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Sample records for glandular trichome transcriptome

  1. Differential transcriptome analysis of glandular and filamentous trichomes in Artemisia annua

    PubMed Central

    2013-01-01

    Background The medicinal plant Artemisia annua is covered with filamentous trichomes and glandular, artemisinin producing trichomes. A high artemisinin supply is needed at a reduced cost for treating malaria. Artemisinin production in bioreactors can be facilitated if a better insight is obtained in the biosynthesis of artemisinin and other metabolites. Therefore, metabolic activities of glandular and filamentous trichomes were investigated at the transcriptome level. Results By laser pressure catapulting, glandular and filamentous trichomes as well as apical and sub-apical cells from glandular trichomes were collected and their transcriptome was sequenced using Illumina RNA-Seq. A de novo transcriptome was assembled (Trinity) and studied with a differential expression analysis (edgeR). A comparison of the transcriptome from glandular and filamentous trichomes shows that MEP, MVA, most terpene and lipid biosynthesis pathways are significantly upregulated in glandular trichomes. Conversely, some transcripts coding for specific sesquiterpenoid and triterpenoid enzymes such as 8-epi-cedrol synthase and an uncharacterized oxidosqualene cyclase were significantly upregulated in filamentous trichomes. All known artemisinin biosynthesis genes are upregulated in glandular trichomes and were detected in both the apical and sub-apical cells of the glandular trichomes. No significant differential expression could be observed between the apical and sub-apical cells. Conclusions Our results underscore the vast metabolic capacities of A. annua glandular trichomes but nonetheless point to the existence of specific terpene metabolic pathways in the filamentous trichomes. Candidate genes that might be involved in artemisinin biosynthesis are proposed based on their putative function and their differential expression level. PMID:24359620

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

    PubMed

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

    2017-02-11

    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 was carried out. In addition to the MVA and MEP pathway genes, about 210 and 196 different terpene synthases (TPS) 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 (3 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. Abbreviations - AACT, acetyl-CoA C-acetyltransferase; CMK, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase; DGE, digital gene expression; DXR, 1-deoxy-D-xylulose-5-phosphate reductoisomerase; DXS, 1-deoxy-D-xylulose-5-phosphate synthase; FPPS, farnesyl pyrophosphate synthase; GC, gas chromatography; GPPS, geranyl pyrophosphate synthase; GT, glandular trichome; HDR, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; HDS, (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase; HMGR, 3-hydroxy-3-methylglutaryl-coenzyme A reductase; HMGS, hydroxymethylglutaryl-CoA synthase; IDI, isopentenyl-diphosphate delta-isomerase; IPD, isopiperitenol dehydrogenase; IPI

  3. Comparative functional genomic analysis of Solanum glandular trichome types.

    PubMed

    McDowell, Eric T; Kapteyn, Jeremy; Schmidt, Adam; Li, Chao; Kang, Jin-Ho; Descour, Anne; Shi, Feng; Larson, Matthew; Schilmiller, Anthony; An, Lingling; Jones, A Daniel; Pichersky, Eran; Soderlund, Carol A; Gang, David R

    2011-01-01

    Glandular trichomes play important roles in protecting plants from biotic attack by producing defensive compounds. We investigated the metabolic profiles and transcriptomes to characterize the differences between different glandular trichome types in several domesticated and wild Solanum species: Solanum lycopersicum (glandular trichome types 1, 6, and 7), Solanum habrochaites (types 1, 4, and 6), Solanum pennellii (types 4 and 6), Solanum arcanum (type 6), and Solanum pimpinellifolium (type 6). Substantial chemical differences in and between Solanum species and glandular trichome types are likely determined by the regulation of metabolism at several levels. Comparison of S. habrochaites type 1 and 4 glandular trichomes revealed few differences in chemical content or transcript abundance, leading to the conclusion that these two glandular trichome types are the same and differ perhaps only in stalk length. The observation that all of the other species examined here contain either type 1 or 4 trichomes (not both) supports the conclusion that these two trichome types are the same. Most differences in metabolites between type 1 and 4 glands on the one hand and type 6 glands on the other hand are quantitative but not qualitative. Several glandular trichome types express genes associated with photosynthesis and carbon fixation, indicating that some carbon destined for specialized metabolism is likely fixed within the trichome secretory cells. Finally, Solanum type 7 glandular trichomes do not appear to be involved in the biosynthesis and storage of specialized metabolites and thus likely serve another unknown function, perhaps as the site of the synthesis of protease inhibitors.

  4. Comparative Functional Genomic Analysis of Solanum Glandular Trichome Types1[W][OA

    PubMed Central

    McDowell, Eric T.; Kapteyn, Jeremy; Schmidt, Adam; Li, Chao; Kang, Jin-Ho; Descour, Anne; Shi, Feng; Larson, Matthew; Schilmiller, Anthony; An, Lingling; Jones, A. Daniel; Pichersky, Eran; Soderlund, Carol A.; Gang, David R.

    2011-01-01

    Glandular trichomes play important roles in protecting plants from biotic attack by producing defensive compounds. We investigated the metabolic profiles and transcriptomes to characterize the differences between different glandular trichome types in several domesticated and wild Solanum species: Solanum lycopersicum (glandular trichome types 1, 6, and 7), Solanum habrochaites (types 1, 4, and 6), Solanum pennellii (types 4 and 6), Solanum arcanum (type 6), and Solanum pimpinellifolium (type 6). Substantial chemical differences in and between Solanum species and glandular trichome types are likely determined by the regulation of metabolism at several levels. Comparison of S. habrochaites type 1 and 4 glandular trichomes revealed few differences in chemical content or transcript abundance, leading to the conclusion that these two glandular trichome types are the same and differ perhaps only in stalk length. The observation that all of the other species examined here contain either type 1 or 4 trichomes (not both) supports the conclusion that these two trichome types are the same. Most differences in metabolites between type 1 and 4 glands on the one hand and type 6 glands on the other hand are quantitative but not qualitative. Several glandular trichome types express genes associated with photosynthesis and carbon fixation, indicating that some carbon destined for specialized metabolism is likely fixed within the trichome secretory cells. Finally, Solanum type 7 glandular trichomes do not appear to be involved in the biosynthesis and storage of specialized metabolites and thus likely serve another unknown function, perhaps as the site of the synthesis of protease inhibitors. PMID:21098679

  5. Terpene biosynthesis in glandular trichomes of hop.

    PubMed

    Wang, Guodong; Tian, Li; Aziz, Naveed; Broun, Pierre; Dai, Xinbin; He, Ji; King, Andrew; Zhao, Patrick X; Dixon, Richard A

    2008-11-01

    Hop (Humulus lupulus L. Cannabaceae) is an economically important crop for the brewing industry, where it is used to impart flavor and aroma to beer, and has also drawn attention in recent years due to its potential pharmaceutical applications. Essential oils (mono- and sesquiterpenes), bitter acids (prenylated polyketides), and prenylflavonoids are the primary phytochemical components that account for these traits, and all accumulate at high concentrations in glandular trichomes of hop cones. To understand the molecular basis for terpene accumulation in hop trichomes, a trichome cDNA library was constructed and 9,816 cleansed expressed sequence tag (EST) sequences were obtained from random sequencing of 16,152 cDNA clones. The ESTs were assembled into 3,619 unigenes (1,101 contigs and 2,518 singletons). Putative functions were assigned to the unigenes based on their homology to annotated sequences in the GenBank database. Two mono- and two sesquiterpene synthases identified from the EST collection were expressed in Escherichia coli. Hop MONOTERPENE SYNTHASE2 formed the linear monterpene myrcene from geranyl pyrophosphate, whereas hop SESQUITERPENE SYNTHASE1 (HlSTS1) formed both caryophyllene and humulene from farnesyl pyrophosphate. Together, these enzymes account for the production of the major terpene constituents of the hop trichomes. HlSTS2 formed the minor sesquiterpene constituent germacrene A, which was converted to beta-elemene on chromatography at elevated temperature. We discuss potential functions for other genes expressed at high levels in developing hop trichomes.

  6. Glandular Trichomes and Essential Oil of Thymus quinquecostatus

    PubMed Central

    Jia, Ping; Liu, Hanzhu; Gao, Ting; Xin, Hua

    2013-01-01

    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. PMID:24250266

  7. Localization of Salvinorin A and Related Compounds in Glandular Trichomes of the Psychoactive Sage, Salvia divinorum

    PubMed Central

    SIEBERT, DANIEL J.

    2004-01-01

    • Background and Aims Salvia divinorum produces several closely related neoclerodane diterpenes. The most abundant of these, salvinorin A, is responsible for the psychoactive properties of the plant. To determine where these compounds occur in the plant, various organs, tissues and glandular secretions were chemically analysed. A microscopic survey of the S. divinorum plant was performed to examine the various types of trichomes present and to determine their distribution. • Methods Chemical analyses were performed using thin layer chromatographic and histochemical techniques. Trichomes were examined using conventional light microscopy and scanning electron microscopy. • Key Results It was found that neoclerodane diterpenes are secreted as components of a resin that accumulates in peltate glandular trichomes, specifically in the subcuticular space that exists between the trichome head cells and the cuticle that encloses them. Four main types of trichomes were observed: peltate glandular trichomes, short‐stalked capitate glandular trichomes, long‐stalked capitate glandular trichomes and non‐glandular trichomes. Their morphology and distribution is described. Peltate glandular trichomes were only found on the abaxial surfaces of the leaves, stems, rachises, bracts, pedicles and calyces. This was consistent with chemical analyses, which showed the presence of neoclerodane diterpenes in these organs, but not in parts of the plant where peltate glandular trichomes are absent. • Conclusions Salvinorin A and related compounds are secreted as components of a complex resin that accumulates in the subcuticular space of peltate glandular trichomes. PMID:15087301

  8. Autofluorescence as a Signal to Sort Developing Glandular Trichomes by Flow Cytometry

    PubMed Central

    Bergau, Nick; Navarette Santos, Alexander; Henning, Anja; Balcke, Gerd U.; Tissier, Alain

    2016-01-01

    The industrial relevance of a number of metabolites produced in plant glandular trichomes (GTs) has spurred research on these specialized organs for a number of years. Most of the research, however, has focused on the elucidation of secondary metabolite pathways and comparatively little has been undertaken on the development and differentiation of GTs. One way to gain insight into these developmental processes is to generate stage-specific transcriptome and metabolome data. The difficulty for this resides in the isolation of early stages of development of the GTs. Here we describe a method for the separation and isolation of intact young and mature type VI trichomes from the wild tomato species Solanum habrochaites. The final and key step of the method uses cell sorting based on distinct autofluorescence signals of the young and mature trichomes. We demonstrate that sorting by flow cytometry allows recovering pure fractions of young and mature trichomes. Furthermore, we show that the sorted trichomes can be used for transcript and metabolite analyses. Because many plant tissues or cells have distinct autofluorescence components, the principles of this method can be generally applicable for the isolation of specific cell types without prior labeling. PMID:27446176

  9. Transcriptional profiling unravels potential metabolic activities of the olive leaf non-glandular trichome

    PubMed Central

    Koudounas, Konstantinos; Manioudaki, Maria E.; Kourti, Anna; Banilas, Georgios; Hatzopoulos, Polydefkis

    2015-01-01

    The olive leaf trichomes are multicellular peltate hairs densely distributed mainly at the lower leaf epidermis. Although, non-glandular, they have gained much attention since they significantly contribute to abiotic and biotic stress tolerance of olive leaves. The exact mechanisms by which olive trichomes achieve these goals are not fully understood. They could act as mechanical barrier but they also accumulate high amounts of flavonoids among other secondary metabolites. However, little is currently known about the exact compounds they produce and the respective metabolic pathways. Here we present the first EST analysis from olive leaf trichomes by using 454-pyrosequencing. A total of 5368 unigenes were identified out of 7258 high quality reads with an average length of 262 bp. Blast search revealed that 27.5% of them had high homologies to known proteins. By using Blast2GO, 1079 unigenes (20.1%) were assigned at least one Gene Ontology (GO) term. Most of the genes were involved in cellular and metabolic processes and in binding functions followed by catalytic activity. A total of 521 transcripts were mapped to 67 KEGG pathways. Olive trichomes represent a tissue of highly unique transcriptome as per the genes involved in developmental processes and the secondary metabolism. The results indicate that mature olive trichomes are trancriptionally active, mainly through the potential production of enzymes that contribute to phenolic compounds with important roles in biotic and abiotic stress responses. PMID:26322070

  10. Variation in the number of capitate glandular trichomes in wild and cultivated sunflower germplasm and potential for use in host plant resistance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Capitate glandular trichomes of wild sunflower (Helianthus spp.) are considered an effective defense against the sunflower moth, Homoeosoma electellum (Hulst), but cultivated sunflowers are reportedly deficient in glandular trichomes. To investigate whether glandular trichomes have a role in protect...

  11. Genetic basis for glandular trichome formation in cotton

    PubMed Central

    Ma, Dan; Hu, Yan; Yang, Changqing; Liu, Bingliang; Fang, Lei; Wan, Qun; Liang, Wenhua; Mei, Gaofu; Wang, Lingjian; Wang, Haiping; Ding, Linyun; Dong, Chenguang; Pan, Mengqiao; Chen, Jiedan; Wang, Sen; Chen, Shuqi; Cai, Caiping; Zhu, Xiefei; Guan, Xueying; Zhou, Baoliang; Zhu, Shuijin; Wang, Jiawei; Guo, Wangzhen; Chen, Xiaoya; Zhang, Tianzhen

    2016-01-01

    Trichomes originate from epidermal cells and can be classified as either glandular or non-glandular. Gossypium species are characterized by the presence of small and darkly pigmented lysigenous glands that contain large amounts of gossypol. Here, using a dominant glandless mutant, we characterize GoPGF, which encodes a basic helix-loop-helix domain-containing transcription factor, that we propose is a positive regulator of gland formation. Silencing GoPGF leads to a completely glandless phenotype. A single nucleotide insertion in GoPGF, introducing a premature stop codon is found in the duplicate recessive glandless mutant (gl2gl3). The characterization of GoPGF helps to unravel the regulatory network of glandular structure biogenesis, and has implications for understanding the production of secondary metabolites in glands. It also provides a potential molecular basis to generate glandless seed and glanded cotton to not only supply fibre and oil but also provide a source of protein for human consumption. PMID:26795254

  12. Purification and Characterization of Polyphenol Oxidase from Glandular Trichomes of Solanum berthaultii.

    PubMed

    Kowalski, S P; Eannetta, N T; Hirzel, A T; Steffens, J C

    1992-10-01

    Type A glandular trichomes of the wild potato (Solanum berthaultii Hawkes) entrap insects by rapidly polymerizing the trichome contents after breakage by insect contact. Polymerization of trichome exudate appears to be driven by a soluble polyphenol oxidase (PPO). PPO constitutes up to 70% of the protein in individually collected trichomes and reaches a concentration approaching 200 mum in these organs. Trichome PPO has been purified and shown to be a monomeric copper metalloprotein with an isoelectric point of 5.5, possessing only o-diphenol oxygen oxido-reductase activity, and is larger than most other reported PPOs, with relative molecular weight of 59,000. Chlorogenic and caffeic acid were the most readily oxidized of 14 phenolic substrates tested. Polyclonal antibodies raised against the relative molecular weight 59,000 S. berthaultii trichome PPO were used to show that S. tuberosum L. trichomes express low levels of a cross-reactive protein that lacks detectable PPO activity.

  13. Influence of Environment on Glandular Trichomes and Composition of Essential Oil of Perovskia abrotanoides Karel.

    PubMed Central

    Oreizi, Elaheh; Rahiminejad, Mohammad Reza; Asghari, Gholamreza

    2014-01-01

    Background: Perovskia abrotanoides Karel. is a medicinal plant used in Iranian folk medicine as a pain killer. Forty-one components have been identified in P. abrotanoides samples collected from Baluchistan Province, and 29 components have been recognized in samples collected from Khorasan Province. The leaves of P. abrotanoides have glandular trichomes (capitates and peltate) on both sides of the lamina. Objectives: This study aimed to evaluate the variation of oil constituents of the plant and illustrate the glandular trichomes types and then show the influence of environment on oil constituents and glandular trichomes. Materials and Methods: The essential oil of the plant was obtained using hydrodistillation and the analysis of oils carried out using GC-MS. The anatomical analysis of leaves was done by fixing, coloring, and photoing the sections. Results: Glandular trichomes composed of capitates and peltate trichomes. The essential oil composition differs. Viridiflora and neryl acetate were not identified in yellow glandular trichomes. Conclusions: It seems that there is no relation between anatomical characteristics of the plant leaves and its essential oil composition. PMID:25625046

  14. Plant Glandular Trichomes as Targets for Breeding or Engineering of Resistance to Herbivores

    PubMed Central

    Glas, Joris J.; Schimmel, Bernardus C. J.; Alba, Juan M.; Escobar-Bravo, Rocío; Schuurink, Robert C.; Kant, Merijn R.

