggests that their residence on the × chromosome might be sufficient to confer male-biased expression. There are no transcription unit structural features, from a set of features, that are robustly significantly different in the genes with significant sex differences in the ratio of isoform-specific transcripts, as compared to random isoform-specific transcripts, suggesting that there is no single molecular mechanism that generates isoform-specific transcript differences between the sexes, even though the sex hierarchy is known to include three pre-mRNA splicing factors. Conclusions We identify thousands of genes that show sex-specific differences in overall gene expression levels, and identify hundreds of additional genes that have differences in the abundance of isoform

  7. Transcriptomic signatures shaped by cell proportions shed light on comparative developmental biology

    Czech Academy of Sciences Publication Activity Database

    Pantalacci, S.; Gueguen, L.; Petit, C.; Lambert, A.; Peterková, Renata; Sémon, E.

    2017-01-01

    Roč. 18, feb (2017), s. 29 ISSN 1474-760X R&D Projects: GA ČR(CZ) GB14-37368G Institutional support: RVO:68378041 Keywords : comparative transcriptomics * developmental biology * transcriptomic signature Subject RIV: EA - Cell Biology OBOR OECD: Developmental biology Impact factor: 11.908, year: 2016

  8. Transcriptomic impacts of rumen epithelium induced by butyrate infusion in dairy cattle in dry period

    Science.gov (United States)

    Transcriptomics and bioinformatics are utilized to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion. Butyrate, as an essential element of nutrients, is an HDAC inhibitor that can alter histone acetylation and methyl...

  9. Researches on Transcriptome Sequencing in the Study of Traditional Chinese Medicine

    Science.gov (United States)

    Xin, Jie; Zhang, Rong-chao; Wang, Lei

    2017-01-01

    Due to its incomparable advantages, the application of transcriptome sequencing in the study of traditional Chinese medicine attracts more and more attention of researchers, which greatly promote the development of traditional Chinese medicine. In this paper, the applications of transcriptome sequencing in traditional Chinese medicine were summarized by reviewing recent related papers. PMID:28900463

  10. A whole-blood transcriptome meta-analysis identifies gene expression signatures of cigarette smoking

    NARCIS (Netherlands)

    Huan, T. (Tianxiao); R. Joehanes (Roby); C. Schurmann (Claudia); K. Schramm (Katharina); L.C. Pilling (Luke); M.J. Peters (Marjolein); R. Mägi (Reedik); D.L. Demeo (Dawn L.); G.T. O'Connor (George); L. Ferrucci (Luigi); A. Teumer (Alexander); G. Homuth (Georg); R. Biffar (Reiner); U. Völker (Uwe); C. Herder (Christian); M. Waldenberger (Melanie); A. Peters (Annette); S. Zeilinger (Sonja); A. Metspalu (Andres); A. Hofman (Albert); A.G. Uitterlinden (André); D.G. Hernandez (Dena); A. Singleton (Andrew); S. Bandinelli (Stefania); P.J. Munson (Peter); H. Lin (Honghuang); E.J. Benjamin (Emelia); T. Esko (Tõnu); H.J. Grabe (Hans Jörgen); H. Prokisch (Holger); J.B.J. van Meurs (Joyce); D. Melzer (David); D. Levy (Daniel)

    2016-01-01

    textabstractCigarette smoking is a leading modifiable cause of death worldwide. We hypothesized that cigarette smoking induces extensive transcriptomic changes that lead to target-organ damage and smoking-related diseases. We performed a metaanalysis of transcriptome-wide gene expression using whole

  11. Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish

    NARCIS (Netherlands)

    Palstra, A.P.; Beltran, S.; Burgerhout, E.; Brittijn, S.A.; Magnoni, L.J.; Henkel, C.V.; Jansen, A.; Thillart, G.E.E.J.M.; Spaink, H.P.; Planas, J.V.

    2013-01-01

    Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of

  12. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

    DEFF Research Database (Denmark)

    Nicolas, Pierre; Mäder, Ulrike; Dervyn, Etienne

    2012-01-01

    Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutrition...

  13. Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

    NARCIS (Netherlands)

    Nicolas, Pierre; Maeder, Ulrike; Dervyn, Etienne; Rochat, Tatiana; Leduc, Aurelie; Pigeonneau, Nathalie; Bidnenko, Elena; Marchadier, Elodie; Hoebeke, Mark; Aymerich, Stephane; Becher, Doerte; Bisicchia, Paola; Botella, Eric; Delumeau, Olivier; Doherty, Geoff; Denham, Emma L.; Fogg, Mark J.; Fromion, Vincent; Goelzer, Anne; Hansen, Annette; Haertig, Elisabeth; Harwood, Colin R.; Homuth, Georg; Jarmer, Hanne; Jules, Matthieu; Klipp, Edda; Le Chat, Ludovic; Lecointe, Francois; Lewis, Peter; Liebermeister, Wolfram; March, Anika; Mars, Ruben A. T.; Nannapaneni, Priyanka; Noone, David; Pohl, Susanne; Rinn, Bernd; Ruegheimer, Frank; Sappa, Praveen K.; Samson, Franck; Schaffer, Marc; Schwikowski, Benno; Steil, Leif; Stuelke, Joerg; Wiegert, Thomas; Devine, Kevin M.; Wilkinson, Anthony J.; van Dijl, Jan Maarten; Hecker, Michael; Voelker, Uwe; Bessieres, Philippe; Noirot, Philippe

    2012-01-01

    Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional

  14. Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse

    Directory of Open Access Journals (Sweden)

    Lauren L. Kordonowy

    2016-10-01

    Full Text Available Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and vas deferens of Peromyscus eremicus (Cactus mouse, a desert specialist. The transcriptome assembly process was optimized in order to produce a high quality and substantially complete annotated transcriptome. This composite transcriptome was generated to characterize the expressed transcripts in the male reproductive tract of P. eremicus, which will serve as a crucial resource for future research investigating our hypothesis that the male Cactus mouse possesses an adaptive reproductive phenotype to mitigate water-loss from ejaculate. This study reports genes under positive selection in the male Cactus mouse reproductive transcriptome relative to transcriptomes from Peromyscus maniculatus (deer mouse and Mus musculus. Thus, this study expands upon existing genetic research in this species, and we provide a high quality transcriptome to enable further explorations of our proposed hypothesis for male Cactus mouse reproductive adaptations to minimize seminal fluid loss.

  15. Fish-T1K (Transcriptomes of 1,000 Fishes) Project: large-scale transcriptome data for fish evolution studies.

    Science.gov (United States)

    Sun, Ying; Huang, Yu; Li, Xiaofeng; Baldwin, Carole C; Zhou, Zhuocheng; Yan, Zhixiang; Crandall, Keith A; Zhang, Yong; Zhao, Xiaomeng; Wang, Min; Wong, Alex; Fang, Chao; Zhang, Xinhui; Huang, Hai; Lopez, Jose V; Kilfoyle, Kirk; Zhang, Yong; Ortí, Guillermo; Venkatesh, Byrappa; Shi, Qiong

    2016-01-01

    Ray-finned fishes (Actinopterygii) represent more than 50 % of extant vertebrates and are of great evolutionary, ecologic and economic significance, but they are relatively underrepresented in 'omics studies. Increased availability of transcriptome data for these species will allow researchers to better understand changes in gene expression, and to carry out functional analyses. An international project known as the "Transcriptomes of 1,000 Fishes" (Fish-T1K) project has been established to generate RNA-seq transcriptome sequences for 1,000 diverse species of ray-finned fishes. The first phase of this project has produced transcriptomes from more than 180 ray-finned fishes, representing 142 species and covering 51 orders and 109 families. Here we provide an overview of the goals of this project and the work done so far.

  16. A first insight into Pycnoporus sanguineus BAFC 2126 transcriptome.

    Directory of Open Access Journals (Sweden)

    Cristian O Rohr

    Full Text Available Fungi of the genus Pycnoporus are white-rot basidiomycetes widely studied because of their ability to synthesize high added-value compounds and enzymes of industrial interest. Here we report the sequencing, assembly and analysis of the transcriptome of Pycnoporus sanguineus BAFC 2126 grown at stationary phase, in media supplemented with copper sulfate. Using the 454 pyrosequencing platform we obtained a total of 226,336 reads (88,779,843 bases that were filtered and de novo assembled to generate a reference transcriptome of 7,303 transcripts. Putative functions were assigned for 4,732 transcripts by searching similarities of six-frame translated sequences against a customized protein database and by the presence of conserved protein domains. Through the analysis of translated sequences we identified transcripts encoding 178 putative carbohydrate active enzymes, including representatives of 15 families with roles in lignocellulose degradation. Furthermore, we found many transcripts encoding enzymes related to lignin hydrolysis and modification, including laccases and peroxidases, as well as GMC oxidoreductases, copper radical oxidases and other enzymes involved in the generation of extracellular hydrogen peroxide and iron homeostasis. Finally, we identified the transcripts encoding all of the enzymes involved in terpenoid backbone biosynthesis pathway, various terpene synthases related to the biosynthesis of sesquiterpenoids and triterpenoids precursors, and also cytochrome P450 monooxygenases, glutathione S-transferases and epoxide hydrolases with potential functions in the biodegradation of xenobiotics and the enantioselective biosynthesis of biologically active drugs. To our knowledge this is the first report of a transcriptome of genus Pycnoporus and a resource for future molecular studies in P. sanguineus.

  17. Transcriptomic Response of Chinese Yew (Taxus chinensis to Cold Stress

    Directory of Open Access Journals (Sweden)

    Xianghua Yu

    2017-04-01

    Full Text Available Taxus chinensis is a rare and endangered shrub, highly sensitive to temperature changes and widely known for its potential in cancer treatment. How gene expression of T. chinensis responds to low temperature is still unknown. To investigate cold response of the genus Taxus, we obtained the transcriptome profiles of T. chinensis grown under normal and low temperature (cold stress, 0°C conditions using Illumina Miseq sequencing. A transcriptome including 83,963 transcripts and 62,654 genes were assembled from 4.16 Gb of reads data. Comparative transcriptomic analysis identified 2,025 differently expressed (DE isoforms at p < 0.05, of which 1,437 were up-regulated by cold stress and 588 were down-regulated. Annotation of DE isoforms indicated that transcription factors (TFs in the MAPK signaling pathway and TF families of NAC, WRKY, bZIP, MYB, and ERF were transcriptionally activated. This might have been caused by the accumulation of secondary messengers, such as reactive oxygen species (ROS and Ca2+. While accumulation of ROS will have caused damages to cells, our results indicated that to adapt to low temperatures T. chinensis employed a series of mechanisms to minimize these damages. The mechanisms included: (i cold-enhanced expression of ROS deoxidant systems, such as peroxidase and phospholipid hydroperoxide glutathione peroxidase, to remove ROS. This was further confirmed by analyses showing increased activity of POD, SOD, and CAT under cold stress. (ii Activation of starch and sucrose metabolism, thiamine metabolism, and purine metabolism by cold-stress to produce metabolites which either protect cell organelles or lower the ROS content in cells. These processes are regulated by ROS signaling, as the “feedback” toward ROS accumulation.

  18. Perspectives on the use of transcriptomics to advance biofuels

    Directory of Open Access Journals (Sweden)

    Siseon Lee

    2015-11-01

    Full Text Available As a field within the energy research sector, bioenergy is continuously expanding. Although much has been achieved and the yields of both ethanol and butanol have been improved, many avenues of research to further increase these yields still remain. This review covers current research related with transcriptomics and the application of this high-throughput analytical tool to engineer both microbes and plants with the penultimate goal being better biofuel production and yields. The initial focus is given to the responses of fermentative microbes during the fermentative production of acids, such as butyric acid, and solvents, including ethanol and butanol. As plants offer the greatest natural renewable source of fermentable sugars within the form of lignocellulose, the second focus area is the transcriptional responses of microbes when exposed to plant hydrolysates and lignin-related compounds. This is of particular importance as the acid/base hydrolysis methods commonly employed to make the plant-based cellulose available for enzymatic hydrolysis to sugars also generates significant amounts of lignin-derivatives that are inhibitory to fermentative bacteria and microbes. The article then transitions to transcriptional analyses of lignin-degrading organisms, such as Phanerochaete chrysosporium, as an alternative to acid/base hydrolysis. The final portion of this article will discuss recent transcriptome analyses of plants and, in particular, the genes involved in lignin production. The rationale behind these studies is to eventually reduce the lignin content present within these plants and, consequently, the amount of inhibitors generated during the acid/base hydrolysis of the lignocelluloses. All four of these topics represent key areas where transcriptomic research is currently being conducted to identify microbial genes and their responses to products and inhibitors as well as those related with lignin degradation/formation.