    2012-01-01

    Glandular trichomes are specialized hairs found on the surface of about 30% of all vascular plants and are responsible for a significant portion of a plant’s secondary chemistry. Glandular trichomes are an important source of essential oils, i.e., natural fragrances or products that can be used by the pharmaceutical industry, although many of these substances have evolved to provide the plant with protection against herbivores and pathogens. The storage compartment of glandular trichomes usually is located on the tip of the hair and is part of the glandular cell, or cells, which are metabolically active. Trichomes and their exudates can be harvested relatively easily, and this has permitted a detailed study of their metabolites, as well as the genes and proteins responsible for them. This knowledge now assists classical breeding programs, as well as targeted genetic engineering, aimed to optimize trichome density and physiology to facilitate customization of essential oil production or to tune biocide activity to enhance crop protection. We will provide an overview of the metabolic diversity found within plant glandular trichomes, with the emphasis on those of the Solanaceae, and of the tools available to manipulate their activities for enhancing the plant’s resistance to pests. PMID:23235331

  15. Comparison of polyphenol oxidase expression in glandular trichomes of solanum and lycopersicon species.

    PubMed

    Yu, H; Kowalski, S P; Steffens, J C

    1992-12-01

    Tetralobulate glandular trichomes are present on the foliage of many solanaceous species. Resistance of many of these species to insects is conditioned by the ability of trichomes to rupture upon contact and to rapidly polymerize their contents, resulting in entrapment of insects in hardened trichome exudate. In the wild potato, Solanum berthaultii, polymerization of trichome exudate is initiated by a soluble M(r) 59,000 polyphenol oxidase (PPO), which is a dominant protein constituent of the organ. PPOs, although ubiquitous in angiosperms, typically display great heterogeneity in molecular weight and are found at low levels in plant cells. Because of the unusually high accumulation and tissue-specific expression of the M(r) 59,000 PPO in S. berthaultii glandular trichomes, we analyzed trichome proteins of a number of Lycopersicon and Solanum species to assess the extent to which possession of the M(r) 59,000 PPO is conserved. Trichomes were collected manually and examined for PPO activity, immuno-cross-reactivity with S. berthaultiiM(r) 59,000 PPO, and protein content. In addition, N-terminal amino acid sequences were obtained for five trichome PPOs. All species analyzed possessed trichome PPOs similar in structure and level of expression to that of S. berthaultii. The relationship between sequences and structures of these conserved PPOs and the variable PPOs of leaf is discussed.

  16. Comparison of Polyphenol Oxidase Expression in Glandular Trichomes of Solanum and Lycopersicon Species 1

    PubMed Central

    Yu, Haifeng; Kowalski, Stanley P.; Steffens, John C.

    1992-01-01

    Tetralobulate glandular trichomes are present on the foliage of many solanaceous species. Resistance of many of these species to insects is conditioned by the ability of trichomes to rupture upon contact and to rapidly polymerize their contents, resulting in entrapment of insects in hardened trichome exudate. In the wild potato, Solanum berthaultii, polymerization of trichome exudate is initiated by a soluble Mr 59,000 polyphenol oxidase (PPO), which is a dominant protein constituent of the organ. PPOs, although ubiquitous in angiosperms, typically display great heterogeneity in molecular weight and are found at low levels in plant cells. Because of the unusually high accumulation and tissue-specific expression of the Mr 59,000 PPO in S. berthaultii glandular trichomes, we analyzed trichome proteins of a number of Lycopersicon and Solanum species to assess the extent to which possession of the Mr 59,000 PPO is conserved. Trichomes were collected manually and examined for PPO activity, immuno-cross-reactivity with S. berthaultiiMr 59,000 PPO, and protein content. In addition, N-terminal amino acid sequences were obtained for five trichome PPOs. All species analyzed possessed trichome PPOs similar in structure and level of expression to that of S. berthaultii. The relationship between sequences and structures of these conserved PPOs and the variable PPOs of leaf is discussed. Images Figure 1 Figure 2 Figure 3 PMID:16653213

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

    PubMed Central

    Göpfert, Jens C; MacNevin, Gillian; Ro, Dae-Kyun; Spring, Otmar

    2009-01-01

    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 as well. Conclusion This

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

    PubMed

    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.

  19. Biochemical and histochemical localization of monoterpene biosynthesis in the glandular trichomes of spearmint (Mentha spicata)

    SciTech Connect

    Gershenzon, J.; Maffei, M.; Croteau, R. )

    1989-04-01

    The primary monoterpene accumulated in the glandular trichomes of spearmint (Mentha spicata) is the ketone (-)-carvone which is formed by cyclization of the C{sub 10} isoprenoid intermediate geranyl pyrophosphate to the olefin (-)-limonene, hydroxylation to (-)-trans-carveol and subsequent dehydrogenation. Selective extraction of the contents of the glandular trichomes indicated that essentially all of the cyclase and hydroxylase activities resided in these structures, whereas only about 30% of the carveol dehydrogenase was located here with the remainder located in the rest of the leaf. This distribution of carveol dehydrogenase activity was confirmed by histochemical methods. Electrophoretic analysis of the partially purified carveol dehydrogenase from extracts of both the glands and the leaves following gland removal indicated the presence of a unique carveol dehydrogenase species in the glandular trichomes, suggesting that the other dehydrogenase found throughout the leaf probably utilizes carveol only as an adventitious substrate. These results demonstrate that carvone biosynthesis takes place exclusively in the glandular trichomes in which this natural product accumulates.

  20. Phytotoxicity of Constituents of Glandular Trichomes and the Leaf Surface of Camphorweed, Heterotheca subaxillaris

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Camphorweed, Heterotheca subaxillaris (Lam.) Britt. & Rusby has a camphor-like odor, and its leaf surfaces contain glandular trichomes of the type shown to contain high levels of isoprenoids in other species. Phytotoxic calamenene-type sesquiterpenes (1-4, 8-10), borneol (11) and methylated flavone...

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

    PubMed

    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.

  2. Biological activity of acyl glucose esters from Datura wrightii glandular trichomes against three native insect herbivores.

    PubMed

    Hare, J Daniel

    2005-07-01

    Datura wrightii is dimorphic for leaf trichome type in southern California. "Sticky" plants produce glandular trichomes that secrete acylsugars, whereas velvety plants produce nonglandular trichomes. Glandular trichomes confer resistance to some potential insect herbivores and are associated with reduced feeding in the field by two native coleopteran herbivores: the tobacco flea beetle, Epitrix hirtipennis, and a weevil, Trichobaris compacta. In contrast, another native beetle, Lema daturaphila, damages sticky and velvety plants similarly in the field. A series of choice and no-choice "ester removal" and "ester addition" feeding experiments were performed in the laboratory to evaluate the role of acylsugars in feeding by all three insect species. Consumption of sticky leaves after their esters were removed by washing was compared to consumption of unwashed sticky leaves and velvety leaves in ester removal experiments. Consumption of velvety leaves was measured after acylsugars were applied to those leaves in controlled amounts in the ester addition experiments. Consumption by E. hirtipennis was reduced by acylsugars in all experiments. Consumption by T. compacta was reduced by acylsugars in the ester removal experiments, but not in the ester addition experiments. The location of the acylsugars at the tip of a long trichome, rather than simply on the leaf surface, may be an important component of the biological activity of acylsugars against T. compacta in nature. Consumption by L. daturaphila was not significantly reduced by acylsugars in any experiment. The acylsugars caused no significant mortality of any of the three insect species.

  3. Transcriptome profiling of trichome-less reveals genes associated with multicellular trichome development in Cucumis sativus.

    PubMed

    Zhao, Jun-Long; Wang, Yun-Li; Yao, Dan-Qing; Zhu, Wen-Ying; Chen, Long; He, Huan-Le; Pan, Jun-Song; Cai, Run

    2015-10-01

    Trichomes on plants, similar to fine hairs on animal and human bodies, play important roles in plant survival and development. They also represent a useful model for the study of cell differentiation. Although the regulatory gene network of unicellular trichome development in Arabidopsis thaliana has been well studied, the genes that regulate multicellular trichome development remain unclear. We confirmed that Cucumis sativus (cucumber) trichomes are multicellular and unbranched, but identified a spontaneous mutant, trichome-less (tril), which presented a completely glabrous phenotype. We compared the transcriptome profilings of the tril mutant and wild type using the Illumina HiSeq 2000 sequencing technology. A total of 991 genes exhibited differential expression: 518 were up-regulated and 473 were down-regulated. We further identified 62 differentially expressed genes that encoded crucial transcription factors and were subdivided into seven categories: homeodomain, MADS, MYB, and WRKY domains, ethylene-responsive, zinc finger, and other transcription factor genes. We further analyzed the tissue-expression profiles of two candidate genes, GLABRA2-like and ATHB51-like, using qRT-PCR and found that these two genes were specifically expressed in the epidermis and trichomes, respectively. These results and the tril mutant provide useful tools to study the molecular networks associated with multicellular trichome development.

  4. Terpene Biosynthesis in Glandular Trichomes of Hop12[W][OA

    PubMed Central

    Wang, Guodong; Tian, Li; Aziz, Naveed; Broun, Pierre; Dai, Xinbin; He, Ji; King, Andrew; Zhao, Patrick X.; Dixon, Richard A.

    2008-01-01

    Hop (Humulus lupulus L. Cannabaceae) is an economically important crop for the brewing industry, where it is used to impart flavor and aroma to beer, and has also drawn attention in recent years due to its potential pharmaceutical applications. Essential oils (mono- and sesquiterpenes), bitter acids (prenylated polyketides), and prenylflavonoids are the primary phytochemical components that account for these traits, and all accumulate at high concentrations in glandular trichomes of hop cones. To understand the molecular basis for terpene accumulation in hop trichomes, a trichome cDNA library was constructed and 9,816 cleansed expressed sequence tag (EST) sequences were obtained from random sequencing of 16,152 cDNA clones. The ESTs were assembled into 3,619 unigenes (1,101 contigs and 2,518 singletons). Putative functions were assigned to the unigenes based on their homology to annotated sequences in the GenBank database. Two mono- and two sesquiterpene synthases identified from the EST collection were expressed in Escherichia coli. Hop MONOTERPENE SYNTHASE2 formed the linear monterpene myrcene from geranyl pyrophosphate, whereas hop SESQUITERPENE SYNTHASE1 (HlSTS1) formed both caryophyllene and humulene from farnesyl pyrophosphate. Together, these enzymes account for the production of the major terpene constituents of the hop trichomes. HlSTS2 formed the minor sesquiterpene constituent germacrene A, which was converted to β-elemene on chromatography at elevated temperature. We discuss potential functions for other genes expressed at high levels in developing hop trichomes. PMID:18775972

  5. Genetic elaborations of glandular and non-glandular trichomes in Mentha arvensis genotypes: assessing genotypic and phenotypic correlations along with gene expressions.

    PubMed

    Mishra, Anand; Lal, R K; Chanotiya, C S; Dhawan, Sunita Singh

    2017-03-01

    Mentha arvensis (corn mint) is well known for the production of menthol, a widely used commodity in pharma and flavoring industries and provides natural fragrances and products. Glandular trichomes are specialized hairs found on the aerial surface of vascular plants species producing specific secondary metabolite chemistry. Correlations were established among trichomes, oil yield, and major secondary metabolites. Nine improved, elite cultivars representing different M. arvensis genotypes were used for analysis. Phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) were estimated; results indicated the presence of considerable amount of genetic variability, thereby emphasizing wide scope of selection. Positive and significant associations were found among glandular trichomes, oil yield, essential oil constituents, and leaf morphology itself, whereas morphological parameters of leaf show positive and negative correlations to average number of trichome and essential oil constituents. Average number of glandular, non-glandular trichomes, their ratios, menthol content, and trichome number showed a good heritability. Trichomes were studied microscopically in leaf parts in all varieties for analyzing their distribution pattern. The trichome number variations showed significant correlation throughout the genotypes with essential oil yield and monoterpenoid constituents. Differential changes were analyzed for Glutathione S-transferases, Glutathione reductase, Malondialdehyde, phenolics, and chlorophyll content. Gene expressions were analyzed for biosynthesis genes and selected transcription factors TRANSPARENT TESTA GLABRA 1 (TTG1), ENOLASE 1, GLABRA 3, GTL 1, NUCLEAR TRANSCRIPTION FACTOR Y SUBUNIT B-6, WRKY transcription factor 22, putative WRKY 33, WRKY 17, WRKY 1, and WRKY 65-like for harnessing their relation with trichome development in M. arvensis genotypes.

  6. Tetrahydrocannabinolic acid synthase, the enzyme controlling marijuana psychoactivity, is secreted into the storage cavity of the glandular trichomes.

    PubMed

    Sirikantaramas, Supaart; Taura, Futoshi; Tanaka, Yumi; Ishikawa, Yu; Morimoto, Satoshi; Shoyama, Yukihiro

    2005-09-01

    Tetrahydrocannabinolic acid (THCA) synthase is the enzyme responsible for the production of tetrahydrocannabinol (THC), the psychoactive component of marijuana (Cannabis sativa L.). We suggest herein that THCA is biosynthesized in the storage cavity of the glandular trichomes based on the following observations. (i) The exclusive expression of THCA synthase was confirmed in the secretory cells of glandular trichomes by reverse transcription-PCR (RT-PCR) analysis. (ii) THCA synthase activity was detected in the storage cavity content. (iii) Transgenic tobacco expressing THCA synthase fused to green fluorescent protein showed fluorescence in the trichome head corresponding to the storage cavity. These results also showed that secretory cells of the glandular trichomes secrete not only metabolites but also biosynthetic enzyme.

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

    PubMed

    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.

  8. The Key Role of Peltate Glandular Trichomes in Symbiota Comprising Clavicipitaceous Fungi of the Genus Periglandula and Their Host Plants

    PubMed Central

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

    2015-01-01

    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. PMID:25894995

  9. The flavonoid biosynthetic enzyme chalcone isomerase modulates terpenoid production in glandular trichomes of tomato.

    PubMed

    Kang, Jin-Ho; McRoberts, John; Shi, Feng; Moreno, Javier E; Jones, A Daniel; Howe, Gregg A

    2014-03-01

    Flavonoids and terpenoids are derived from distinct metabolic pathways but nevertheless serve complementary roles in mediating plant interactions with the environment. Here, we show that glandular trichomes of the anthocyanin free (af) mutant of cultivated tomato (Solanum lycopersicum) fail to accumulate both flavonoids and terpenoids. This pleiotropic metabolic deficiency was associated with loss of resistance to native populations of coleopteran herbivores under field conditions. We demonstrate that Af encodes an isoform (SlCHI1) of the flavonoid biosynthetic enzyme chalcone isomerase (CHI), which catalyzes the conversion of naringenin chalcone to naringenin and is strictly required for flavonoid production in multiple tissues of tomato. Expression of the wild-type SlCHI1 gene from its native promoter complemented the anthocyanin deficiency in af. Unexpectedly, the SlCHI1 transgene also complemented the defect in terpenoid production in glandular trichomes. Our results establish a key role for SlCHI1 in flavonoid production in tomato and reveal a link between CHI1 and terpenoid production. Metabolic coordination of the flavonoid and terpenoid pathways may serve to optimize the function of trichome glands in dynamic environments.

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

    PubMed Central

    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. PMID:26406988

  11. Phytotoxicity of constituents of glandular trichomes and the leaf surface of camphorweed, Heterotheca subaxillaris.

    PubMed

    Morimoto, Masanori; Cantrell, Charles L; Libous-Bailey, Lynn; Duke, Stephen O

    2009-01-01

    Camphorweed, Heterotheca subaxillaris (Lam.) Britt. & Rusby, has a camphor-like odor, and its leaf surfaces contain glandular trichomes of the type shown to contain high levels of isoprenoids in other species. Borneol (1), the phytotoxic calamenene-type sesquiterpenes (2-5, 9-11), and methylated flavones (12-15) were isolated from the dichloromethane rinsate of camphorweed aerial tissues. The strongest plant growth inhibitor against Agrostis stolonifera and Lactuca sativa seedlings, as well as duckweed (Lemna pausicostata), was 2-methoxy-calamenene-14-carboxylic acid (2). Esterification of calamenene carboxylic acids decreased their biological activity.

  12. Transcriptome profiling reveals roles of meristem regulators and polarity genes during fruit trichome development in cucumber (Cucumis sativus L.).

    PubMed

    Chen, Chunhua; Liu, Meiling; Jiang, Li; Liu, Xiaofeng; Zhao, Jianyu; Yan, Shuangshuang; Yang, Sen; Ren, Huazhong; Liu, Renyi; Zhang, Xiaolan

    2014-09-01

    Trichomes are epidermal hair-like structures that function in plant defence against biotic and abiotic stresses. Extensive studies have been performed on foliar trichomes development in Arabidopsis and tomato, but the molecular mechanism of fruit trichome formation remains elusive. Cucumber fruit is covered with trichomes (spines) that directly affect the appearance and quality of cucumber products. Here, we characterized the fruit spine development in wild-type (WT) cucumber and a spontaneous mutant, tiny branched hair (tbh). Our data showed that the cucumber trichome was multicellular and non-glandular, with malformed organelles and no endoreduplication. Fruit spine development was generally homogenous and marked by a rapid base expansion stage. Trichomes in the tbh mutant were tiny and branched, with increased density and aberrant cell shape. Transcriptome profiling indicated that meristem-related genes were highly enriched in the upregulated genes in the tbh versus the WT, as well as in WT spines after versus before base expansion, and that polarity regulators were greatly induced during spine base expansion. Quantitative reverse transcription PCR and in situ hybridization confirmed the differential expression of CUP-SHAPED COTYLEDON3 (CUC3) and SHOOT MERISTEMLESS (STM) during spine development. Therefore, cucumber trichomes are morphologically different from those of Arabidopsis and tomato, and their development may be regulated by a distinct pathway involving meristem genes and polarity regulators.

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

    PubMed

    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.

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

    PubMed

    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.