  19. The draft genome and transcriptome of Cannabis sativa.

    Science.gov (United States)

    van Bakel, Harm; Stout, Jake M; Cote, Atina G; Tallon, Carling M; Sharpe, Andrew G; Hughes, Timothy R; Page, Jonathan E

    2011-10-20

    Cannabis sativa has been cultivated throughout human history as a source of fiber, oil and food, and for its medicinal and intoxicating properties. Selective breeding has produced cannabis plants for specific uses, including high-potency marijuana strains and hemp cultivars for fiber and seed production. The molecular biology underlying cannabinoid biosynthesis and other traits of interest is largely unexplored. We sequenced genomic DNA and RNA from the marijuana strain Purple Kush using shortread approaches. We report a draft haploid genome sequence of 534 Mb and a transcriptome of 30,000 genes. Comparison of the transcriptome of Purple Kush with that of the hemp cultivar 'Finola' revealed that many genes encoding proteins involved in cannabinoid and precursor pathways are more highly expressed in Purple Kush than in 'Finola'. The exclusive occurrence of Δ9-tetrahydrocannabinolic acid synthase in the Purple Kush transcriptome, and its replacement by cannabidiolic acid synthase in 'Finola', may explain why the psychoactive cannabinoid Δ9-tetrahydrocannabinol (THC) is produced in marijuana but not in hemp. Resequencing the hemp cultivars 'Finola' and 'USO-31' showed little difference in gene copy numbers of cannabinoid pathway enzymes. However, single nucleotide variant analysis uncovered a relatively high level of variation among four cannabis types, and supported a separation of marijuana and hemp. The availability of the Cannabis sativa genome enables the study of a multifunctional plant that occupies a unique role in human culture. Its availability will aid the development of therapeutic marijuana strains with tailored cannabinoid profiles and provide a basis for the breeding of hemp with improved agronomic characteristics.

  20. Transcriptome and proteome analysis of Eucalyptus infected with Calonectria pseudoreteaudii.

    Science.gov (United States)

    Chen, Quanzhu; Guo, Wenshuo; Feng, Lizhen; Ye, Xiaozhen; Xie, Wanfeng; Huang, Xiuping; Liu, Jinyan

    2015-02-06

    Cylindrocladium leaf blight is one of the most severe diseases in Eucalyptus plantations and nurseries. There are Eucalyptus cultivars with resistance to the disease. However, little is known about the defense mechanism of resistant cultivars. Here, we investigated the transcriptome and proteome of Eucalyptus leaves (E. urophylla×E. tereticornis M1), infected or not with Calonectria pseudoreteaudii. A total of 8585 differentially expressed genes (|log2 ratio| ≥1, FDR ≤0.001) at 12 and 24hours post-inoculation were detected using RNA-seq. Transcriptional changes for five genes were further confirmed by qRT-PCR. A total of 3680 proteins at the two time points were identified using iTRAQ technique.The combined transcriptome and proteome analysis revealed that the shikimate/phenylpropanoid pathway, terpenoid biosynthesis, signalling pathway (jasmonic acid and sugar) were activated. The data also showed that some proteins (WRKY33 and PR proteins) which have been reported to involve in plant defense response were up-regulated. However, photosynthesis, nucleic acid metabolism and protein metabolism were impaired by the infection of C. pseudoreteaudii. This work will facilitate the identification of defense related genes and provide insights into Eucalyptus defense responses to Cylindrocladium leaf blight. In this study, a total of 130 proteins and genes involved in the shikimate/phenylpropanoid pathway, terpenoid biosynthesis, signalling pathway, cell transport, carbohydrate and energy metabolism, nucleic acid metabolism and protein metabolism in Eucalyptus leaves after infected with C. pseudoreteaudii were identified. This is the first report of a comprehensive transcriptomic and proteomic analysis of Eucalyptus in response to Calonectria sp. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Construction of coffee transcriptome networks based on gene annotation semantics

    Directory of Open Access Journals (Sweden)

    Castillo Luis F.

    2012-12-01

    Full Text Available Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models. When thousands of gene models are being described in an organism genome, construction and visualization of gene networks impose novel challenges in the understanding of complex expression patterns and the generation of new knowledge in genomics research. In order to take advantage of accumulated text data after conventional gene sequence analysis, this work applied semantics in combination with visualization tools to build transcriptome networks from a set of coffee gene annotations. A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST and Interproscan, were filtered out by coverage, identity, length of the query, and e-values. Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF using Ruby scripts and Methontology to find associations between concepts. Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations. A large gene network connecting transcripts by way of relational concepts was created where detailed connections remain to be validated for biological significance based on current biochemical and genetics frameworks. Besides reusing text information in the generation of gene connections and for data mining purposes, this tool development opens the possibility to visualize complex and abundant transcriptome data, and triggers the formulation of new hypotheses in metabolic pathways analysis.

  2. Transcriptomic analysis of flower development in wintersweet (Chimonanthus praecox).

    Science.gov (United States)

    Liu, Daofeng; Sui, Shunzhao; Ma, Jing; Li, Zhineng; Guo, Yulong; Luo, Dengpan; Yang, Jianfeng; Li, Mingyang

    2014-01-01

    Wintersweet (Chimonanthus praecox) is familiar as a garden plant and woody ornamental flower. On account of its unique flowering time and strong fragrance, it has a high ornamental and economic value. Despite a long history of human cultivation, our understanding of wintersweet genetics and molecular biology remains scant, reflecting a lack of basic genomic and transcriptomic data. In this study, we assembled three cDNA libraries, from three successive stages in flower development, designated as the flower bud with displayed petal, open flower and senescing flower stages. Using the Illumina RNA-Seq method, we obtained 21,412,928, 26,950,404, 24,912,954 qualified Illumina reads, respectively, for the three successive stages. The pooled reads from all three libraries were then assembled into 106,995 transcripts, 51,793 of which were annotated in the NCBI non-redundant protein database. Of these annotated sequences, 32,649 and 21,893 transcripts were assigned to gene ontology categories and clusters of orthologous groups, respectively. We could map 15,587 transcripts onto 312 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at the open flower and senescing flower stages. An analysis of differentially expressed genes involved in plant hormone signal transduction pathways indicated that although flower opening and senescence may be independent of the ethylene signaling pathway in wintersweet, salicylic acid may be involved in the regulation of flower senescence. We also succeeded in isolating key genes of floral scent biosynthesis and proposed a biosynthetic pathway for monoterpenes and sesquiterpenes in wintersweet flowers, based on the annotated sequences. This comprehensive transcriptomic analysis presents fundamental information on the genes and pathways which are involved in flower development in wintersweet. And our data

  3. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L..

    Directory of Open Access Journals (Sweden)

    Chandra Kant

    Full Text Available A hallmark trait of chickpea (Cicer arietinum L., like other legumes, is the capability to convert atmospheric nitrogen (N2 into ammonia (NH3 in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO, Cluster of Orthologous Groups (COG and Kyoto Encyclopedia of Genes and Genomes (KEGG metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.

  4. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata

    2016-01-01

    A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea.

  5. Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

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    Cseke Leland J

    2011-05-01

    Full Text Available Abstract Background Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. Results We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. Conclusions The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.

  6. The past, present, and future of Leishmania genomics and transcriptomics

    Science.gov (United States)

    Cantacessi, Cinzia; Dantas-Torres, Filipe; Nolan, Matthew J.; Otranto, Domenico

    2015-01-01

    It has been nearly 10 years since the completion of the first entire genome sequence of a Leishmania parasite. Genomic and transcriptomic analyses have advanced our understanding of the biology of Leishmania, and shed new light on the complex interactions occurring within the parasite–host–vector triangle. Here, we review these advances and examine potential avenues for translation of these discoveries into treatment and control programs. In addition, we argue for a strong need to explore how disease in dogs relates to that in humans, and how an improved understanding in line with the ‘One Health’ concept may open new avenues for the control of these devastating diseases. PMID:25638444

  7. Transcriptome profiling of tobacco under water deficit conditions

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    Roel C. Rabara

    2015-09-01

    Full Text Available Drought is one of the limiting environmental factors that affect crop production. Understanding the molecular basis of how plants respond to this water deficit stress is key to developing drought tolerant crops. In this study we generated time course-based transcriptome profiles of tobacco plants under water deficit conditions using microarray technology. In this paper, we describe in detail the experimental procedures and analyses performed in our study. The data set we generated (available in the NCBI/GEO database under GSE67434 has been analysed to identify genes that are involved in the regulation of tobacco's responses to drought.

  8. Ovary transcriptome profiling via artificial intelligence reveals a transcriptomic fingerprint predicting egg quality in striped bass, Morone saxatilis.

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    Robert W Chapman

    Full Text Available Inherited gene transcripts deposited in oocytes direct early embryonic development in all vertebrates, but transcript profiles indicative of embryo developmental competence have not previously been identified. We employed artificial intelligence to model profiles of maternal ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in the striped bass (Morone saxatilis, a farmed species with serious egg quality problems. In models developed using artificial neural networks (ANNs and supervised machine learning, collective changes in the expression of a limited suite of genes (233 representing 90% of the eventual variance in embryo survival. Egg quality related to minor changes in gene expression (<0.2-fold, with most individual transcripts making a small contribution (<1% to the overall prediction of egg quality. These findings indicate that the predictive power of the transcriptome as regards egg quality resides not in levels of individual genes, but rather in the collective, coordinated expression of a suite of transcripts constituting a transcriptomic "fingerprint". Correlation analyses of the corresponding candidate genes indicated that dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence. The affected gene networks are centrally involved in regulation of early development in all vertebrates, including humans. By assessing collective levels of the relevant ovarian transcripts via ANNs we were able, for the first time in any vertebrate, to accurately predict the subsequent embryo developmental potential of eggs from individual females. Our results show that the transcriptomic fingerprint evidencing developmental dysfunction is highly predictive of, and therefore likely to regulate, egg quality, a biologically complex trait crucial to reproductive fitness.

  9. Transcriptomics and comparative analysis of three antarctic notothenioid fishes.

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    Seung Chul Shin

    Full Text Available For the past 10 to 13 million years, Antarctic notothenioid fish have undergone extraordinary periods of evolution and have adapted to a cold and highly oxygenated Antarctic marine environment. While these species are considered an attractive model with which to study physiology and evolutionary adaptation, they are poorly characterized at the molecular level, and sequence information is lacking. The transcriptomes of the Antarctic fishes Notothenia coriiceps, Chaenocephalus aceratus, and Pleuragramma antarcticum were obtained by 454 FLX Titanium sequencing of a normalized cDNA library. More than 1,900,000 reads were assembled in a total of 71,539 contigs. Overall, 40% of the contigs were annotated based on similarity to known protein or nucleotide sequences, and more than 50% of the predicted transcripts were validated as full-length or putative full-length cDNAs. These three Antarctic fishes shared 663 genes expressed in the brain and 1,557 genes expressed in the liver. In addition, these cold-adapted fish expressed more Ub-conjugated proteins compared to temperate fish; Ub-conjugated proteins are involved in maintaining proteins in their native state in the cold and thermally stable Antarctic environments. Our transcriptome analysis of Antarctic notothenioid fish provides an archive for future studies in molecular mechanisms of fundamental genetic questions, and can be used in evolution studies comparing other fish.