  15. Opposing Roles of Foliar and Glandular Trichome Volatile Components in Cultivated Nightshade Interaction with a Specialist Herbivore

    PubMed Central

    Murungi, Lucy Kananu; Kirwa, Hillary; Salifu, Daisy; Torto, Baldwyn

    2016-01-01

    Plant chemistry is an important contributor to the interaction with herbivores. Here, we report on a previously unknown role for foliar and glandular trichome volatiles in their interaction with the specialist herbivore of solanaceous plants, the tomato red spider mite Tetranychus evansi. We used various bioassays and chemical analyses including coupled gas chromatography-mass spectrometry (GC/MS) and liquid chromatography coupled to quadrupole time of flight mass spectrometry (LC-QToF-MS) to investigate this interaction between cultivated African nightshades and T. evansi. We show that, whereas morphologically different cultivated African nightshade species released similar foliar volatile organic compounds (VOCs) that attracted T. evansi, VOCs released from exudates of ruptured glandular trichomes of one nightshade species influenced local defense on the leaf surface. VOCs from ruptured glandular trichomes comprising mainly saturated and unsaturated fatty acids deterred T. evansi oviposition. Of the fatty acids, the unsaturated fatty acids accounted for >40% of the oviposition deterrent activity. Our findings point to a defense strategy in a plant, based on opposing roles for volatiles released by foliar and glandular trichomes in response to attack by a specialist herbivore. PMID:27556560

  16. Opposing Roles of Foliar and Glandular Trichome Volatile Components in Cultivated Nightshade Interaction with a Specialist Herbivore.

    PubMed

    Murungi, Lucy Kananu; Kirwa, Hillary; Salifu, Daisy; Torto, Baldwyn

    2016-01-01

    Plant chemistry is an important contributor to the interaction with herbivores. Here, we report on a previously unknown role for foliar and glandular trichome volatiles in their interaction with the specialist herbivore of solanaceous plants, the tomato red spider mite Tetranychus evansi. We used various bioassays and chemical analyses including coupled gas chromatography-mass spectrometry (GC/MS) and liquid chromatography coupled to quadrupole time of flight mass spectrometry (LC-QToF-MS) to investigate this interaction between cultivated African nightshades and T. evansi. We show that, whereas morphologically different cultivated African nightshade species released similar foliar volatile organic compounds (VOCs) that attracted T. evansi, VOCs released from exudates of ruptured glandular trichomes of one nightshade species influenced local defense on the leaf surface. VOCs from ruptured glandular trichomes comprising mainly saturated and unsaturated fatty acids deterred T. evansi oviposition. Of the fatty acids, the unsaturated fatty acids accounted for >40% of the oviposition deterrent activity. Our findings point to a defense strategy in a plant, based on opposing roles for volatiles released by foliar and glandular trichomes in response to attack by a specialist herbivore.

  17. Capitate glandular trichomes of Paragutzlaffia henryi harbor new phytotoxic labdane diterpenoids.

    PubMed

    Wang, Ying; Luo, Shi-Hong; Hua, Juan; Liu, Yan; Jing, Shu-Xi; Li, Xiao-Nian; Li, Sheng-Hong

    2015-11-18

    The morphology and chemical profile of the capitate glandular trichomes (CGTs) of Paragutzlaffia henryi (Acanthaceae) were investigated. Four new labdane diterpenoids named paraguhenryisins A-D (1-4), together with the known physacoztomatin (5), were localized to the CGTs using laser microdissection coupled with cryogenic (1)H NMR and HPLC analyses and were traced and isolated from the CGT extract of inflorescences. Their structures were determined by spectroscopic methods and single-crystal X-ray diffraction. Bioassays indicated significant inhibitory effect for these diterpenoids on Arabidopsis thaliana seed germination and seedling root elongation. The most potent inhibitor, paraguhenryisin C (3), was interestingly detected in both the rhizosphere soil and water rinsed inflorescences extract of P. henryi but not the roots, with average contents in the rhizosphere soil relevant to its phytotoxic EC50 values. These results suggested that phytotoxic labdane diterpenoids in the CGTs might be released into the environment as a defensive measure for P. henryi against other competitive plants.

  18. Capitate glandular trichomes of Helianthus annuus (Asteraceae): ultrastructure and cytological development.

    PubMed

    Amrehn, Evelyn; Heller, Annerose; Spring, Otmar

    2014-01-01

    Previous studies have shown that capitate glandular trichomes (CGT) of the common sunflower, Helianthus annuus, produce sesquiterpene lactones (STL) and flavonoids, which are sequestered and accumulated between the apical cuticle and the wall of the tip cells. To explore the cellular structures required and putatively involved in the STL biosynthesis and secretion, the present study was focused on the development of CGT and the comparison of the ultrastructure of its different cell types. Gradual maturation of flowers in the capitulum of the sunflower provided the possibility to study the simultaneous differentiation from the primordial to the secretory stage of CGT located by light microscopy (bright field, differential interference contrast and fluorescence) as well as transmission electron microscopy. It was shown that the CGT of sunflower anthers had a biseriate structure with up to 14 cell pairs. In mature trichomes, the apical cells called secretory cells were covered entirely by a large cuticle globe, which enclosed the resinous terpenoids and was specialised in thickness and structure. The secretory cells lacked chloroplasts and contained mainly smooth endoplasmic reticulum (sER). Conspicuous cell wall protuberances and an accumulation of mitochondria nearby occurred in the horizontally oriented cell walls. The cytological differences between stalk cells and secretory cells indicate a different function. The dominance of sER suggests its involvement in STL biosynthesis and cell wall protuberances enlarge the surface of the plasmamembrane of secretory cells and may be involved in the secretion processes of STL into the subcuticular space.

  19. Localization of sesquiterpene lactone biosynthesis in cells of capitate glandular trichomes of Helianthus annuus (Asteraceae).

    PubMed

    Amrehn, Evelyn; Aschenbrenner, Anna-Katharina; Heller, Annerose; Spring, Otmar

    2016-03-01

    Capitate glandular trichomes (CGT) of sunflower, Helianthus annuus, synthesize bioactive sesquiterpene lactones (STLs) within a short period of only a few days during trichome development. In the current project, the subcellular localization of H. annuus germacrene A monooxygenase (HaGAO), a key enzyme of the STL biosynthesis in sunflower CGT, was investigated. A polyclonal antibody raised against this enzyme was used for immunolabelling. HaGAO was found in secretory and stalk cells of CGT. This correlated with the appearance of smooth endoplasmic reticulum in both cell types. Stalk cells and secretory cells differed in form, size and types of plastids, but both had structures necessary for secretion. No HaGAO-specific immunoreaction was found in sunflower leaf tissue outside of CGT or in developing CGT before the secretory phase had started. Our results indicated that not only secretory cells but also nearly all cells of the CGT were involved in the biosynthesis of STL and that this process was not linked to the presence or absence of a specific type of plastid.

  20. Non-glandular trichomes of Solanum carolinense deter feeding by Manduca sexta caterpillars and cause damage to the gut peritrophic matrix.

    PubMed

    Kariyat, Rupesh R; Smith, Jason D; Stephenson, Andrew G; De Moraes, Consuelo M; Mescher, Mark C

    2017-02-22

    Plant trichomes constitute a first line of defence against insect herbivores. The pre- and post-ingestive defensive functions of glandular trichomes are well documented and include direct toxicity, adhesion, antinutrition and defence gene induction. By contrast, the defensive functions of non-glandular trichomes are less well characterized, although these structures are thought to serve as physical barriers that impede herbivore feeding and movement. We experimentally varied the density of stellate non-glandular trichomes in several ways to explore their pre- and post-ingestive effects on herbivores. Larvae of Manduca sexta (Sphingidae) initiated feeding faster and gained more weight on Solanum carolinense (Solanaceae) leaves having lower trichome densities (or experimentally removed trichomes) than on leaves having higher trichome densities. Adding trichomes to artificial diet also deterred feeding and adversely affected caterpillar growth relative to controls. Scanning electron and light microscopy revealed that the ingestion of stellate trichomes by M. sexta caterpillars caused extensive damage to the peritrophic membrane, a gut lining that is essential to digestion and pathogen isolation. These findings suggest that, in addition to acting as a physical barrier to deter feeding, trichomes can inhibit caterpillar growth and development via post-ingestive effects.

  1. Promoters of AaGL2 and AaMIXTA-Like1 genes of Artemisia annua direct reporter gene expression in glandular and non-glandular trichomes

    PubMed Central

    Jindal, Sunita; Longchar, Bendangchuchang; Singh, Alka; Gupta, Vikrant

    2015-01-01

    Herein, we report cloning and analysis of promoters of GLABRA2 (AaGL2) homolog and a MIXTA-Like (AaMIXTA-Like1) gene from Artemisia annua. The upstream regulatory regions of AaGL2 and AaMIXTA-Like1 showed the presence of several crucial cis-acting elements. Arabidopsis and A. annua seedlings were transiently transfected with the promoter-GUS constructs using a robust agro-infiltration method. Both AaGL2 and AaMIXTA-Like1 promoters showed GUS expression preferentially in Arabidopsis single-celled trichomes and glandular as well as T-shaped trichomes of A. annua. Transgenic Arabidopsis harboring constructs in which AaGL2 or AaMIXTA-Like1 promoters would control GFP expression, showed fluorescence emanating specifically from trichome cells. Our study provides a fast and efficient method to study trichome-specific expression, and 2 promoters that have potential for targeted metabolic engineering in plants. PMID:26340695

  2. EST analysis of hop glandular trichomes identifies an O-methyltransferase that catalyzes the biosynthesis of xanthohumol.

    PubMed

    Nagel, Jana; Culley, Lana K; Lu, Yuping; Liu, Enwu; Matthews, Paul D; Stevens, Jan F; Page, Jonathan E

    2008-01-01

    The glandular trichomes (lupulin glands) of hop (Humulus lupulus) synthesize essential oils and terpenophenolic resins, including the bioactive prenylflavonoid xanthohumol. To dissect the biosynthetic processes occurring in lupulin glands, we sequenced 10,581 ESTs from four trichome-derived cDNA libraries. ESTs representing enzymes of terpenoid biosynthesis, including all of the steps of the methyl 4-erythritol phosphate pathway, were abundant in the EST data set, as were ESTs for the known type III polyketide synthases of bitter acid and xanthohumol biosynthesis. The xanthohumol biosynthetic pathway involves a key O-methylation step. Four S-adenosyl-l-methionine-dependent O-methyltransferases (OMTs) with similarity to known flavonoid-methylating enzymes were present in the EST data set. OMT1, which was the most highly expressed OMT based on EST abundance and RT-PCR analysis, performs the final reaction in xanthohumol biosynthesis by methylating desmethylxanthohumol to form xanthohumol. OMT2 accepted a broad range of substrates, including desmethylxanthohumol, but did not form xanthohumol. Mass spectrometry and proton nuclear magnetic resonance analysis showed it methylated xanthohumol to 4-O-methylxanthohumol, which is not known from hop. OMT3 was inactive with all substrates tested. The lupulin gland-specific EST data set expands the genomic resources for H. lupulus and provides further insight into the metabolic specialization of glandular trichomes.

  3. EST Analysis of Hop Glandular Trichomes Identifies an O-Methyltransferase That Catalyzes the Biosynthesis of Xanthohumol[W][OA

    PubMed Central

    Nagel, Jana; Culley, Lana K.; Lu, Yuping; Liu, Enwu; Matthews, Paul D.; Stevens, Jan F.; Page, Jonathan E.

    2008-01-01

    The glandular trichomes (lupulin glands) of hop (Humulus lupulus) synthesize essential oils and terpenophenolic resins, including the bioactive prenylflavonoid xanthohumol. To dissect the biosynthetic processes occurring in lupulin glands, we sequenced 10,581 ESTs from four trichome-derived cDNA libraries. ESTs representing enzymes of terpenoid biosynthesis, including all of the steps of the methyl 4-erythritol phosphate pathway, were abundant in the EST data set, as were ESTs for the known type III polyketide synthases of bitter acid and xanthohumol biosynthesis. The xanthohumol biosynthetic pathway involves a key O-methylation step. Four S-adenosyl-l-methionine–dependent O-methyltransferases (OMTs) with similarity to known flavonoid-methylating enzymes were present in the EST data set. OMT1, which was the most highly expressed OMT based on EST abundance and RT-PCR analysis, performs the final reaction in xanthohumol biosynthesis by methylating desmethylxanthohumol to form xanthohumol. OMT2 accepted a broad range of substrates, including desmethylxanthohumol, but did not form xanthohumol. Mass spectrometry and proton nuclear magnetic resonance analysis showed it methylated xanthohumol to 4-O-methylxanthohumol, which is not known from hop. OMT3 was inactive with all substrates tested. The lupulin gland-specific EST data set expands the genomic resources for H. lupulus and provides further insight into the metabolic specialization of glandular trichomes. PMID:18223037

  4. Effect of prolonged water stress on specialized secondary metabolites, peltate glandular trichomes, and pathway gene expression in Artemisia annua L.

    PubMed

    Yadav, Ritesh K; Sangwan, Rajender S; Sabir, Farzana; Srivastava, Awadesh K; Sangwan, Neelam S

    2014-01-01

    Artemisia annua L. accumulates substantial quantities of unique sesquiternoid artemisinin and related phytomolecules and characteristic essential oil in glandular trichomes, present on its leaves and inflorescence. Water stress is a major concern in controlling plant growth and productivity. In this study, our aim was to find out the modulation of artemisinin and essential oil constituents in plants grown under prolonged water stress conditions. A. annua CIM-Arogya plants grown in pots were subjected to mild (60% ± 5) and moderate (40% ± 5) water stress treatment and continued during entire developmental period. Results revealed that artemisinin, arteannuin-B, artemisinic acid, dihydroartemisinic acid and essential oil content were positively controlled by the growth and development however negatively modulated by water deficit stress. Interestingly, some of minor monoterpenes, all sesquiterpenes and other low molecular weight volatiles of essential oil components were induced by water deficit treatment. Camphor which is the major essential oil constituents did not alter much while 1, 8 cineole was modulated during development of plant as well as under water stress conditions. Water deficit stress induces a decrease in glandular trichome density and size as well. The dynamics of various secondary metabolites is discussed in the light of growth responses, trichomes and pathway gene expression in plants grown under two levels of prolonged water stress conditions.

  5. The Flavonoid Biosynthetic Enzyme Chalcone Isomerase Modulates Terpenoid Production in Glandular Trichomes of Tomato1[C][W][OPEN

    PubMed Central

    Kang, Jin-Ho; McRoberts, John; Shi, Feng; Moreno, Javier E.; Jones, A. Daniel; Howe, Gregg A.

    2014-01-01

    Flavonoids and terpenoids are derived from distinct metabolic pathways but nevertheless serve complementary roles in mediating plant interactions with the environment. Here, we show that glandular trichomes of the anthocyanin free (af) mutant of cultivated tomato (Solanum lycopersicum) fail to accumulate both flavonoids and terpenoids. This pleiotropic metabolic deficiency was associated with loss of resistance to native populations of coleopteran herbivores under field conditions. We demonstrate that Af encodes an isoform (SlCHI1) of the flavonoid biosynthetic enzyme chalcone isomerase (CHI), which catalyzes the conversion of naringenin chalcone to naringenin and is strictly required for flavonoid production in multiple tissues of tomato. Expression of the wild-type SlCHI1 gene from its native promoter complemented the anthocyanin deficiency in af. Unexpectedly, the SlCHI1 transgene also complemented the defect in terpenoid production in glandular trichomes. Our results establish a key role for SlCHI1 in flavonoid production in tomato and reveal a link between CHI1 and terpenoid production. Metabolic coordination of the flavonoid and terpenoid pathways may serve to optimize the function of trichome glands in dynamic environments. PMID:24424324

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

    PubMed

    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.

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

    PubMed

    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.

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

    PubMed

    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.

  9. Effects of Plant Density on the Number of Glandular Trichomes and on Yield and Quality of Essential Oils from Oregano.

    PubMed

    Tuttolomondo, Teresa; La Bella, Salvatore; Leto, Claudio; Bonsangue, Giuseppe; Leone, Raffaele; Gennaro, Maria Cristina; Virga, Giuseppe; Inguanta, Rosalinda; Licata, Mario

    2016-06-01

    Plants yields are influenced by agronomic techniques. Plant density is a complex issue and extremely important when maximizing both crop quality, and biomass and essential oil yields. Plants belonging to the Origanum vulgare subspecies hirtum (Link) Ietswaart were grown adopting four types of plant density and were characterized in biometric and chemical terms. The samples were analyzed using the ANOVA (Principal Component Analysis) statistical method regarding biometric aspects, EO yield and peltate hair density. Essential oil (EO) was extracted by hydrodistillation and analyzed using GC-FID and GC-MS. GC-FID and GC-MS analysis led to the identification of 45 compounds from the EO. Plant density affected production both in terms of biomass and EO. However, it was not found to have affected peltate glandular trichome density or EO quality.

  10. Transcriptome analysis in Cucumis sativus identifies genes involved in multicellular trichome development.

    PubMed

    Zhao, Jun-Long; Pan, Jun-Song; Guan, Yuan; Nie, Jing-Tao; Yang, Jun-Jun; Qu, Mei-Ling; He, Huan-Le; Cai, Run

    2015-05-01

    The regulatory gene network of unicellular trichome development in Arabidopsis thaliana has been studied intensively, but that of multicellular remains unclear. In the present study, we characterized cucumber trichomes as representative multicellular and unbranched structures, but in a spontaneous mutant, mict (micro-trichome), all trichomes showed a micro-size and stunted morphologies. We revealed the transcriptome profile using Illumina HiSeq 2000 sequencing technology, and determined that a total of 1391 genes exhibited differential expression. We further validated the accuracy of the transcriptome data by RT-qPCR and found that 43 genes encoding critical transcription factors were likely involved in multicellular trichome development. These 43 candidate genes were subdivided into seven groups: homeodomain, MYB-domain, WRKY-domain, bHLH-domain, ethylene-responsive, zinc finger and other transcription factor genes. Our findings also serve as a powerful tool to further study the relevant molecular networks, and provide a new perspective for investigating this complex and species-specific developmental process.