  10. Similarities between Reproductive and Immune Pistil Transcriptomes of Arabidopsis Species.

    Science.gov (United States)

    Mondragón-Palomino, Mariana; John-Arputharaj, Ajay; Pallmann, Maria; Dresselhaus, Thomas

    2017-07-01

    Independent lines of evidence suggest that members from ancient and polymorphic gene families such as defensins and receptor-like kinases mediate intercellular communication during both the immune response and reproduction. Here, we report a large-scale analysis to investigate the extent of overlap between these processes by comparing differentially expressed genes (DEGs) in the pistil transcriptomes of Arabidopsis thaliana and Arabidopsis halleri during self-pollination and interspecific pollination and during infection with Fusarium graminearum In both Arabidopsis species, the largest number of DEGs was identified in infected pistils, where genes encoding regulators of cell division and development were most frequently down-regulated. Comparison of DEGs between infection and various pollination conditions showed that up to 79% of down-regulated genes are shared between conditions and include especially defensin-like genes. Interspecific pollination of A. thaliana significantly up-regulated thionins and defensins. The significant overrepresentation of similar groups of DEGs in the transcriptomes of reproductive and immune responses of the pistil makes it a prime system in which to study the consequences of plant-pathogen interactions on fertility and the evolution of intercellular communication in pollination. © 2017 American Society of Plant Biologists. All Rights Reserved.

  11. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae

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    Samuel E. Fox

    2013-03-01

    Full Text Available Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis, 104,950 (Spain, and 177,682 (Greece transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum. The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium sylvaticum sequence reads aligned against the Bd21 genome revealed 394,654 single-nucleotide polymorphisms (SNPs and >20,000 simple sequence repeat (SSR DNA sites. Conclusions: To our knowledge, this is the first report of transcriptome sequencing of invasive plant species with a closely related sequenced reference genome. The sequences and identified SNP variant and SSR sites will provide tools for developing novel genetic markers for use in genotyping and characterization of invasive behavior of B. sylvaticum.

  12. Transcriptome analysis of Haloquadratum walsbyi: vanity is but the surface.

    Science.gov (United States)

    Bolhuis, Henk; Martín-Cuadrado, Ana Belén; Rosselli, Riccardo; Pašić, Lejla; Rodriguez-Valera, Francisco

    2017-07-03

    Haloquadratum walsbyi dominates saturated thalassic lakes worldwide where they can constitute up to 80-90% of the total prokaryotic community. Despite the abundance of the enigmatic square-flattened cells, only 7 isolates are currently known with 2 genomes fully sequenced and annotated due to difficulties to grow them under laboratory conditions. We have performed a transcriptomic analysis of one of these isolates, the Spanish strain HBSQ001 in order to investigate gene transcription under light and dark conditions. Despite a potential advantage for light as additional source of energy, no significant differences were found between light and dark expressed genes. Constitutive high gene expression was observed in genes encoding surface glycoproteins, light mediated proton pumping by bacteriorhodopsin, several nutrient uptake systems, buoyancy and storage of excess carbon. Two low expressed regions of the genome were characterized by a lower codon adaptation index, low GC content and high incidence of hypothetical genes. Under the extant cultivation conditions, the square hyperhalophile devoted most of its transcriptome towards processes maintaining cell integrity and exploiting solar energy. Surface glycoproteins are essential for maintaining the large surface to volume ratio that facilitates light and organic nutrient harvesting whereas constitutive expression of bacteriorhodopsin warrants an immediate source of energy when light becomes available.

  13. Spatial transcriptomes within the Pseudomonas aeruginosa biofilm architecture.

    Science.gov (United States)

    Heacock-Kang, Yun; Sun, Zhenxin; Zarzycki-Siek, Jan; McMillan, Ian A; Norris, Michael H; Bluhm, Andrew P; Cabanas, Darlene; Fogen, Dawson; Vo, Hung; Donachie, Stuart P; Borlee, Bradley R; Sibley, Christopher D; Lewenza, Shawn; Schurr, Michael J; Schweizer, Herbert P; Hoang, Tung T

    2017-12-01

    Bacterial cooperative associations and dynamics in biofilm microenvironments are of special interest in recent years. Knowledge of localized gene-expression and corresponding bacterial behaviors within the biofilm architecture at a global scale has been limited, due to a lack of robust technology to study limited number of cells in stratified layers of biofilms. With our recent pioneering developments in single bacterial cell transcriptomic analysis technology, we generated herein an unprecedented spatial transcriptome map of the mature in vitro Pseudomonas aeruginosa biofilm model, revealing contemporaneous yet altered bacterial behaviors at different layers within the biofilm architecture (i.e., surface, middle and interior of the biofilm). Many genes encoding unknown functions were highly expressed at the biofilm-solid interphase, exposing a critical gap in the knowledge of their activities that may be unique to this interior niche. Several genes of unknown functions are critical for biofilm formation. The in vivo importance of these unknown proteins was validated in invertebrate (fruit fly) and vertebrate (mouse) models. We envisage the future value of this report to the community, in aiding the further pathophysiological understanding of P. aeruginosa biofilms. Our approach will open doors to the study of bacterial functional genomics of different species in numerous settings. © 2017 The Authors. Molecular Microbiology Published by John Wiley & Sons Ltd.

  14. Leading edge analysis of transcriptomic changes during pseudorabies virus infection

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    Damarius S. Fleming

    2016-12-01

    Full Text Available Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO (GSE74473 database.

  15. Characterization of gonadal transcriptomes from the turbot (Scophthalmus maximus).

    Science.gov (United States)

    Hu, Yulong; Huang, Meng; Wang, Weiji; Guan, Jiantao; Kong, Jie

    2016-01-01

    The mechanisms underlying sexual reproduction and sex ratio determination remains unclear in turbot, a flatfish of great commercial value. And there is limited information in the turbot database regarding genes related to the reproductive system. Here, we conducted high-throughput transcriptome profiling of turbot gonad tissues to better understand their reproductive functions and to supply essential gene sequence information for marker-assisted selection programs in the turbot industry. In this study, two gonad libraries representing sex differences in Scophthalmus maximus yielded 453 818 high-quality reads that were assembled into 24 611 contigs and 33 713 singletons by using 454 pyrosequencing, 13 936 contigs and singletons (CS) of which were annotated using BLASTx. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analyses revealed that various biological functions and processes were associated with many of the annotated CS. Expression analyses showed that 510 genes were differentially expressed in males versus females; 80% of these genes were annotated. In addition, 6484 and 6036 single nucleotide polymorphisms (SNPs) were identified in male and female libraries, respectively. This transcriptome resource will serve as the foundation for cDNA or SNP microarray construction, gene expression characterization, and sex-specific linkage mapping in turbot.