  11. Methylerythritol and mevalonate pathway contributions to biosynthesis of mono-, sesqui-, and diterpenes in glandular trichomes and leaves of Stevia rebaudiana Bertoni.

    PubMed

    Wölwer-Rieck, Ursula; May, Bianca; Lankes, Christa; Wüst, Matthias

    2014-03-19

    The biosynthesis of the diterpenoid steviol glycosides rebaudioside A and stevioside in nonrooted cuttings of Stevia rebaudiana was investigated by feeding experiments using the labeled key precursors [5,5-(2)H2]-mevalonic acid lactone (d2-MVL) and [5,5-(2)H2]-1-deoxy-d-xylulose (d2-DOX). Labeled glycosides were extracted from the leaves and stems and were directly analyzed by LC-(-ESI)-MS/MS and by GC-MS after hydrolysis and derivatization of the resulting isosteviol to the corresponding TMS-ester. Additionally, the incorporation of the proffered d2-MVL and d2-DOX into volatile monoterpenes, sesquiterpenes, and diterpenes in glandular trichomes on leaves and stems was investigated by headspace-solid phase microextraction-GC-MS (HS-SPME-GC-MS). Incorporation of the labeled precursors indicated that diterpenes in leaves and monoterpenes and diterpenes in glandular trichomes are predominately biosynthesized via the methylerythritol phosphate (MEP) pathway, whereas both the MEP and mevalonate (MVA) pathways contribute to the biosynthesis of sesquiterpenes at equal rates in glandular trichomes. These findings give evidence for a transport of MEP pathway derived farnesyl diphosphate precursors from plastids to the cytosol. Contrarily, the transport of MVA pathway derived geranyl diphosphate and geranylgeranyl diphosphate precursors from the cytosol to the plastid is limited.

  12. Purification and characterization of an NADPH-cytochrome P450 (cytochrome c) reductase from spearmint (Mentha spicata) glandular trichomes.

    PubMed

    Ponnamperuma, K; Croteau, R

    1996-05-01

    Solubilized NADPH-cytochrome c (P450) reductase was purified to homogeneity from an extract of spearmint (Mentha spicata) glandular trichomes by dye-ligand interaction chromatography on Matrex-Gel Red A and affinity chromatography on 2', 5'-adenosine diphosphate agarose. SDS-PAGE of the purified enzyme preparation revealed the presence of two similar proteins with masses of 82 kDa (major) and 77 kDa (minor) that crossreacted on immunoblot analysis with polyclonal antibodies directed against NADPH-cytochrome P450 reductase from Jerusalem artichoke and from mung bean. Complete immunoinhibition of reductase activity was observed with both types of polyclonal antibodies, while only partial inhibition of activity resulted using a family of monoclonal antibodies directed against the Jerusalem artichoke cytochrome P450 reductase. Inhibition of the spearmint oil gland cytochrome c reductase was also observed with the diphenyliodonium ion. The K(m) values for the cosubstrates NADPH and cytochrome c were 6.2 and 3.7 microM, respectively, and the pH optimum for activity was at 8.5. The NADPH-cytochrome c reductase reconstituted NADPH-dependent (-)-4S-limonene-6-hydroxylase activity in the presence of cytochrome P450, purified from the microsomal fraction of spearmint oil gland cells and dilauroyl phosphatidyl choline. These characteristics establish the identity of the purified enzyme as a NADPH-cytochrome P450 reductase.

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

    PubMed

    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.

  14. Characterization of the formation of branched short-chain fatty acid:CoAs for bitter acid biosynthesis in hop glandular trichomes.

    PubMed

    Xu, Haiyang; Zhang, Fengxia; Liu, Baoxiu; Huhman, David V; Sumner, Lloyd W; Dixon, Richard A; Wang, Guodong

    2013-07-01

    Bitter acids, known for their use as beer flavoring and for their diverse biological activities, are predominantly formed in hop (Humulus lupulus) glandular trichomes. Branched short-chain acyl-CoAs (e.g. isobutyryl-CoA, isovaleryl-CoA and 2-methylbutyryl-CoA), derived from the degradation of branched-chain amino acids (BCAAs), are essential building blocks for the biosynthesis of bitter acids in hops. However, little is known regarding what components are needed to produce and maintain the pool of branched short-chain acyl-CoAs in hop trichomes. Here, we present several lines of evidence that both CoA ligases and thioesterases are likely involved in bitter acid biosynthesis. Recombinant HlCCL2 (carboxyl CoA ligase) protein had high specific activity for isovaleric acid as a substrate (K cat /K m = 4100 s(-1) M(-1)), whereas recombinant HlCCL4 specifically utilized isobutyric acid (Kcat/K m = 1800 s(-1) M(-1)) and 2-methylbutyric acid (Kcat/K m = 6900 s(-1) M(-1)) as substrates. Both HlCCLs, like hop valerophenone synthase (HlVPS), were expressed strongly in glandular trichomes and localized to the cytoplasm. Co-expression of HlCCL2 and HlCCL4 with HlVPS in yeast led to significant production of acylphloroglucinols (the direct precursors for bitter acid biosynthesis), which further confirmed the biochemical function of these two HlCCLs in vivo. Functional identification of a thioesterase that catalyzed the reverse reaction of CCLs in mitochondria, together with the comprehensive analysis of genes involved BCAA catabolism, supported the idea that cytosolic CoA ligases are required for linking BCAA degradation and bitter acid biosynthesis in glandular trichomes. The evolution and other possible physiological roles of branched short-chain fatty acid:CoA ligases in planta are also discussed.

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

    PubMed

    Brückner, Kathleen; Božić, Dragana; Manzano, David; Papaefthimiou, Dimitra; Pateraki, Irini; Scheler, Ulschan; Ferrer, Albert; de Vos, Ric C H; Kanellis, Angelos K; Tissier, Alain

    2014-05-01

    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 biosynthesis of these diterpenes. Here we show that the biosynthesis of phenolic diterpenes in rosemary predominantly takes place in the glandular trichomes of young leaves, and used this feature to identify the first committed steps. Thus, a copalyl diphosphate synthase (RoCPS1) and two kaurene synthase-like (RoKSL1 and RoKSL2) encoding genes were identified and characterized. Expression in yeast (Saccharomyces cerevisiae) and Nicotiana benthamiana demonstrate that RoCPS1 converts geranylgeranyl diphosphate (GGDP) to copalyl diphosphate (CDP) of normal stereochemistry and that both RoKSL1 and RoKSL2 use 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 the dicot-monocot split.

  16. Quantitative determination of enhydrin in leaf rinse extracts and in glandular trichomes of Smallanthus sonchifolius (Asteraceae) by reversed-phase high-performance liquid chromatography.

    PubMed

    Schorr, Karin; Da Costa, Fernando B

    2005-01-01

    A simple, reliable and rapid reversed-phase HPLC-PAD procedure for the characterisation and quantitative determination of the anti-diabetic sesquiterpene lactone enhydrin (1) from Smallanthus sonchifolius (yacón) has been evaluated and validated. The approach focused on the analysis of various leaf rinse extracts, as well as the glandular trichomes of intact leaves, in which 1 was the major compound detected. The best sample preparation of a rinse extract yielded 0.67 mg/mL of 1, whilst a rapid rinse of a small piece of one dried leaf gave 0.09 mg/mL of 1; the highest concentration obtained from a glandular extract was 0.07 mg/mL. The dried leaves of S. sonchifolius were found to contain a total of 0.97% of 1.

  17. A Geranylfarnesyl Diphosphate Synthase Provides the Precursor for Sesterterpenoid (C25) Formation in the Glandular Trichomes of the Mint Species Leucosceptrum canum

    PubMed Central

    Luo, Shi-Hong; Schmidt, Axel; Sun, Gui-Ling; Kuang, Ce; Yang, Min-Jie; Jing, Shu-Xi; Li, Chun-Huan

    2016-01-01

    Plant sesterterpenoids, an important class of terpenoids, are widely distributed in various plants, including food crops. However, little is known about their biosynthesis. Here, we cloned and functionally characterized a plant geranylfarnesyl diphosphate synthase (Lc-GFDPS), the enzyme producing the C25 prenyl diphosphate precursor to all sesterterpenoids, from the glandular trichomes of the woody plant Leucosceptrum canum. GFDPS catalyzed the formation of GFDP after expression in Escherichia coli. Overexpressing GFDPS in Arabidopsis thaliana also gave an extract catalyzing GFDP formation. GFDPS was strongly expressed in glandular trichomes, and its transcript profile was completely in accordance with the sesterterpenoid accumulation pattern. GFDPS is localized to the plastids, and inhibitor studies indicated its use of isoprenyl diphosphate substrates supplied by the 2-C-methyl-d-erythritol 4-phosphate pathway. Application of a jasmonate defense hormone induced GFDPS transcript and sesterterpenoid accumulation, while reducing feeding and growth of the generalist insect Spodoptera exigua, suggesting that these C25 terpenoids play a defensive role. Phylogenetic analysis suggested that GFDPS probably evolved from plant geranylgeranyl diphosphate synthase under the influence of positive selection. The isolation of GFDPS provides a model for investigating sesterterpenoid formation in other species and a tool for manipulating the formation of this group in plants and other organisms. PMID:26941091

  18. Sucrose esters of carboxylic acids in glandular trichomes ofSolanum berthaultii deter settling and probing by green peach aphid.

    PubMed

    Neal, J J; Tingey, W M; Steffens, J C

    1990-02-01

    Removal of type B trichome exudate fromSolanum berthaultii leaflets leads to a decrease in tarsal gumming and mortality and an increase in feeding by the green peach aphid,Myzus persicae. Type B trichome exudate of theS. berthaultii accession PI 473331 is composed of a complex of 3',3,4,6-tetra-O-acyl sucroses containing primarily short-chain branched carboxylic acids. The acyl constituents are primarily derived from 2-methylpropanoic, 2-methylbutyric, and 8-methylnonanoic acids but constituents derived fromn-decanoic and dodecanoic acids are also present. Sucrose esters inhibit settling and probing by aphids in glass feeding cages.

  19. Si-Accumulation In Artemisia annua Glandular Trichomes Increases Artemisinin Concentration, but Does Not Interfere In the Impairment of Toxoplasma gondii Growth

    PubMed Central

    Rostkowska, Cristina; Mota, Caroline M.; Oliveira, Taísa C.; Santiago, Fernanda M.; Oliveira, Lilian A.; Korndörfer, Gaspar H.; Lana, Regina M. Q.; Rossi, Monica L.; Nogueira, Neusa L.; Simonnet, Xavier; Mineo, Tiago W. P.; Silva, Deise A.O.; Mineo, José R.

    2016-01-01

    Artemisia annua is used as a source of artemisinin, a potent therapeutic agent used for the treatment of infectious diseases, chiefly malaria. However, the low concentration (from 0.01 to 1.4% of dried leaf matter) of artemisinin in the plant obtained with the traditional cropping system makes it a relatively expensive drug, especially in developing countries. Considering that artemisinin and silicon (Si) are both stored in A. annua glandular trichomes, and that Si accumulation has never been investigated, this study aimed to look into Si effects on A. annua trichome artemisinin concentration, and whether leaf infusion from Si-treated A. annua plants is able to control Toxoplasma gondii growth. T. gondii is the etiologic agent of toxoplasmosis, a zoonotic parasitic disease whose traditional treatment shows significant side effects. The experimental design consisted of A. annua seedlings randomly planted in soil treated with different doses of calcium/magnesium silicate (0, 200, 400, 800, and 1600 kg ha-1). Analysis of foliar macronutrients showed significant increases of nitrogen content only at the highest dose of silicate. Foliar micronutrients, Si concentrations, and plant height were not affected by any of the silicate doses. However, the dose of 400 kg ha-1 of silicate increased the trichome size, which in turn raised artemisinin concentration in leaves and the infusion. In contrast, the 800 and 1600 kg ha-1 doses dramatically decreased artemisinin concentration. HeLa cell treatment with the infusion of A. annua grown in soil treated with 400 kg ha-1 of silicate decreased parasite proliferation in a dose-dependent manner when the treatment was carried out after or along with T. gondii infection. However, this effect was similar to A. annua grown in soil without silicate treatment. Thus, it can be concluded that, even though Si applied to the soil at 400 kg ha-1 has a positive effect on the A. annua glandular trichome size and the artemisinin concentration

  20. Effect of external stress on density and size of glandular trichomes in full-grown Artemisia annua, the source of anti-malarial artemisinin

    PubMed Central

    Kjær, Anders; Grevsen, Kai; Jensen, Martin

    2012-01-01

    Background and aims Glandular trichomes (GT) of Artemisia annua produce valuable compounds for pharmaceutical and industrial uses, most notably the anti-malarial artemisinin. Our aim was to find out whether the density, number and size of GT can be manipulated to advantage by environmental stress. A range of external stress treatments, including stress response regulators, was therefore given to fully grown plants under field and greenhouse conditions. Methodology In a field experiment (Ex1), seed-grown plants were subjected to chemical or physical stress and plants analysed after 5 weeks. In a greenhouse experiment (Ex2), three groups of clonally derived plants were stressed at weekly intervals for 5 weeks. Stress treatments included sandblasting, leaf cutting and spraying with jasmonic acid, salicylic acid, chitosan oligosaccharide (COS), H2O2 (HP) and NaCl (SC)at different concentrations. Leaves from an upper and a lower position on the plants were analysed by fluorescence microscopy to determine the density and size of GT. Principal results Densities of GT on upper leaves of full-grown A. annua plants generally showed no response to external stress and only plants from one clone of Ex2 supported the hypothesis that increased density of GT was inducible in upper leaves by stress (significant for SC, HP and COS). The density of GT on lower leaves was not affected by stress in any experiment. Glandular trichomes were significantly smaller on the lower leaves in response to stress in Ex2, and a similar non-significant trend was observed in Ex1. Conclusions The results indicate a dynamic system in which stress treatments of large A. annua plants had a minor promoting effect on the initiation of GT in developing leaves, and a maturing effect of GT later in the lifetime of the individual GT. The hypothesis that applying stress can induce larger GT or more numerous GT was rejected. PMID:22833781

  1. A comprehensive proteome map of glandular trichomes of hop (Humulus lupulus L.) female cones: Identification of biosynthetic pathways of the major terpenoid-related compounds and possible transport proteins.

    PubMed

    Champagne, Antoine; Boutry, Marc

    2017-02-15

    Female flowers of hop (Humulus lupulus) are an essential source of terpenoid-related compounds, which are mainly used as flavoring in the beer brewing process. The compounds involved are bitter acids, terpenophenolics, as well as mono- and sesquiterpenoids. In this work, we analyzed the proteome of purified glandular trichomes (lupulin glands) from female flowers, which produce and accumulate these compounds. An extensive 2D-LC-MS/MS analysis identified 1,015 proteins. Of these, most correspond to housekeeping and primary metabolism-related proteins, albeit predominantly including amino acid and lipid metabolism, which feeds the specialized (secondary) metabolism. Indeed, 75 proteins belong to the specialized metabolism. No less than 40 enzymes are involved in the synthesis of terpenoid-derived compounds and 21 are predicted transporters, some of which might be involved in the transport of specialized metabolites. We discuss the possible routes involved in the intra- and intercellular translocation of terpenoids and their precursors. This comprehensive proteomic map of the glandular trichomes of hop female flowers represents a valuable resource to improve our knowledge on the function of glandular trichomes. This article is protected by copyright. All rights reserved.

  2. Trichome structure and evolution in Neotropical lianas

    PubMed Central

    Nogueira, Anselmo; El Ottra, Juliana Hanna Leite; Guimarães, Elza; Machado, Silvia Rodrigues; Lohmann, Lúcia G.

    2013-01-01

    Background and Aims Trichomes are epidermal outgrowths generally associated with protection against herbivores and/or desiccation that are widely distributed from ferns to angiosperms. Patterns of topological variation and morphological evolution of trichomes are still scarce in the literature, preventing valid comparisons across taxa. This study integrates detailed morphoanatomical data and the evolutionary history of the tribe Bignonieae (Bignoniaceae) in order to gain a better understanding of current diversity and evolution of trichome types. Methods Two sampling schemes were used to characterize trichome types: (1) macromorphological characterization of all 105 species currently included in Bignonieae; and (2) micromorphological characterization of 16 selected species. Individual trichome morphotypes were coded as binary in each vegetative plant part, and trichome density and size were coded as multistate. Ancestral character state reconstructions were conducted using maximum likelihood (ML) assumptions. Key Results Two main functional trichome categories were found: non-glandular and glandular. In glandular trichomes, three morphotypes were recognized: peltate (Pg), stipitate (Sg) and patelliform/cupular (P/Cg) trichomes. Non-glandular trichomes were uniseriate, uni- or multicellular and simple or branched. Pg and P/Cg trichomes were multicellular and non-vascularized with three clearly distinct cell layers. Sg trichomes were multicellular, uniseriate and long-stalked. ML ancestral character state reconstructions suggested that the most recent common ancestor (MRCA) of Bignonieae probably had non-glandular, Pg and P/Cg trichomes, with each trichome type presenting alternative histories of appearance on the different plant parts. For example, the MRCA of Bignonieae probably had non-glandular trichomes on the stems, prophylls, petiole, petiolule and leaflet veins while P/Cg trichomes were restricted to leaflet blades. Sg trichomes were not present in the MRCA

  3. Morphology, Structure, and Ontogeny of Trichomes of the Grape Genus (Vitis, Vitaceae)

    PubMed Central

    Ma, Zhi-Yao; Wen, Jun; Ickert-Bond, Stefanie M.; Chen, Long-Qing; Liu, Xiu-Qun

    2016-01-01

    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. We observed that glandular trichomes of V. romanetii secrete mucilage and volatile substances which trap insectes on the 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. PMID:27252720

  4. New Approaches for Studying and Exploiting an Old Protuberance, the Plant Trichome

    PubMed Central

    WAGNER, G. J.; WANG, E.; SHEPHERD, R. W.