  16. High-throughput sequencing of black pepper root transcriptome

    Science.gov (United States)

    2012-01-01

    Background Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms. PMID:22984782

  17. Differential Transcriptome Analysis between Paulownia fortunei and Its Synthesized Autopolyploid

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    Xiaoshen Zhang

    2014-03-01

    Full Text Available Paulownia fortunei is an ecologically and economically important tree species that is widely used as timber and chemical pulp. Its autotetraploid, which carries a number of valuable traits, was successfully induced with colchicine. To identify differences in gene expression between P. fortunei and its synthesized autotetraploid, we performed transcriptome sequencing using an Illumina Genome Analyzer IIx (GAIIx. About 94.8 million reads were generated and assembled into 383,056 transcripts, including 18,984 transcripts with a complete open reading frame. A conducted Basic Local Alignment Search Tool (BLAST search indicated that 16,004 complete transcripts had significant hits in the National Center for Biotechnology Information (NCBI non-redundant database. The complete transcripts were given functional assignments using three public protein databases. One thousand one hundred fifty eight differentially expressed complete transcripts were screened through a digital abundance analysis, including transcripts involved in energy metabolism and epigenetic regulation. Finally, the expression levels of several transcripts were confirmed by quantitative real-time PCR. Our results suggested that polyploidization caused epigenetic-related changes, which subsequently resulted in gene expression variation between diploid and autotetraploid P. fortunei. This might be the main mechanism affected by the polyploidization. Our results represent an extensive survey of the P. fortunei transcriptome and will facilitate subsequent functional genomics research in P. fortunei. Moreover, the gene expression profiles of P. fortunei and its autopolyploid will provide a valuable resource for the study of polyploidization.

  18. Transcriptomic Analysis of Young and Old Erythrocytes of Fish

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    Miriam Götting

    2017-12-01

    Full Text Available Understanding gene expression changes over the lifespan of cells is of fundamental interest and gives important insights into processes related to maturation and aging. This study was undertaken to understand the global transcriptome changes associated with aging in fish erythrocytes. Fish erythrocytes retain their nuclei throughout their lifetime and they are transcriptionally and translationally active. However, they lose important functions during their lifespan in the circulation. We separated rainbow trout (Oncorhynchus mykiss erythrocytes into young and old fractions using fixed angle-centrifugation and analyzed transcriptome changes using RNA sequencing (RNA-seq technology and quantitative real-time PCR. We found 930 differentially expressed between young and old erythrocyte fractions; 889 of these showed higher transcript levels in young, while only 34 protein-coding genes had higher transcript levels in old erythrocytes. In particular genes involved in ion binding, signal transduction, membrane transport, and those encoding various enzyme classes are affected in old erythrocytes. The transcripts with higher levels in old erythrocytes were associated with seven different GO terms within biological processes and nine within molecular functions and cellular components, respectively. Our study furthermore found several highly abundant transcripts as well as a number of differentially expressed genes (DEGs for which the protein products are currently not known revealing the gaps of knowledge in most non-mammalian vertebrates. Our data provide the first insight into changes involved in aging on the transcriptional level and thus opens new perspectives for the study of maturation processes in fish erythrocytes.

  19. Functional organization of the transcriptome in human brain

    Science.gov (United States)

    Oldham, Michael C; Konopka, Genevieve; Iwamoto, Kazuya; Langfelder, Peter; Kato, Tadafumi; Horvath, Steve; Geschwind, Daniel H

    2009-01-01

    The enormous complexity of the human brain ultimately derives from a finite set of molecular instructions encoded in the human genome. These instructions can be directly studied by exploring the organization of the brain’s transcriptome through systematic analysis of gene coexpression relationships. We analyzed gene coexpression relationships in microarray data generated from specific human brain regions and identified modules of coexpressed genes that correspond to neurons, oligodendrocytes, astrocytes and microglia. These modules provide an initial description of the transcriptional programs that distinguish the major cell classes of the human brain and indicate that cell type–specific information can be obtained from whole brain tissue without isolating homogeneous populations of cells. Other modules corresponded to additional cell types, organelles, synaptic function, gender differences and the subventricular neurogenic niche. We found that subventricular zone astrocytes, which are thought to function as neural stem cells in adults, have a distinct gene expression pattern relative to protoplasmic astrocytes. Our findings provide a new foundation for neurogenetic inquiries by revealing a robust and previously unrecognized organization to the human brain transcriptome. PMID:18849986

  20. Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Ciobanu, Doina; Clum, Alicia; Singh, Vasanth; Salamov, Asaf; Han, James; Copeland, Alex; Grigoriev, Igor; James, Timothy; Singer, Steven; Woyke, Tanja; Malmstrom, Rex; Cheng, Jan-Fang

    2014-03-14

    Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.

  1. De novo transcriptome assembly of Sorghum bicolor variety Taejin

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    Yeonhwa Jo

    2016-06-01

    Full Text Available Sorghum (Sorghum bicolor, also known as great millet, is one of the most popular cultivated grass species in the world. Sorghum is frequently consumed as food for humans and animals as well as used for ethanol production. In this study, we conducted de novo transcriptome assembly for sorghum variety Taejin by next-generation sequencing, obtaining 8.748 GB of raw data. The raw data in this study can be available in NCBI SRA database with accession number of SRX1715644. Using the Trinity program, we identified 222,161 transcripts from sorghum variety Taejin. We further predicted coding regions within the assembled transcripts by the TransDecoder program, resulting in a total of 148,531 proteins. We carried out BLASTP against the Swiss-Prot protein sequence database to annotate the functions of the identified proteins. To our knowledge, this is the first transcriptome data for a sorghum variety derived from Korea, and it can be usefully applied to the generation of genetic markers.

  2. Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

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    Nagesh A. Kuravadi

    2015-08-01

    Full Text Available Neem (Azadirachta indica A. Juss is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC. Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways.

  3. Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

    Science.gov (United States)

    Rangiah, Kannan; Mahesh, HB; Rajamani, Anantharamanan; Shirke, Meghana D.; Russiachand, Heikham; Loganathan, Ramya Malarini; Shankara Lingu, Chandana; Siddappa, Shilpa; Ramamurthy, Aishwarya; Sathyanarayana, BN

    2015-01-01

    Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways. PMID:26290780

  4. Application of transcriptomics in Chinese herbal medicine studies

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    Hsin-Yi Lo

    2012-04-01

    Full Text Available Transcriptomics using DNA microarray has become a practical and popular tool for herbal medicine study because of high throughput, sensitivity, accuracy, specificity, and reproducibility. Therefore, this article focuses on the overview of DNA microarray technology and the application of DNA microarray in Chinese herbal medicine study. To understand the number and the objectives of articles utilizing DNA microarray for herbal medicine study, we surveyed 297 frequently used Chinese medicinal herbs listed in Pharmacopoeia Commission of People’s Republic of China. We classified these medicinal herbs into 109 families and then applied PudMed search using “microarray” and individual herbal family as keywords. Although thousands of papers applying DNA microarray in Chinese herbal studies have been published since 1998, most of the articles focus on the elucidation of mechanisms of certain biological effects of herbs. Construction of the bioactivity database containing large-scaled gene expression profiles of quality control herbs can be applied in the future to analyze the biological events induced by herbs, predict the therapeutic potential of herbs, evaluate the safety of herbs, and identify the drug candidate of herbs. Moreover, the linkage of systems biology tools, such as functional genomics, transcriptomics, proteomics, metabolomics, pharmacogenomics and toxicogenomics, will become a new translational platform between Western medicine and Chinese herbal medicine.

  5. High-throughput sequencing of black pepper root transcriptome

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    Gordo Sheila MC

    2012-09-01

    Full Text Available Abstract Background Black pepper (Piper nigrum L. is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.

  6. De novo transcriptome assembly of Setatria italica variety Taejin

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2016-06-01

    Full Text Available Foxtail millet (Setaria italica belonging to the family Poaceae is an important millet that is widely cultivated in East Asia. Of the cultivated millets, the foxtail millet has the longest history and is one of the main food crops in South India and China. Moreover, foxtail millet is a model plant system for biofuel generation utilizing the C4 photosynthetic pathway. In this study, we carried out de novo transcriptome assembly for the foxtail millet variety Taejin collected from Korea using next-generation sequencing. We obtained a total of 8.676 GB raw data by paired-end sequencing. The raw data in this study can be available in NCBI SRA database with accession number of SRR3406552. The Trinity program was used to de novo assemble 145,332 transcripts. Using the TransDecoder program, we predicted 82,925 putative proteins. BLASTP was performed against the Swiss-Prot protein sequence database to annotate the functions of identified proteins, resulting in 20,555 potentially novel proteins. Taken together, this study provides transcriptome data for the foxtail millet variety Taejin by RNA-Seq.

  7. De novo transcriptome assembly of the mycoheterotrophic plant Monotropa hypopitys

    Directory of Open Access Journals (Sweden)

    Alexey V. Beletsky

    2017-03-01

    Full Text Available Monotropa hypopitys (pinesap is a non-photosynthetic obligately mycoheterotrophic plant of the family Ericaceae. It obtains the carbon and other nutrients from the roots of surrounding autotrophic trees through the associated mycorrhizal fungi. In order to understand the evolutionary changes in the plant genome associated with transition to a heterotrophic lifestyle, we performed de novo transcriptomic analysis of M. hypopitys using next-generation sequencing. We obtained the RNA-Seq data from flowers, flower bracts and roots with haustoria using Illumina HiSeq2500 platform. The raw data obtained in this study can be available in NCBI SRA database with accession number of SRP069226. A total of 10.3 GB raw sequence data were obtained, corresponding to 103,357,809 raw reads. A total of 103,025,683 reads were filtered after removing low-quality reads and trimming the adapter sequences. The Trinity program was used to de novo assemble 98,349 unigens with an N50 of 1342 bp. Using the TransDecoder program, we predicted 43,505 putative proteins. 38,416 unigenes were annotated in the Swiss-Prot protein sequence database using BLASTX. The obtained transcriptomic data will be useful for further studies of the evolution of plant genomes upon transition to a non-photosynthetic lifestyle and the loss of photosynthesis-related functions.

  8. Coral host transcriptomic states are correlated with Symbiodinium genotypes

    KAUST Repository

    DeSalvo, Michael K.

    2010-03-01

    A mutualistic relationship between reef-building corals and endosymbiotic dinoflagellates (Symbiodinium spp.) forms the basis for the existence of coral reefs. Genotyping tools for Symbiodinium spp. have added a new level of complexity to studies concerning cnidarian growth, nutrient acquisition, and stress. For example, the response of the coral holobiont to thermal stress is connected to the host-Symbiodinium genotypic combination, as different partnerships can have different bleaching susceptibilities. In this study, we monitored Symbiodinium physiological parameters and profiled the coral host transcriptional responses in acclimated, thermally stressed, and recovered fragments of the coral Montastraea faveolata using a custom cDNA gene expression microarray. Interestingly, gene expression was more similar among samples with the same Symbiodinium content rather than the same experimental condition. In order to discount for host-genotypic effects, we sampled fragments from a single colony of M. faveolata containing different symbiont types, and found that the host transcriptomic states grouped according to Symbiodinium genotype rather than thermal stress. As the first study that links coral host transcriptomic patterns to the clade content of their Symbiodinium community, our results provide a critical step to elucidating the molecular basis of the apparent variability seen among different coral-Symbiodinium partnerships. © 2010 Blackwell Publishing Ltd.