    2004-01-01

    • Background and aims Much recent study of plant trichomes has focused on various aspects of glandular secreting trichomes (GSTs) and differentiation of simple trichomes. This Botanical Briefing will highlight: ‐ research on various aspects of, and manipulation of glandular secreting trichomes; ‐ molecular aspects of the differentiation and development of simple trichomes of arabidopsis and cotton; ‐ how methods for manipulation of model systems used in the above work can be applied to expand our understanding of less studied surface structures of plants. • Scope The Briefing will cover: ‐ established and suggested roles of simple and glandular secreting trichomes; ‐ recent results regarding solute and ion movement in trichomes; ‐ methods for isolating trichomes; ‐ recent studies of trichome differentiation and development; ‐ attempts to modify metabolism in secreting trichomes; ‐ efforts to exploit trichomes for commercial and agronomic purposes. PMID:14678941

  5. Multicellular Secretory Trichome Development on Soybean and Related Glycine Gynoecia

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Multicellular glandular trichomes form on gynoecia of wild Glycine annual species, annual soybean cultivars, and wild perennial species. These trichomes occur on gynoecia of annual taxa from ovary base to style base, and along style of perennial species. Trichomes form at least two days prior to ant...

  6. 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.

    PubMed

    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.

  7. Trichomes as sensors: detecting activity on the leaf surface.

    PubMed

    Tooker, John F; Peiffer, Michelle; Luthe, Dawn S; Felton, Gary W

    2010-01-01

    The dramatic movements of some carnivorous plants species are triggered by sensory structures derived from trichomes. While unusual plant species such as the Venus fly trap and sundews may be expected to have elaborate sensors to capture their insect prey, more modest plant species might not be expected to have similar sensory capabilities. Our recent work, however, has revealed that glandular trichomes on tomato (Solanum lycopersicum) appear to have a function similar to trigger hairs of carnivorous species, acting as "early warning" sensors. Using a combination of behavioral, molecular, and biochemical techniques, we determined that caterpillars, moths and mechanical disruption upregulate signaling molecules and defensive genes found in glandular trichomes. Importantly, we discovered that plants whose trichomes have been broken respond more vigorously when their defenses were induced. Taken together, our results suggest that glandular trichomes can act as sensors that detect activity on the leaf surface, and ready plants for herbivore attack.

  8. Trichoderma species form endophytic associations within Theobroma cacao trichomes.

    PubMed

    Bailey, Bryan A; Strem, Mary D; Wood, Delilah

    2009-12-01

    Trichoderma species are usually considered soil organisms that colonize plant roots, sometimes forming a symbiotic relationship. Recent studies demonstrate that Trichoderma species are also capable of colonizing the above ground tissues of Theobroma cacao (cacao) in what has been characterized as an endophytic relationship. Trichoderma species can be re-isolated from surface sterilized cacao stem tissue, including the bark and xylem, the apical meristem, and to a lesser degree from leaves. SEM analysis of cacao stems colonized by strains of four Trichoderma species (Trichoderma ovalisporum-DIS 70a, Trichoderma hamatum-DIS 219b, Trichoderma koningiopsis-DIS 172ai, or Trichoderma harzianum-DIS 219f) showed a preference for surface colonization of glandular trichomes versus non-glandular trichomes. The Trichoderma strains colonized the glandular trichome tips and formed swellings resembling appresoria. Hyphae were observed emerging from the glandular trichomes on surface sterilized stems from cacao seedlings that had been inoculated with each of the four Trichoderma strains. Fungal hyphae were observed under the microscope emerging from the trichomes as soon as 6h after their isolation from surface sterilized cacao seedling stems. Hyphae were also observed, in some cases, emerging from stalk cells opposite the trichome head. Repeated single trichome/hyphae isolations verified that the emerging hyphae were the Trichoderma strains with which the cacao seedlings had been inoculated. Strains of four Trichoderma species were able to enter glandular trichomes during the colonization of cacao stems where they survived surface sterilization and could be re-isolated. The penetration of cacao trichomes may provide the entry point for Trichoderma species into the cacao stem allowing systemic colonization of this tissue.

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

    PubMed Central

    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. PMID:27625674

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

    PubMed

    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.

  11. Mining the mouse transcriptome of receptive endometrium reveals distinct molecular signatures for the luminal and glandular epithelium.

    PubMed

    Niklaus, Andrea L; Pollard, Jeffrey W

    2006-07-01

    Epithelia coat most tissues where they sense and respond to the environment and participate in innate immune responses. In the adult mouse uterus, columnar epithelium lines the central lumen and the glands that penetrate the underlying stroma. A nidatory surge of estrogen causes differentiation of the luminal epithelium to the receptive state that permits blastocyst attachment and allows subsequent implantation. Here, using laser-capture microdissection to isolate the luminal and glandular epithelia separately, we have profiled gene expression 2 h before embryo attachment to determine whether there are unique roles for these two epithelial structures in this process. Although most genes were expressed in both compartments, there was greater expression of 153 and 118 genes in the lumen and glands, respectively. In the luminal epithelium, there is enrichment in lipid, metal-ion binding, and carbohydrate-metabolizing enzymes, whereas in the glands, immune response genes are emphasized. In situ hybridization to uterine sections obtained from mice during the preimplantation period validated these data and indicated an array of previously undocumented genes expressed with unique patterns in these epithelia. The data show that each epithelial compartment has a distinct molecular signature and that they act differentially and synergistically to permit blastocyst implantation.

  12. Micro-trichome as a class I homeodomain-leucine zipper gene regulates multicellular trichome development in Cucumis sativus.

    PubMed

    Zhao, Jun-Long; Pan, Jun-Song; Guan, Yuan; Zhang, Wei-Wei; Bie, Bei-Bei; Wang, Yun-Li; He, Huan-Le; Lian, Hong-Li; Cai, Run

    2015-11-01

    Plant trichomes serve as a highly suitable model for investigating cell differentiation at the single-cell level. The regulatory genes involved in unicellular trichome development in Arabidopsis thaliana have been intensively studied, but genes regulating multicellular trichome development in plants remain unclear. Here, we characterized Cucumis sativus (cucumber) trichomes as representative multicellular and unbranched structures, and identified Micro-trichome (Mict), using map-based cloning in an F2 segregating population of 7,936 individuals generated from a spontaneous mict mutant. In mict plants, trichomes in both leaves and fruits, are small, poorly developed, and denser than in the wild type. Sequence analysis revealed that a 2,649-bp genomic deletion, spanning the first and second exons, occurred in a plant-specific class I homeodomain-leucine zipper gene. Tissue-specific expression analysis indicated that Mict is strongly expressed in the trichome cells. Transcriptome profiling identified potential targets of Mict including putative homologs of genes known in other systems to regulate trichome development, meristem determinacy, and hormone responsiveness. Phylogenic analysis charted the relationships among putative homologs in angiosperms. Our paper represents initial steps toward understanding the development of multicellular trichomes.

  13. Trichomes related to an unusual method of water retention and protection of the stem apex in an arid zone perennial species

    PubMed Central

    Lusa, Makeli Garibotti; Cardoso, Elaine Cristina; Machado, Silvia Rodrigues; Appezzato-da-Glória, Beatriz

    2015-01-01

    It is well known that trichomes protect plant organs, and several studies have investigated their role in the adaptation of plants to harsh environments. Recent studies have shown that the production of hydrophilic substances by glandular trichomes and the deposition of this secretion on young organs may facilitate water retention, thus preventing desiccation and favouring organ growth until the plant develops other protective mechanisms. Lychnophora diamantinana is a species endemic to the Brazilian ‘campos rupestres’ (rocky fields), a region characterized by intense solar radiation and water deficits. This study sought to investigate trichomes and the origin of the substances observed on the stem apices of L. diamantinana. Samples of stem apices, young and expanded leaves were studied using standard techniques, including light microscopy and scanning and transmission electron microscopy. Histochemical tests were used to identify the major groups of metabolites present in the trichomes and the hyaline material deposited on the apices. Non-glandular trichomes and glandular trichomes were observed. The material deposited on the stem apices was hyaline, highly hydrophilic and viscous. This hyaline material primarily consists of carbohydrates that result from the partial degradation of the cell wall of uniseriate trichomes. This degradation occurs at the same time that glandular trichomes secrete terpenoids, phenolic compounds and proteins. These results suggest that the non-glandular trichomes on the leaves of L. diamantinana help protect the young organ, particularly against desiccation, by deposition of highly hydrated substances on the apices. Furthermore, the secretion of glandular trichomes probably repels herbivore and pathogen attacks. PMID:25527474

  14. Morphology of foliar trichomes of the Chinese cork oak Quercus variabilis by electron microscopy and three-dimensional surface profiling.

    PubMed

    Kim, Ki Woo; Cho, Do-Hyun; Kim, Pan-Gi

    2011-06-01

    Morphology of foliar trichomes was analyzed in Quercus variabilis by electron microscopy and three-dimensional surface profiling. Leaves from suppressed or dominant sprouts of the oak species were collected after a forest fire to unravel the effects of the disturbance factor on sprouting of the oak species. Scanning electron microscopy revealed two types of trichomes depending on the leaf surface. The trichomes on the adaxial surface were branched and constricted, and possessed a single row of thin-walled cells with a collapsed morphology (glandular branched uniseriate trichomes). Meanwhile, the trichomes on the abaxial surface were star-shaped, unfused with each other, and had 6 to 10 rays (nonglandular simple stellate trichomes). An apparent proliferation of trichomes was evident on the adaxial surface of the dominant sprouts. Uniseriate trichomes could be discernable as an elevation from the surface by white light scanning interferometry. By transmission electron microscopy, thin and convoluted cell wall, degenerated cytoplasm, and a single row of cells were characteristic of the trichomes on the adaxial surface. The thick cell walls of the mature trichomes on the abaxial surface represented the nonglandular nature. This is the first report on the morphological and ultrastructural characterization of foliar trichomes of the oak species.

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

    PubMed

    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. Polymethylated Myricetin in Trichomes of the Wild Tomato Species Solanum habrochaites and Characterization of Trichome-Specific 3′/5′- and 7/4′-Myricetin O-Methyltransferases1[C][W][OA

    PubMed Central

    Schmidt, Adam; Li, Chao; Shi, Feng; Jones, A. Daniel; Pichersky, Eran

    2011-01-01

    Flavonoids are a class of metabolites found in many plant species. They have been reported to serve several physiological roles, such as in defense against herbivores and pathogens and in protection against harmful ultraviolet radiation. They also serve as precursors of pigment compounds found in flowers, leaves, and seeds. Highly methylated, nonglycosylated derivatives of the flavonoid myricetin flavonoid, have been previously reported from a variety of plants, but O-methyltransferases responsible for their synthesis have not yet been identified. Here, we show that secreting glandular trichomes (designated types 1 and 4) and storage glandular trichomes (type 6) on the leaf surface of wild tomato (Solanum habrochaites accession LA1777) plants contain 3,7,3′-trimethyl myricetin, 3,7,3′,5′-tetramethyl myricetin, and 3,7,3′,4′,5′-pentamethyl myricetin, with gland types 1 and 4 containing severalfold more of these compounds than type 6 glands and with the tetramethylated compound predominating in all three gland types. We have also identified transcripts of two genes expressed in the glandular trichomes and showed that they encode enzymes capable of methylating myricetin at the 3′ and 5′ and the 7 and 4′ positions, respectively. Both genes are preferentially expressed in secreting glandular trichome types 1 and 4 and to a lesser degree in storage trichome type 6, and the levels of the proteins they encode are correspondingly higher in types 1 and 4 glands compared with type 6 glands. PMID:21343428

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

    PubMed

    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.

  18. Trichome-derived O-acyl sugars are a first meal for caterpillars that tags them for predation

    PubMed Central

    Weinhold, Alexander; Baldwin, Ian Thomas

    2011-01-01

    Plant glandular trichomes exude secondary metabolites with defensive functions, but these epidermal protuberances are surprisingly the first meal of Lepidopteran herbivores on Nicotiana attenuata. O-acyl sugars, the most abundant metabolite of glandular trichomes, impart a distinct volatile profile to the body and frass of larvae that feed on them. The headspace composition of Manduca sexta larvae is dominated by the branched chain aliphatic acids hydrolyzed from ingested O-acyl sugars, which waxes and wanes rapidly with trichome ingestion. In native habitats a ground-hunting predator, the omnivorous ant Pogonomyrmex rugosus, but not the big-eyed bug Geocoris spp., use these volatile aliphatic acids to locate their prey. PMID:21518882

  19. Trichomes as dangerous lollipops

    PubMed Central

    Stork, William F. J.; Weinhold, Alexander; Baldwin, Ian T.

    2011-01-01

    When attacked by herbivores, plants produce toxic secondary metabolites that function as direct defenses, as well as indirect defenses that attract and reward predators of the offending herbivores. These indirect defenses include both nutritive rewards such as extra floral nectar, as well as informational rewards, such as the production and release of volatile compounds that betray the location of feeding herbivores to predators. Herbivory of Nicotiana attenuata by the tobacco hornworm (Manduca larvae) alters the volatile profiles of both the plant and larval headspace. Herbivory-elicited specific changes in the volatile profiles are detected by arthropod predators of Manduca larvae. The known predators that perceive volatile cues induced by Manduca herbivory of N. attenuata are insects that target Manduca at early developmental stages, when the larvae are still small; large, late-instar larvae may have outgrown these predation risks. However, here we offer evidence that branched chain aliphatic acids derived from the digestion of plant O-acyl sugars from trichomes may betray Manduca larvae to lizard predators during late developmental stages as well. PMID:22095147

  20. Photosynthetic Trichomes Contain a Specific Rubisco with a Modified pH-Dependent Activity1[OPEN

    PubMed Central

    Laterre, Raphaëlle; Remacle, Claire

    2017-01-01

    Ribulose-1,5-biphosphate carboxylase/oxygenase (Rubisco) is the most abundant enzyme in plants and is responsible for CO2 fixation during photosynthesis. This enzyme is assembled from eight large subunits (RbcL) encoded by a single chloroplast gene and eight small subunits (RbcS) encoded by a nuclear gene family. Rubisco is primarily found in the chloroplasts of mesophyll (C3 plants), bundle-sheath (C4 plants), and guard cells. In certain species, photosynthesis also takes place in the secretory cells of glandular trichomes, which are epidermal outgrowths (hairs) involved in the secretion of specialized metabolites. However, photosynthesis and, in particular, Rubisco have not been characterized in trichomes. Here, we show that tobacco (Nicotiana tabacum) trichomes contain a specific Rubisco small subunit, NtRbcS-T, which belongs to an uncharacterized phylogenetic cluster (T). This cluster contains RbcS from at least 33 species, including monocots, many of which are known to possess glandular trichomes. Cluster T is distinct from the cluster M, which includes the abundant, functionally characterized RbcS isoforms expressed in mesophyll or bundle-sheath cells. Expression of NtRbcS-T in Chlamydomonas reinhardtii and purification of the full Rubisco complex showed that this isoform conferred higher Vmax and Km values as well as higher acidic pH-dependent activity than NtRbcS-M, an isoform expressed in the mesophyll. This observation was confirmed with trichome extracts. These data show that an ancient divergence allowed for the emergence of a so-far-uncharacterized RbcS cluster. We propose that secretory trichomes have a particular Rubisco uniquely adapted to secretory cells where CO2 is released by the active specialized metabolism. PMID:28250069

  1. A cold-tolerant evergreen interspecific hybrid of Ocimum kilimandscharicum and Ocimum basilicum: analyzing trichomes and molecular variations.

    PubMed

    Dhawan, Sunita Singh; Shukla, Preeti; Gupta, Pankhuri; Lal, R K

    2016-05-01

    Ocimum (Lamiaceae) is an important source of essential oils and aroma chemicals especially eugenol, methyl eugenol, linalool, methyl chavicol etc. An elite evergreen hybrid has been developed from Ocimum kilimandscharicum and Ocimum basilicum, which demonstrated adaptive behavior towards cold stress. A comparative molecular analysis has been done through RAPD, AFLP, and ISSR among O. basilicum and O. kilimandscharicum and their evergreen cold-tolerant hybrid. The RAPD and AFLP analyses demonstrated similar results, i.e., the hybrid of O. basilicum and O. kilimandscharicum shares the same cluster with O. kilimandscharicum, while O. basilicum behaves as an outgroup, whereas in ISSR analysis, the hybrid genotype grouped in the same cluster with O. basilicum. Ocimum genotypes were analyzed and compared for their trichome density. There were distinct differences on morphology, distribution, and structure between the two kinds of trichomes, i.e., glandular and non-glandular. Glandular trichomes contain essential oils, polyphenols, flavonoids, and acid polysaccharides. Hair-like trichomes, i.e., non-glandular trichomes, help in keeping the frost away from the living surface cells. O. basilicum showed less number of non-glandular trichomes on leaves compared to O. kilimandscharicum and the evergreen cold-tolerant hybrid. Trichomes were analyzed in O. kilimandscharicum, O. basilicum, and their hybrid. An increased proline content at the biochemical level represents a higher potential to survive in a stress condition like cold stress. In our analysis, the proline content is quite higher in tolerant variety O. kilimandscharicum, low in susceptible variety O. basilicum, and intermediate in the hybrid. Gene expression analysis was done in O. basilicum, O. kilimandscharicum and their hybrid for TTG1, GTL1, and STICHEL gene locus which regulates trichome development and its formation and transcription factors WRKY and MPS involved in the regulation of plant responses to freezing

  2. Ecological distribution of leaf stomata and trichomes among tree species in a Malaysian lowland tropical rain forest.

    PubMed

    Ichie, Tomoaki; Inoue, Yuta; Takahashi, Narumi; Kamiya, Koichi; Kenzo, Tanaka

    2016-07-01

    The vertical structure of a tropical rain forest is complex and multilayered, with strong variation of micro-environment with height up to the canopy. We investigated the relation between morphological traits of leaf surfaces and tree ecological characteristics in a Malaysian tropical rain forest. The shapes and densities of stomata and trichomes on the abaxial leaf surfaces and their relation with leaf characteristics such as leaf area and leaf mass per area (LMA) were studied in 136 tree species in 35 families with different growth forms in the tropical moist forest. Leaf physiological properties were also measured in 50 canopy and emergent species. Most tree species had flat type (40.4 %) or mound type (39.7 %) stomata. In addition, 84 species (61.76 %) in 22 families had trichomes, including those with glandular (17.65 %) and non-glandular trichomes (44.11 %). Most leaf characteristics significantly varied among the growth form types: species in canopy and emergent layers and canopy gap conditions had higher stomatal density, stomatal pore index (SPI), trichome density and LMA than species in understory and subcanopy layers, though the relation of phylogenetically independent contrasts to each characteristic was not statistically significant, except for leaf stomatal density, SPI and LMA. Intrinsic water use efficiency in canopy and emergent tree species with higher trichome densities was greater than in species with lower trichome densities. These results suggest that tree species in tropical rain forests adapt to a spatial difference in their growth forms, which are considerably affected by phylogenetic context, by having different stomatal and trichome shapes and/or densities.

  3. Molecular cloning of the tomato Hairless gene implicates actin dynamics in trichome-mediated defense and mechanical properties of stem tissue

    PubMed Central

    Kang, Jin-Ho; Campos, Marcelo L.; Zemelis-Durfee, Starla; Al-Haddad, Jameel M.; Jones, A. Daniel; Telewski, Frank W.; Brandizzi, Federica; Howe, Gregg A.

    2016-01-01

    Trichomes are epidermal structures that provide a first line of defense against arthropod herbivores. The recessive hairless (hl) mutation in tomato (Solanum lycopersicum L.) causes severe distortion of trichomes on all aerial tissues, impairs the accumulation of sesquiterpene and polyphenolic compounds in glandular trichomes, and compromises resistance to the specialist herbivore Manduca sexta. Here, we demonstrate that the tomato Hl gene encodes a subunit (SRA1) of the highly conserved WAVE regulatory complex that controls nucleation of actin filaments in a wide range of eukaryotic cells. The tomato SRA1 gene spans a 42-kb region containing both Solyc11g013280 and Solyc11g013290. The hl mutation corresponds to a complex 3-kb deletion that removes the last exon of the gene. Expression of a wild-type SRA1 cDNA in the hl mutant background restored normal trichome development, accumulation of glandular trichome-derived metabolites, and resistance to insect herbivory. These findings establish a role for SRA1 in the development of tomato trichomes and also implicate the actin-cytoskeleton network in cytosolic control of specialized metabolism for plant defense. We also show that the brittleness of hl mutant stems is associated with altered mechanical and cell morphological properties of stem tissue, and demonstrate that this defect is directly linked to the mutation in SRA1. PMID:27481446

  4. Molecular cloning of the tomato Hairless gene implicates actin dynamics in trichome-mediated defense and mechanical properties of stem tissue.

    PubMed

    Kang, Jin-Ho; Campos, Marcelo L; Zemelis-Durfee, Starla; Al-Haddad, Jameel M; Jones, A Daniel; Telewski, Frank W; Brandizzi, Federica; Howe, Gregg A

    2016-10-01

    Trichomes are epidermal structures that provide a first line of defense against arthropod herbivores. The recessive hairless (hl) mutation in tomato (Solanum lycopersicum L.) causes severe distortion of trichomes on all aerial tissues, impairs the accumulation of sesquiterpene and polyphenolic compounds in glandular trichomes, and compromises resistance to the specialist herbivore Manduca sexta Here, we demonstrate that the tomato Hl gene encodes a subunit (SRA1) of the highly conserved WAVE regulatory complex that controls nucleation of actin filaments in a wide range of eukaryotic cells. The tomato SRA1 gene spans a 42-kb region containing both Solyc11g013280 and Solyc11g013290 The hl mutation corresponds to a complex 3-kb deletion that removes the last exon of the gene. Expression of a wild-type SRA1 cDNA in the hl mutant background restored normal trichome development, accumulation of glandular trichome-derived metabolites, and resistance to insect herbivory. These findings establish a role for SRA1 in the development of tomato trichomes and also implicate the actin-cytoskeleton network in cytosolic control of specialized metabolism for plant defense. We also show that the brittleness of hl mutant stems is associated with altered mechanical and cell morphological properties of stem tissue, and demonstrate that this defect is directly linked to the mutation in SRA1.

  5. The Tomato odorless-2 Mutant Is Defective in Trichome-Based Production of Diverse Specialized Metabolites and Broad-Spectrum Resistance to Insect Herbivores1[W][OA

    PubMed Central

    Kang, Jin-Ho; Liu, Guanghui; Shi, Feng; Jones, A. Daniel; Beaudry, Randolph M.; Howe, Gregg A.

    2010-01-01

    Glandular secreting trichomes of cultivated tomato (Solanum lycopersicum) produce a wide array of volatile and nonvolatile specialized metabolites. Many of these compounds contribute to the characteristic aroma of tomato foliage and constitute a key part of the language by which plants communicate with other organisms in natural environments. Here, we describe a novel recessive mutation called odorless-2 (od-2) that was identified on the basis of an altered leaf-aroma phenotype. od-2 plants exhibit pleiotrophic phenotypes, including alterations in the morphology, density, and chemical composition of glandular trichomes. Type VI glandular trichomes isolated from od-2 leaves accumulate only trace levels of monoterpenes, sesquiterpenes, and flavonoids. Other foliar defensive compounds, including acyl sugars, glycoalkaloids, and jasmonate-regulated proteinase inhibitors, are produced in od-2 leaves. Growth of od-2 plants under natural field conditions showed that the mutant is highly susceptible to attack by an indigenous flea beetle, Epitrix cucumeris, and the Colorado potato beetle, Leptinotarsa decemlineata. The increased susceptibility of od-2 plants to Colorado potato beetle larvae and to the solanaceous specialist Manduca sexta was verified in no-choice bioassays. These findings indicate that Od-2 is essential for the synthesis of diverse trichome-borne compounds and further suggest that these compounds influence host plant selection and herbivore community composition under natural conditions. PMID:20668059

  6. The tomato odorless-2 mutant is defective in trichome-based production of diverse specialized metabolites and broad-spectrum resistance to insect herbivores.

    PubMed

    Kang, Jin-Ho; Liu, Guanghui; Shi, Feng; Jones, A Daniel; Beaudry, Randolph M; Howe, Gregg A

    2010-09-01

    Glandular secreting trichomes of cultivated tomato (Solanum lycopersicum) produce a wide array of volatile and nonvolatile specialized metabolites. Many of these compounds contribute to the characteristic aroma of tomato foliage and constitute a key part of the language by which plants communicate with other organisms in natural environments. Here, we describe a novel recessive mutation called odorless-2 (od-2) that was identified on the basis of an altered leaf-aroma phenotype. od-2 plants exhibit pleiotrophic phenotypes, including alterations in the morphology, density, and chemical composition of glandular trichomes. Type VI glandular trichomes isolated from od-2 leaves accumulate only trace levels of monoterpenes, sesquiterpenes, and flavonoids. Other foliar defensive compounds, including acyl sugars, glycoalkaloids, and jasmonate-regulated proteinase inhibitors, are produced in od-2 leaves. Growth of od-2 plants under natural field conditions showed that the mutant is highly susceptible to attack by an indigenous flea beetle, Epitrix cucumeris, and the Colorado potato beetle, Leptinotarsa decemlineata. The increased susceptibility of od-2 plants to Colorado potato beetle larvae and to the solanaceous specialist Manduca sexta was verified in no-choice bioassays. These findings indicate that Od-2 is essential for the synthesis of diverse trichome-borne compounds and further suggest that these compounds influence host plant selection and herbivore community composition under natural conditions.

  7. Hydathode trichomes actively secreting water from leaves play a key role in the physiology and evolution of root-parasitic rhinanthoid Orobanchaceae

    PubMed Central

    Světlíková, Petra; Hájek, Tomáš; Těšitel, Jakub

    2015-01-01

    Background and Aims Root hemiparasites from the rhinanthoid clade of Orobanchaceae possess metabolically active glandular trichomes that have been suggested to function as hydathode trichomes actively secreting water, a process that may facilitate resource acquisition from the host plant’s root xylem. However, no direct evidence relating the trichomes to water secretion exists, and carbon budgets associated with this energy-demanding process have not been determined. Methods Macro- and microscopic observations of the leaves of hemiparasitic Rhinanthus alectorolophus were conducted and night-time gas exchange was measured. Correlations were examined among the intensity of guttation, respiration and transpiration, and analysis of these correlations allowed the carbon budget of the trichome activity to be quantified. We examined the intensity of guttation, respiration and transpiration, correlations among which indicate active water secretion. Key Results Guttation was observed on the leaves of 50 % of the young, non-flowering plants that were examined, and microscopic observations revealed water secretion from the glandular trichomes present on the abaxial leaf side. Night-time rates of respiration and transpiration and the presence of guttation drops were positively correlated, which is a clear indicator of hydathode trichome activity. Subsequent physiological measurements on older, flowering plants indicated neither intense guttation nor the presence of correlations, which suggests that the peak activity of hydathodes is in the juvenile stage. Conclusions This study provides the first unequivocal evidence for the physiological role of the hydathode trichomes in active water secretion in the rhinanthoid Orobanchaceae. Depending on the concentration of organic elements calculated to be in the host xylem sap, the direct effect of water secretion on carbon balance ranges from close to neutral to positive. However, it is likely to be positive in the xylem-only feeding

  8. Glandular hairs of Sigesbeckia jorullensis Kunth (Asteraceae): morphology, histochemistry and composition of essential oil.

    PubMed

    Heinrich, G; Pfeifhofer, H W; Stabentheiner, E; Sawidis, T

    2002-04-01

    Long-stalked glandular hairs of outer and inner involucral bracts of Sigesbeckia jorullensis, which are important for epizoic fruit propagation, were investigated using light and scanning electron microscopy. The essential oil secreted by the hairs was analysed by chromatographic methods including gas chromatography/mass spectrometry and with a laser microprobe mass analyser. The glandular hairs consisted of a large multicellular stalk and a multicellular secreting head. The apical layer of glandular head cells was characterized by leucoplasts and calcium oxalate crystals. Below the apical cells there were up to six layers of cells containing many chloroplasts around the nucleus and surrounded by vacuoles filled with flavonoids and tannins. The essential oil originating in the head cells was secreted into the subcuticular space and may be liberated by rupture of the cuticle. It was mainly composed of sesqui- and diterpenes, with the sesquiterpene hydrocarbon germacrene-D as the main component. Monoterpenes, n-alkanes and their derivatives as well as flavonoid aglycones were also detected. The stickiness of the essential oil is probably associated with the high content of oxygenated sesqui- and diterpenes. In addition to long-stalked trichomes, small biseriate trichomes occurred, secreting small quantities of essential oil into a subcuticular space.

  9. Secretory trichomes, a substitutive floral nectar source in Lundia A. DC. (Bignoniaceae), a genus lacking a functional disc.

    PubMed

    Lopes, Ariadna Valentina; Vogel, Stefan; Machado, Isabel Cristina

    2002-08-01

    This is the first report of corolla-borne secretory trichomes that substitute in role for a non-functional disc in a species of the neotropical genus Lundia A. DC. (Bignoniaceae). The floral biology and flowering phenology of Lundia cordata were investigated at two remnants of tropical rainforest in northeastern Brazil. This species is a typically omithophilous liana, with reddish, tubular, scentless flowers. The flowers are resupinate, protandrous and last for 2 d. There is a vestigial non-functional perigynous disc and nectar is secreted by glandular trichomes distributed along the internal surface of the corolla. The nectar is stored at the base of the corolla tube, thus showing secondary nectar presentation. The nectariferous trichomes are multi-cellular, uniseriate, with a basal foot cell rooting in the epidermis, one neck cell, and a glandular head with 13 cells on average. Three species of hummingbirds (Amazilia fimbriata, Eupetomena macroura and Phaethornis pretrei) serve as pollinators. Phaethornis ruber, Xylocopa bees, wasps and diurnal moths are considered nectar thieves.

  10. Leaf trichome density may explain herbivory patterns of Actinote sp. (Lepidoptera: Acraeidae) on Liabum mandonii (Asteraceae) in a montane humid forest (Nor Yungas, Bolivia)

    NASA Astrophysics Data System (ADS)

    Molina-Montenegro, Marco A.; Ávila, Pamela; Hurtado, Rosember; Valdivia, Alejandra I.; Gianoli, Ernesto

    2006-09-01

    Increasing evidence shows that most insect herbivores of tropical forests show specific associations with their hosts. Environmental factors as well as foliar characters can modify insect preference. In the present work, we evaluated in a montane humid forest the preference and herbivory rate of Actinote sp. caterpillars (Lepidoptera: Acraeidae) on mature and young leaves of their specific host plant Liabum mandonii (Asteraceae) in two contrasting sites. Additionally, the density of non-glandular trichomes in young and mature leaves of plant at each site was evaluated. Analysis of variance of herbivory showed significant effects of site, leaf age, and the interaction of these factors. Higher herbivory levels were found on leaves from the site with lower levels of radiation and on mature leaves. On the other hand, trichome density was significantly higher in leaves from the site with higher levels of radiation and in young leaves. This suggests trichomes may explain the observed pattern of herbivory.

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

    PubMed

    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. Ultrastructure of hydathode trichomes of hemiparasitic Rhinanthus alectorolophus and Odontites vernus: how important is their role in physiology and evolution of parasitism in Orobanchaceae?

    PubMed

    Těšitel, J; Tesařová, M

    2013-01-01

    The Rhinanthoid clade of the family Orobanchaceae comprises plants displaying a hemiparasitic or holoparasitic strategy of resource acquisition. Some of its species (mainly Rhinanthus spp.) are often used as models for studies of hemiparasite physiology. Although there is a well-developed concept covering their physiological processes, most recent studies have neglected the existence of hydathode trichomes present on leaves of these hemiparasitic plants. As a first step for the proposed integration of these structures in the theory of physiological processes of the hemiparasites, we described the outer micromorphology and ultrastructure of the hydathode trichomes on leaves of hemiparasitic Rhinanthus alectorolophus and Odontites vernus with scanning and transmission electron microscopy (SEM and TEM, respectively). The TEM inspections of both types of trichome revealed typical ultrastructural features: labyrinthine cell wall, high content of cytoplasm in cells with numerous mitochondria and presence of plasmodesmata. All these features indicate high metabolic activity complying with their function as glandular trichomes actively secreting water. The active secretion of water by the hydathode trichomes (evidence for which is summarised here) also presents a possible mechanism explaining results of previous gas exchange measurements detecting high dark respiration and transpiration rates and a tight inter-correlation between them in hemiparasitic Orobanchaceae. In addition, this process is hypothesised to have allowed multiple evolutionary transitions from facultative to obligate hemiparasitism and unique xylem-feeding holoparasitism of Lathraea with a long-lived underground stage featuring a rhizome covered by scales of leaf origin.

  13. Taxonomic significance of trichomes micromorphology in cucurbits.

    PubMed

    Ali, Mohammad Ajmal; Al-Hemaid, Fahad M A

    2011-01-01

    Studies on trichomes micromorphology using Scanning Electron Microscope (SEM) were undertaken in 23 species with one variety under 13 genera of the family Cucurbitaceae (viz., Benincasa hispida (Thunb.) Cogn., Citrullus lanatus (Thunb.) Matsum. & Nakai, Cucumis melo var. agrestis Naudin, Cucumis sativus L., Diplocyclos palmatus (L.) C. Jeffrey, Edgaria dargeelingensis C.B. Clarke, Gynostemma burmanicum King ex Chakr., Gynostemma pentaphyllum (Thunb.) Makino, Gynostemma pubescens (Gagnep.) C.Y. Wu, Hemsleya dipterygia Kuang & A.M. Lu, Lagenaria siceraria (Molina) Standl., Luffa acutangula (L.) Roxb., Luffa cylindrica M. Roem., Luffa echinata Roxb., Melothria heterophylla (Lour.) Cogn., Melothria leucocarpa (Blume) Cogn., Melothria maderspatana (L.) Cogn., Sechium edule (Jacq.) Sw., Thladiantha cordifolia (Blume) Cogn., Trichosanthes cucumerina L., T. cucumerina var. anguina (L.) Haines, Trichosanthes dioica Roxb., Trichosanthes lepiniana (Naudin) Cogn. and T. tricuspidata Lour.). The trichomes in the family Cucurbitaceae vary from unicellular to multicellular, conical to elongated, smooth to ridges, with or without flattened disk at base and cyctolithic appendages, thin to thick walled, curved at apices to blunt. Trichomes micromorphology in the family Cucurbitaceae was found significant taxonomically.