  9. Influence of Organic Farming on the Potato Transcriptome

    Directory of Open Access Journals (Sweden)

    Daniela Pacifico

    2017-05-01

    Full Text Available Organic agriculture sparks a lively debate on its potential health and environmental benefits. Comparative studies often investigate the response of crops to organic farming through targeted approaches and within a limited experimental work. To clarify this issue, the transcriptomic profile of a cultivar of the potato grown for two years under organic and conventional farming was compared with the profile of an experimental clone grown in the same location of Southern Italy for one year. Transcriptomic raw data were obtained through Potato Oligo Chip Initiative (POCI microarrays and were processed using unsupervised coupling multivariate statistical analysis and bioinformatics (MapMan software. One-hundred-forty-four genes showed the same expression in both years, and 113 showed the same expression in both genotypes. Their functional characterization revealed the strong involvement of the farming system in metabolism associated with the nutritional aspects of organic tubers (e.g., phenylpropanoid, flavonoid, glycoalcaloid, asparagine, ascorbic acid. Moreover, further investigation showed that eight of 42,034 features exhibited the same trend of expression irrespective of the year and genotype, making them possible candidates as markers of traceability. This paper raises the issue regarding the choice of genotype in organic management and the relevance of assessing seasonal conditions effects when studying the effects of organic cultivation on tuber metabolism.

  10. The head-regeneration transcriptome of the planarian Schmidtea mediterranea

    Science.gov (United States)

    2011-01-01

    Background Planarian flatworms can regenerate their head, including a functional brain, within less than a week. Despite the enormous potential of these animals for medical research and regenerative medicine, the mechanisms of regeneration and the molecules involved remain largely unknown. Results To identify genes that are differentially expressed during early stages of planarian head regeneration, we generated a de novo transcriptome assembly from more than 300 million paired-end reads from planarian fragments regenerating the head at 16 different time points. The assembly yielded 26,018 putative transcripts, including very long transcripts spanning multiple genomic supercontigs, and thousands of isoforms. Using short-read data from two platforms, we analyzed dynamic gene regulation during the first three days of head regeneration. We identified at least five different temporal synexpression classes, including genes specifically induced within a few hours after injury. Furthermore, we characterized the role of a conserved Runx transcription factor, smed-runt-like1. RNA interference (RNAi) knockdown and immunofluorescence analysis of the regenerating visual system indicated that smed-runt-like1 encodes a transcriptional regulator of eye morphology and photoreceptor patterning. Conclusions Transcriptome sequencing of short reads allowed for the simultaneous de novo assembly and differential expression analysis of transcripts, demonstrating highly dynamic regulation during head regeneration in planarians. PMID:21846378

  11. Transcriptomics and the Mediterranean Diet: A Systematic Review

    Science.gov (United States)

    Herrera-Marcos, Luis V.; Lou-Bonafonte, José M.; Arnal, Carmen; Navarro, María A.; Osada, Jesús

    2017-01-01

    The Mediterranean diet has been proven to be highly effective in the prevention of cardiovascular diseases and cancer and in decreasing overall mortality. Nowadays, transcriptomics is gaining particular relevance due to the existence of non-coding RNAs capable of regulating many biological processes. The present work describes a systematic review of current evidence supporting the influence of the Mediterranean diet on transcriptomes of different tissues in various experimental models. While information on regulatory RNA is very limited, they seem to contribute to the effect. Special attention has been given to the oily matrix of virgin olive oil. In this regard, monounsaturated fatty acid-rich diets prevented the expression of inflammatory genes in different tissues, an action also observed after the administration of olive oil phenolic compounds. Among these, tyrosol, hydroxytyrosol, and secoiridoids have been found to be particularly effective in cell cycle expression. Less explored terpenes, such as oleanolic acid, are important modulators of circadian clock genes. The wide range of studied tissues and organisms indicate that response to these compounds is universal and poses an important level of complexity considering the different genes expressed in each tissue and the number of different tissues in an organism. PMID:28486416

  12. The Transcriptomics of Secondary Growth and Wood Formation in Conifers

    Science.gov (United States)

    Carvalho, Ana; Paiva, Jorge; Louzada, José; Lima-Brito, José

    2013-01-01

    In the last years, forestry scientists have adapted genomics and next-generation sequencing (NGS) technologies to the search for candidate genes related to the transcriptomics of secondary growth and wood formation in several tree species. Gymnosperms, in particular, the conifers, are ecologically and economically important, namely, for the production of wood and other forestry end products. Until very recently, no whole genome sequencing of a conifer genome was available. Due to the gradual improvement of the NGS technologies and inherent bioinformatics tools, two draft assemblies of the whole genomes sequence of Picea abies and Picea glauca arose in the current year. These draft genome assemblies will bring new insights about the structure, content, and evolution of the conifer genomes. Furthermore, new directions in the forestry, breeding and research of conifers will be discussed in the following. The identification of genes associated with the xylem transcriptome and the knowledge of their regulatory mechanisms will provide less time-consuming breeding cycles and a high accuracy for the selection of traits related to wood production and quality. PMID:24288610

  13. Leading edge analysis of transcriptomic changes during pseudorabies virus infection.

    Science.gov (United States)

    Fleming, Damarius S; Miller, Laura C

    2016-12-01

    Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi) that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA) to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO) (GSE74473) database.

  14. Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers.

    Directory of Open Access Journals (Sweden)

    Yuichi Shiraishi

    Full Text Available Recent studies applying high-throughput sequencing technologies have identified several recurrently mutated genes and pathways in multiple cancer genomes. However, transcriptional consequences from these genomic alterations in cancer genome remain unclear. In this study, we performed integrated and comparative analyses of whole genomes and transcriptomes of 22 hepatitis B virus (HBV-related hepatocellular carcinomas (HCCs and their matched controls. Comparison of whole genome sequence (WGS and RNA-Seq revealed much evidence that various types of genomic mutations triggered diverse transcriptional changes. Not only splice-site mutations, but also silent mutations in coding regions, deep intronic mutations and structural changes caused splicing aberrations. HBV integrations generated diverse patterns of virus-human fusion transcripts depending on affected gene, such as TERT, CDK15, FN1 and MLL4. Structural variations could drive over-expression of genes such as WNT ligands, with/without creating gene fusions. Furthermore, by taking account of genomic mutations causing transcriptional aberrations, we could improve the sensitivity of deleterious mutation detection in known cancer driver genes (TP53, AXIN1, ARID2, RPS6KA3, and identified recurrent disruptio