  14. Proteomic snapshot of spearmint (Mentha spicata L.) leaf trichomes: a genuine terpenoid factory.

    PubMed

    Champagne, Antoine; Boutry, Marc

    2013-11-01

    Peltate glandular trichomes from Mentha spicata were purified on a Percoll gradient and soluble and membrane proteins were trypsinized and the peptides were separated by nano-LC fractionation and analyzed by MALDI-MS/MS. The vast majority of the 1666 proteins identified were housekeeping proteins or involved in the primary metabolism. However, 57 were predicted to be involved in the secondary metabolism. Of these, 21 were involved in the synthesis of phenylpropanoids and phenolics and 32 in terpenoid synthesis. Of the 14 membrane transporters identified, the 11 ATP-binding cassette transporters provide good material for assessing whether active transport is required for the transfer of monoterpenoid intermediates between cellular compartments and for the secretion of the final products into the subcuticular storage cavity. In conclusion, this proteome analysis of M. spicata peltate trichomes has identified several candidate proteins that might be involved in terpenoid synthesis and transport. The data have been deposited to the ProteomeXchange with identifier PXD000352 (http://proteomecentral.proteomexchange.org/dataset/PXD000352).

  15. Studies of a Biochemical Factory: Tomato Trichome Deep Expressed Sequence Tag Sequencing and Proteomics1[W][OA

    PubMed Central

    Schilmiller, Anthony L.; Miner, Dennis P.; Larson, Matthew; McDowell, Eric; Gang, David R.; Wilkerson, Curtis; Last, Robert L.

    2010-01-01

    Shotgun proteomics analysis allows hundreds of proteins to be identified and quantified from a single sample at relatively low cost. Extensive DNA sequence information is a prerequisite for shotgun proteomics, and it is ideal to have sequence for the organism being studied rather than from related species or accessions. While this requirement has limited the set of organisms that are candidates for this approach, next generation sequencing technologies make it feasible to obtain deep DNA sequence coverage from any organism. As part of our studies of specialized (secondary) metabolism in tomato (Solanum lycopersicum) trichomes, 454 sequencing of cDNA was combined with shotgun proteomics analyses to obtain in-depth profiles of genes and proteins expressed in leaf and stem glandular trichomes of 3-week-old plants. The expressed sequence tag and proteomics data sets combined with metabolite analysis led to the discovery and characterization of a sesquiterpene synthase that produces β-caryophyllene and α-humulene from E,E-farnesyl diphosphate in trichomes of leaf but not of stem. This analysis demonstrates the utility of combining high-throughput cDNA sequencing with proteomics experiments in a target tissue. These data can be used for dissection of other biochemical processes in these specialized epidermal cells. PMID:20431087

  16. Arabidopsis GLASSY HAIR genes promote trichome papillae development

    PubMed Central

    Kirik, Viktor

    2013-01-01

    Specialized plant cells form cell walls with distinct composition and properties pertinent to their function. Leaf trichomes in Arabidopsis form thick cell walls that support the upright growth of these large cells and, curiously, have strong light-reflective properties. To understand the process of trichome cell-wall maturation and the molecular origins of this optical property, mutants affected in trichome light reflection were isolated and characterized. It was found that GLASSY HAIR (GLH) genes are required for the formation of surface papillae structures at late stages of trichome development. Trichomes in these mutants appeared transparent due to unobstructed light transmission. Genetic analysis of the isolated mutants revealed seven different gene loci. Two—TRICHOME BIREFRINGENCE (TBR) and NOK (Noeck)—have been reported previously to have the glassy trichome mutant phenotype. The other five glh mutants were analysed for cell-wall-related phenotypes. A significant reduction was found in cellulose content in glh2 and glh4 mutant trichomes. In addition to the glassy trichome phenotype, the glh6 mutants showed defects in leaf cuticular wax, and glh6 was found to represent a new allele of the eceriferum 10 (cer10) mutation. Trichomes of the glh1 and glh3 mutants did not show any other phenotypes beside reduced papillae formation. These data suggest that the GLH1 and GLH3 genes may have specific functions in trichome papillae formation, whereas GLH2, GLH4, and GLH6 genes are also involved in deposition of other cell-wall components. PMID:24014871

  17. Divergent Regulation of Terpenoid Metabolism in the Trichomes of Wild and Cultivated Tomato Species1[W][OA

    PubMed Central

    Besser, Katrin; Harper, Andrea; Welsby, Nicholas; Schauvinhold, Ines; Slocombe, Stephen; Li, Yi; Dixon, Richard A.; Broun, Pierre

    2009-01-01

    The diversification of chemical production in glandular trichomes is important in the development of resistance against pathogens and pests in two species of tomato. We have used genetic and genomic approaches to uncover some of the biochemical and molecular mechanisms that underlie the divergence in trichome metabolism between the wild species Solanum habrochaites LA1777 and its cultivated relative, Solanum lycopersicum. LA1777 produces high amounts of insecticidal sesquiterpene carboxylic acids (SCAs), whereas cultivated tomatoes lack SCAs and are more susceptible to pests. We show that trichomes of the two species have nearly opposite terpenoid profiles, consisting mainly of monoterpenes and low levels of sesquiterpenes in S. lycopersicum and mainly of SCAs and very low monoterpene levels in LA1777. The accumulation patterns of these terpenoids are different during development, in contrast to the developmental expression profiles of terpenoid pathway genes, which are similar in the two species, but they do not correlate in either case with terpenoid accumulation. However, our data suggest that the accumulation of monoterpenes in S. lycopersicum and major sesquiterpenes in LA1777 are linked both genetically and biochemically. Metabolite analyses after targeted gene silencing, inhibitor treatments, and precursor feeding all show that sesquiterpene biosynthesis relies mainly on products from the plastidic 2-C-methyl-d-erythritol-4-phosphate pathway in LA1777 but less so in the cultivated species. Furthermore, two classes of sesquiterpenes produced by the wild species may be synthesized from distinct pools of precursors via cytosolic and plastidial cyclases. However, highly trichome-expressed sesquiterpene cyclase-like enzymes were ruled out as being involved in the production of major LA1777 sesquiterpenes. PMID:18997116

  18. Trichome-Related Mutants Provide a New Perspective on Multicellular Trichome Initiation and Development in Cucumber (Cucumis sativus L)

    PubMed Central

    Liu, Xingwang; Bartholomew, Ezra; Cai, Yanling; Ren, Huazhong

    2016-01-01

    Trichomes are specialized epidermal cells located in aerial parts of plants that function in plant defense against biotic and abiotic stresses. The simple unicellular trichomes of Arabidopsis serve as an excellent model to study the molecular mechanism of cell differentiation and pattern formation in plants. Loss-of-function mutations in Arabidopsis thaliana have suggested that the core genes GL1 (which encodes a MYB transcription factor) and TTG1 (which encodes a WD40 repeat-containing protein) are important for the initiation and spacing of leaf trichomes, while for normal trichome initiation, the genes GL3, and EGL3 (which encode a bHLH protein) are needed. However, the positive regulatory genes involved in multicellular trichrome development in cucumber remain unclear. This review focuses on the phenotype of mutants (csgl3, tril, tbh, mict, and csgl1) with disturbed trichomes in cucumber and then infers which gene(s) play key roles in trichome initiation and development in those mutants. Evidence indicates that MICT, TBH, and CsGL1 are allelic with alternative splicing. CsGL3 and TRIL are allelic and override the effect of TBH, MICT, and CsGL1 on the regulation of multicellular trichome development; and affect trichome initiation. CsGL3, TRIL, MICT, TBH, and CsGL1 encode HD-Zip proteins with different subfamilies. Genetic and molecular analyses have revealed that CsGL3, TRIL, MICT, TBH, and CsGL1 are responsible for the differentiation of epidermal cells and the development of trichomes. Based on current knowledge, a positive regulator pathway model for trichome development in cucumber was proposed and compared to a model in Arabidopsis. These data suggest that trichome development in cucumber may differ from that in Arabidopsis. PMID:27559338

  19. Influence of plant ontogeny and abiotic factors on resistance of glandular-haired alfalfa to potato leafhopper (Hemiptera: Cicadellidae).

    PubMed

    Casteel, Clare L; Ranger, Christopher M; Backus, Elaine A; Ellersieck, Mark R; Johnson, David W

    2006-04-01

    Laboratory experiments were conducted to characterize the trichome-based defense of glandular-haired alfalfa, Medicago sativa L., against the potato leafhopper, Empoasca fabae (Harris). Within-plant variability in leafhopper resistance was examined by caging adult leafhoppers to either basal or apical stem internodes of the leafhopper-resistant, glandular-haired M. sativa genotype G98A or the susceptible, nonglandular-haired M. sativa 'Ranger'. Young, actively secreting glandular trichomes are located on apical internodes of G98A, whereas senesced gland heads are found on older, basal internodes of G98A. After 96 h, the highest cumulative leafhopper mortality and lowest number of excretory droplets were associated with apical internodes of G98A. No difference was detected in mortality and feeding levels among insects caged to basal internodes of G98A and basal and apical internodes of Ranger. The influence of abiotic factors on leafhopper resistance was evaluated by caging adult leafhoppers to either G98A or Ranger under four combinations of low and high light (250 and 1,000 micromol s(-1) m(-2)) and temperature regimes (17 and 30 degrees C). After 96 h, the highest cumulative mortality was associated with leafhoppers confined to G98A under high light and high temperature conditions. Temperature level and plant type also had an effect on the production of excretory droplets, resulting in the highest number of excretory droplets being associated with Ranger under the high temperature regime. These results indicate that certain regions of M. sativa G98A are better protected against the potato leafhopper than others and that temperature influences resistance levels of glandular-haired alfalfa.

  20. Are plant trichomes harmful to predatory insects and mites?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants may use epidermal hairs (trichomes) to defend themselves from attack by herbivores. Predatory arthropods may serve as biocontrol agents against herbivores. Whether or not plant trichomes work in concert with predators is undocumented in many cases. We reviewed the peer-reviewed literature ...

  1. Plant trichomes have mixed impacts on predatory insects

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In response to our review article on the role of plant trichomes on insect predators (Riddick & Simmons 2014), Krimmel (2014) acknowledged the challenges that are faced in bringing together the varied publications on the subject of impact of plant trichomes on predatory insects. He also suggested t...

  2. Hydrophobic trichome layers and epicuticular wax powders in Bromeliaceae.

    PubMed

    Pierce, S; Maxwell, K; Griffiths, H; Winter, K

    2001-08-01

    The distinctive foliar trichome of Bromeliaceae has promoted the evolution of an epiphytic habit in certain taxa by allowing the shoot to assume a significant role in the uptake of water and mineral nutrients. Despite the profound ecophysiological and taxonomic importance of this epidermal structure, the functions of nonabsorbent trichomes in remaining Bromeliaceae are not fully understood. The hypothesis that light reflection from these trichome layers provides photoprotection was not supported by spectroradiometry and fluorimetry in the present study; the mean reflectance of visible light from trichome layers did not exceed 6.4% on the adaxial surfaces of species representing a range of ecophysiological types nor was significant photoprotection provided by their presence. Several reports suggesting water repellency in some terrestrial Bromeliaceae were investigated. Scanning electron microscopy (SEM) and a new technique-fluorographic dimensional imaging (FDI)-were used to assess the interaction between aqueous droplets and the leaf surfaces of 86 species from 25 genera. In the majority of cases a dense layer of overlapping, stellate or peltate trichomes held water off the leaf epidermis proper. In the case of hydrophobic tank-forming tillandsioideae, a powdery epicuticular wax layer provided water repellency. The irregular architecture of these indumenta resulted in relatively little contact with water droplets. Most mesic terrestrial Pitcairnioideae examined either possessed glabrous leaf blades or hydrophobic layers of confluent trichomes on the abaxial surface. Thus, the present study indicates that an important ancestral function of the foliar trichome in Bromeliaceae was water repellency. The ecophysiological consequences of hydrophobia are discussed.

  3. Glandular prediction: the pride and the prejudice.

    PubMed

    Waddell, C

    2004-08-01

    For the cytologist and clinician alike, glandular lesions pose possibly the greatest challenge in cervical screening. Worldwide, with increasing confidence in cytological prediction, terminology is evolving. In the UK, with the adoption of liquid based methods, the technical aspects of cervical cytology are being addressed, it is now time to standardise our terminology in glandular reporting. Consideration of the cytological complexity, clinical needs and international protocols is essential in this endeavour.

  4. Glandular odontogenic cyst: systematic review

    PubMed Central

    MacDonald-Jankowski, D S

    2010-01-01

    Objectives The aim of this study was to evaluate the principal features of “glandular odontogenic cyst” (GOC), by systematic review (SR), and to compare their frequencies among four global groups. Methods The databases searched were the PubMed interface of MEDLINE and LILACS. Only those reports of GOCs that occurred in a series in the reporting authors' caseload were considered. All cases were confirmed histopathologically. Results 18 reports on 17 series of consecutive cases were included in the SR. GOC affected males twice as frequently and the mandible almost three times as frequently. The mean age at first presentation was 44 years, coincident with that of the Western global group, in which the largest proportion of reports and cases first presented in the second half of the fifth decade. However, age at presentation of GOCs in the East Asian and sub-Saharan African global groups was nearly a decade younger, this was significant. Six reports included details of at least one clinical presentation. Eight reports included at least one conventional radiological feature. There were some significant differences between global groups. The Western global group had a particular predilection for the anterior sextants of both jaws. The sub-Saharan African group displayed buccolingual expansion (as did the Latin American group) and tooth displacement in every case. 18% of GOCs recurred overall, except in the sub-Saharan African global group. Conclusions GOCs have a marked propensity to recur in most global groups. GOCs presented in older patients and with swellings, affected the anterior sextants of both jaws, and radiologically were more likely to present as a well-defined unilocular radiolucency with buccolingual expansion. Tooth displacement, root resorption and an association with unerupted teeth occurred in 50%, 30% and 11% of cases, respectively. PMID:20203274

  5. Acylsugar Acylhydrolases: Carboxylesterase-Catalyzed Hydrolysis of Acylsugars in Tomato Trichomes1[OPEN

    PubMed Central

    Gilgallon, Karin; Ghosh, Banibrata

    2016-01-01

    Glandular trichomes of cultivated tomato (Solanum lycopersicum) and many other species throughout the Solanaceae produce and secrete mixtures of sugar esters (acylsugars) on the plant aerial surfaces. In wild and cultivated tomato, these metabolites consist of a sugar backbone, typically glucose or sucrose, and two to five acyl chains esterified to various positions on the sugar core. The aliphatic acyl chains vary in length and branching and are transferred to the sugar by a series of reactions catalyzed by acylsugar acyltransferases. A phenotypic screen of a set of S. lycopersicum M82 × Solanum pennellii LA0716 introgression lines identified a dominant genetic locus on chromosome 5 from the wild relative that affected total acylsugar levels. Genetic mapping revealed that the reduction in acylsugar levels was consistent with the presence and increased expression of two S. pennellii genes (Sopen05g030120 and Sopen05g030130) encoding putative carboxylesterase enzymes of the α/β-hydrolase superfamily. These two enzymes, named ACYLSUGAR ACYLHYDROLASE1 (ASH1) and ASH2, were shown to remove acyl chains from specific positions of certain types of acylsugars in vitro. A survey of related genes in M82 and LA0716 identified another trichome-expressed ASH gene on chromosome 9 (M82, Solyc09g075710; LA0716, Sopen09g030520) encoding a protein with similar activity. Characterization of the in vitro activities of the SpASH enzymes showed reduced activities with acylsugars produced by LA0716, presumably contributing to the high-level production of acylsugars in the presence of highly expressed SpASH genes. PMID:26811191

  6. Trichomes control flower bud shape by linking together young petals.

    PubMed

    Tan, Jiafu; Walford, Sally-Anne; Dennis, Elizabeth S; Llewellyn, Danny

    2016-06-20

    Trichomes are widespread in plants and develop from surface cells on different tissues(1). They have many forms and functions, from defensive spines to physical barriers that trap layers of air to insulate against desiccation, but there is growing evidence that trichomes can also have developmental roles in regulating flower structure(2,3). We report here that the trichomes on petals of cotton, Gossypium hirsutum L., are essential for correct flower bud shape through a mechanical entanglement of the trichomes on adjacent petals that anchor the edges to counter the opposing force generated by asymmetric expansion of overlapping petals. Silencing a master regulator of petal trichomes, GhMYB-MIXTA-Like10 (GhMYBML10), by RNA interference (RNAi) suppressed petal trichome growth and resulted in flower buds forming into abnormal corkscrew shapes that exposed developing anthers and stigmas to desiccation damage. Artificially gluing petal edges together could partially restore correct bud shape and fertility. Such petal 'Velcro' is present in other Malvaceae and perhaps more broadly in other plant families, although it is not ubiquitous. This mechanism for physical association between separate organs to regulate flower shape and function is different from the usual organ shape control(4) exerted through cell-to-cell communication and differential cell expansion within floral tissues(5,6).

  7. Functionally Divergent Alleles and Duplicated Loci Encoding an Acyltransferase Contribute to Acylsugar Metabolite Diversity in Solanum Trichomes[OPEN

    PubMed Central

    Schilmiller, Anthony L.; Moghe, Gaurav D.; Fan, Pengxiang; Ghosh, Banibrata; Ning, Jing; Jones, A. Daniel; Last, Robert L.

    2015-01-01

    Glandular trichomes from tomato (Solanum lycopersicum) and other species in the Solanaceae produce and secrete a mixture of O-acylsugars (aliphatic esters of sucrose and glucose) that contribute to insect defense. Despite their phylogenetic distribution and diversity, relatively little is known about how these specialized metabolites are synthesized. Mass spectrometric profiling of acylsugars in the S. lycopersicum x Solanum pennellii introgression lines identified a chromosome 11 locus containing a cluster of BAHD acyltransferases with one gene (named Sl-ASAT3) expressed in tip cells of type I trichomes where acylsugars are made. Sl-ASAT3 was shown to encode an acyl-CoA-dependent acyltransferase that catalyzes the transfer of short (four to five carbons) branched acyl chains to the furanose ring of di-acylsucrose acceptors to produce tri-acylsucroses, which can be further acetylated by Sl-ASAT4 (previously Sl-AT2). Among the wild tomatoes, diversity in furanose ring acyl chains on acylsucroses was most striking in Solanum habrochaites. S. habrochaites accessions from Ecuador and northern Peru produced acylsucroses with short (≤C5) or no acyl chains on the furanose ring. Accessions from central and southern Peru had the ability to add short or long (up to C12) acyl chains to the furanose ring. Multiple ASAT3-like sequences were found in most accessions, and their in vitro activities correlated with observed geographical diversity in acylsugar profiles. PMID:25862303

  8. New developments in endocervical glandular lesions.

    PubMed

    McCluggage, W Glenn

    2013-01-01

    McCluggage W G (2012) Histopathology New developments in endocervical glandular lesions There is evidence that the prevalence of premalignant and malignant endocervical glandular lesions is increasing in real as well as in apparent terms. In this review, new developments and selected controversial aspects of endocervical glandular lesions are covered, concentrating mainly on premalignant and malignant lesions. The terminology of premalignant endocervical glandular lesions is discussed with a comparison of the World Health Organization classification and the cervical glandular intraepithelial neoplasia (CGIN) system, which is in widespread use in the United Kingdom. Primary cervical adenocarcinomas comprise a heterogeneous group of different morphological types, and while it is known that the majority of these are associated with high-risk human papillomavirus (HPV), it has become clear in recent years that most of the more uncommon morphological types are unassociated with HPV, although they may sometimes be p16-positive. A spectrum of benign, premalignant and malignant cervical glandular lesions exhibiting gastric differentiation is now recognized; these include type A tunnel clusters, typical and atypical lobular endocervical glandular hyperplasia, adenoma malignum and gastric-type adenocarcinoma. The latter is a recently described variant of primary cervical adenocarcinoma which has a different morphological appearance to the usual endocervical type and which is probably associated with different patterns of spread and a worse prognosis. There is accumulating evidence that 'early invasive' cervical adenocarcinomas have an excellent prognosis and are suitable for conservative management. Immunohistochemical markers of value in the distinction between a primary cervical and endometrial adenocarcinoma are discussed. While it is well known that a panel of markers comprising oestrogen receptor (ER), vimentin, p16 and monoclonal carcinoembryonic antigen (CEA) is

  9. Malignant glandular lesions and glandular differentiation in invasive/noninvasive urothelial carcinoma of the urinary bladder.

    PubMed

    Behzatoğlu, Kemal

    2011-12-01

    Although the lumen of the urinary bladder is covered with only urothelial epithelium, malign glandular lesions (eg, nonurachal adenocarcinoma) and benign lesions (eg, cystitis cystica and cystitis glandularis) can also rarely occur in this site due to its characteristic embryologic development. Glandular differentiation is uncommon in urothelial carcinomas and is even less common in noninvasive urothelial cancers. In addition, in situ urothelial carcinomas are more likely to progress in the presence of glandular differentiation toward high-grade urothelial carcinomas and/or aggressive urothelial carcinomas. Pure nonurachal adenocarcinomas and mixed carcinomas (urothelial carcinoma and adenocarcinoma) are very rare, and their pathogenesis is not clear. Most of the nonurachal adenocarcinomas are thought to arise on the grounds of cystitis glandularus with intestinal metaplasia. Here, I present 2 cases with noninvasive urothelial carcinoma with substantial glandular differentiation showing progression to signet ring cell carcinoma and invasive urothelial carcinoma, one case with mixed carcinoma (urothelial carcinoma and adenocarcinoma) and another case with pure adenocarcinoma developing from cystitis glandularis with intestinal metaplasia, and discuss malign glandular lesions in the bladder and invasive/noninvasive urothelial carcinomas with glandular differentiation.

  10. One, two, three...models for trichome patterning in Arabidopsis?

    PubMed

    Pesch, Marina; Hülskamp, Martin

    2009-10-01

    Trichome patterning in Arabidopsis rosette leaves serves as a model system to study how individual cells are determined in a regular spacing pattern from initially equivalent cells. A conserved gene cassette regulates this spacing pattern. bHLH, MYB, and WD40 factors are positive regulators of trichome development that are inhibited by R3 single-repeat MYB proteins. One positive regulator, the WD40-protein, and the negative regulators are mobile and are transported in opposite directions: the WD40 factor moves to the negative regulators away from trichome initials. This movement behavior and the genetic and molecular interactions between the contributing genes and proteins make it very difficult to derive the mechanistic core behind pattern formation. Attempts to develop mathematical models toward this end are critically discussed.

  11. Differential expression of trichomes on the leaves of upland cotton (Gossypium hirsutum L)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This study evaluated and quantified trichome diversity on various cotton lines. Leaf trichomes were evaluated with scanning electron and light microscopy on fixed and live samples. Observations indicated that trichome complexity and quantity increased on the mainstem leaves as sampling progressed ...

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

    PubMed

    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.

  13. Low Reynolds number flow near tiny leaves, stems, and trichomes

    NASA Astrophysics Data System (ADS)

    Strickland, Christopher; Pasour, Virginia; Miller, Laura

    2016-11-01

    In terrestrial and aquatic environments such as forest canopies, grass fields, and seagrass beds, the density and shape of trunks, branches, stems, leaves and trichomes (the hairs or fine outgrowths on plants) can drastically alter both the average wind speed and profile through these environments and near each plant. While many studies of flow in these environments have focused on bulk properties of the flow at scales on the order of meters, the low Reynolds number flow close to vegetative structures is especially complex and relevant to nutrient exchange. Using three-dimensional immersed boundary simulations, we resolve the flow around trichomes and small leaves and quantify velocities, shear stresses, and mixing while varying the height and density of idealized structures. National Science Foundation Grant DMS-1127914 to the Statistical and Applied Mathematical Sciences Institute, and the Army Research Office.

  14. T-shaped trichome-specific expression of monoterpene synthase ADH2 using promoter-β-GUS fusion in transgenic Artemisia annua L.

    PubMed

    Fu, Xueqing; Shi, Pu; Shen, Qian; Jiang, Weimin; Tang, Yueli; Lv, Zongyou; Yan, Tingxiang; Li, Ling; Wang, Guofeng; Sun, Xiaofen; Tang, Kexuan

    2016-11-01

    Artemisinin, a sesquiterpene lactone isolated from Artemisia annua L. (sweet wormwood), is extensively used in the treatment of malaria. In order to better understand the metabolism of terpenes in A. annua and the influence of terpene synthases on artemisinin yield, the expression pattern of a monoterpene alcohol dehydrogenase (ADH2) has been studied using transgenic plants expressing promoter-β-glucuronidase (GUS) fusion. ADH2 played a major role in monoterpenoid biosynthesis including carveol, borneol, and artemisia ketone through in vitro biochemical analysis. In this study, the ADH2 promoter was cloned by the genome walking method. A number of putative cis-acting elements were predicted in promoter region, suggesting that the ADH2 is driven by a complex regulation mechanism. ADH2 gene was highly expressed in old leaves, whereas the artemisinin biosynthetic genes were mainly expressed in bud and young leaves. The expression of ADH2 gene increased quickly during leaf development, revealed by qRT-PCR. GUS expression analysis in different tissues of transgenic A. annua demonstrates that ADH2 expression is exclusively located to T-shaped trichome, not glandular secretory trichome.

  15. Effect of gibberellic acid and calliterpenone on plant growth attributes, trichomes, essential oil biosynthesis and pathway gene expression in differential manner in Mentha arvensis L.

    PubMed

    Bose, Subir K; Yadav, Ritesh Kumar; Mishra, Smrati; Sangwan, Rajender S; Singh, A K; Mishra, B; Srivastava, A K; Sangwan, Neelam S

    2013-05-01

    Extensive research is going on throughout the world to find out new molecules from natural sources to be used as plant growth promoter. Mentha arvensis L. is the main source of menthol rich essential oil used commercially in various food, pharmaceutical and other preparations. Experiments were conducted on field grown plants for understanding the effect of calliterpenone (CA), a stereo-isomer of abbeokutone, in comparison to gibberellic acid (GA3) on growth attributes, trichomes, essential oil biosynthesis and expression of some oil biosynthetic pathway genes. The exogenous application of CA (1 μM, 10 μM and 100 μM) was found to be better in improving plant biomass and stolon yield, leaf area, branching and leaf stem ratio than with counterpart GA3 at the same concentrations. CA treated plants showed higher glandular trichome number, density and diameter and also correlated with enhanced oil biogenetic capacity as revealed by feeding labeled (14)C-sucrose for 72 h to excised shoots. Semi-quantitative PCR analysis of key pathway genes revealed differential up regulation under CA treatments. Transcript level of menthol dehydrogenase/menthone reductase was found highly up regulated in CA treated plants with increased content of menthone and menthol in oil. These findings demonstrate that CA positively regulated the yields by enhanced branching and higher density of trichomes resulting into higher accumulation of essential oil. The results suggest CA as a novel plant derived diterpenoid with growth promoting action and opens up new possibilities for improving the crop yields and essential oil biosynthesis in qualitative and quantitative manner.

  16. Roles of the GLABROUS1 and TRANSPARENT TESTA GLABRA Genes in Arabidopsis Trichome Development.

    PubMed Central

    Larkin, J. C.; Oppenheimer, D. G.; Lloyd, A. M.; Paparozzi, E. T.; Marks, M. D.

    1994-01-01

    Arabidopsis trichomes are branched, single-celled epidermal hairs. These specialized cells provide a convenient model for investigating the specification of cell fate in plants. Two key genes regulating the initiation of trichome development are GLABROUS1 (GL1) and TRANSPARENT TESTA GLABRA (TTG). GL1 is a member of the myb gene family. The maize R gene, which can functionally complement the Arabidopsis ttg mutation, encodes a basic helix-loop-helix protein. We used constitutively expressed copies of the GL1 and R genes to test hypotheses about the roles of GL1 and TTG in trichome development. The results support the hypothesis that TTG and GL1 cooperate at the same point in the trichome developmental pathway. Furthermore, the constitutive expression of both GL1 and R in the same plant caused trichomes to develop on all shoot epidermal surfaces. Results were also obtained indicating that TTG plays an additional role in inhibiting neighboring cells from becoming trichomes. PMID:12244266

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

    SciTech Connect

    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.

  18. TEMPRANILLO Reveals the Mesophyll as Crucial for Epidermal Trichome Formation1[OPEN

    PubMed Central

    Aguilar-Jaramillo, Andrea E.; Osnato, Michela; Shani, Eilon

    2016-01-01

    Plant trichomes are defensive specialized epidermal cells. In all accepted models, the epidermis is the layer involved in trichome formation, a process controlled by gibberellins (GAs) in Arabidopsis rosette leaves. Indeed, GA activates a genetic cascade in the epidermis for trichome initiation. Here we report that TEMPRANILLO (TEM) genes negatively control trichome initiation not only from the epidermis but also from the leaf layer underneath the epidermis, the mesophyll. Plants over-expressing or reducing TEM specifically in the mesophyll, display lower or higher trichome numbers, respectively. We surprisingly found that fluorescently labeled GA3 accumulates exclusively in the mesophyll of leaves, but not in the epidermis, and that TEM reduces its accumulation and the expression of several newly identified GA transporters. This strongly suggests that TEM plays an essential role, not only in GA biosynthesis, but also in regulating GA distribution in the mesophyll, which in turn directs epidermal trichome formation. Moreover, we show that TEM also acts as a link between GA and cytokinin signaling in the epidermis by negatively regulating downstream genes of both trichome formation pathways. Overall, these results call for a re-evaluation of the present theories of trichome formation as they reveal mesophyll essential during epidermal trichome initiation. PMID:26802039

  19. Roles of trichomes with silica particles on the surface of leaves in Aphananthe aspera

    NASA Astrophysics Data System (ADS)

    Takeda, Hiroyuki; Ito, Fuyu; Yamanaka, Shigeru; Takiyama, Naoyuki; Yoshino, Katsumi

    2013-03-01

    There exist many trichomes with silica particles on the surface of leaves in Aphananthe aspera (Muku tree). The size of the trichomes is on the order of some tens to hundreds of micrometers. Investigating the electric-field local densities of the states and distributions of electromagnetic wave propagation, we theoretically revealed that while trichomes play a role as waveguides for the far-infrared, silica particles help incident far-infrared light efficiently propagate inside the trichomes and leaves. These properties would be useful for efficiently warming plants, since absorbed far-infrared light is converted to heat.

  20. Correlated evolution of leaf shape and trichomes in Begonia dregei (Begoniaceae).

    PubMed

    McLellan, Tracy

    2005-10-01

    Structural features of leaves, including size, shape, and surfaces, vary greatly throughout the plant kingdom. In both functional and phylogenetic analyses of leaves, the various morphological aspects are often considered independently of each other, although it is likely that many combinations of features do not occur at random due to either functional constraint or genetic correlation. The distribution of variation in leaf morphology in the highly variable Begonia dregei species complex was examined in natural populations and in F(2) offspring from a cross between plants from two populations. Leaf shape was quantified using several morphometric measures, and trichomes on leaves were counted and measured. Correlations between leaf shape and the numbers and size of trichomes were examined. There were significant correlations between the shapes of leaves and the presence, number, and size of trichomes among populations and in hybrid plants. Deeply incised leaves had larger numbers of longer trichomes at the sinuses. Higher numbers of trichomes on upper leaf surfaces occurred together with trichomes at the petiole and on the abaxial surface. The potential for independent evolution of leaf shape and trichomes in this group is limited. Hypotheses to explain the correlated development of leaf shape and trichomes are discussed.

  1. Do plant trichomes cause more harm than good to predatory insects?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants may use epidermal hairs (trichomes) as a morphological defense against attacks from some herbivores. Predatory arthropods can serve plants as biocontrol agents against herbivores. Whether or not plant trichomes work in concert with predators is equivocal. We reviewed the scientific literat...

  2. Fast neutron induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequence-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that ...

  3. Chlamydia muridarum Induction of Glandular Duct Dilation in Mice

    PubMed Central

    Sun, Xin; Yang, Zhangsheng; Zhang, Hongbo; Dai, Jin; Chen, Jianlin; Tang, Lingli; Rippentrop, Sheena; Xue, Min

    2015-01-01

    Although Chlamydia-induced hydrosalpinx in women and mice has been used as a surrogate marker for tubal infertility, the medical relevance of nontubal pathologies, such as uterine horn dilation, developed in mice following chlamydial infection remains unclear. We now report that the uterine horn dilation correlates with glandular duct dilation detected microscopically following Chlamydia muridarum infection. The dilated glandular ducts pushed the uterine horn lumen to closure or dilation and even broke through the myometrium to develop extrusion outside the uterine horn. The severity scores of uterine horn dilation observed macroscopically correlated well with the number of cross sections of the dilated glandular ducts counted under microscopy. Chlamydial infection was detected in the glandular epithelial cells, potentially leading to inflammation and dilation of the glandular ducts. Direct delivery of C. muridarum into the mouse uterus increased both uterine horn/glandular duct dilation and hydrosalpinx. However, the chlamydial plasmid, which is essential for the induction of hydrosalpinx, was not required for the induction of uterine horn/glandular duct dilation. Screening 12 strains of mice for uterine horn dilation following C. muridarum infection revealed that B10.D2, C57BL/10J, and C57BL/6J mice were most susceptible, followed by BALB/cJ and A/J mice. Deficiency in host genes involved in immune responses failed to significantly alter the C. muridarum induction of uterine horn dilation. Nevertheless, the chlamydial induction of uterine horn/glandular duct dilation may be used to evaluate plasmid-independent pathogenicity of Chlamydia in susceptible mice. PMID:25824829

  4. Dosimetric implications of age related glandular changes in screening mammography

    NASA Astrophysics Data System (ADS)

    Beckett, J. R.; Kotre, C. J.

    2000-03-01

    The UK National Health Service Breast Screening Programme is currently organized to routinely screen women between the ages of 50 and 64, with screening for older women available on request. The lower end of this age range closely matches the median age for the menopause (51 years), during which significant changes in the composition of the breast are known to occur. In order to quantify the dosimetric effect of these changes, radiographic factors and compressed breast thickness data for a cohort of 1258 women aged between 35 and 79 undergoing breast screening mammography have been used to derive estimates of breast glandularity and mean glandular dose (MGD), and examine their variation with age. The variation of mean radiographic exposure factors with age is also investigated. The presence of a significant number of age trial women within the cohort allowed an extended age range to be studied. Estimates of MGD including corrections for breast glandularity based on compressed breast thickness only, compressed breast thickness and age and for each individual woman are compared with the MGD based on the conventional assumption of a 50:50 adipose/glandular composition. It has been found that the use of the conventional 50:50 assumption leads to overestimates of MGD of up to 13% over the age range considered. By using compressed breast thickness to estimate breast glandularity, this error range can be reduced to 8%, whilst age and compressed breast thickness based glandularity estimates result in an error range of 1%.

  5. Monte Carlo simulation for correlation analysis of average glandular dose by breast thickness and glandular ratio in breast tissue.

    PubMed

    Kim, Sang-Tae; Cho, Jung-Keun

    2014-01-01

    A glandular breast tissue is a radio-sensitive tissue. So during the evaluation of an X-ray mammography device, Average Glandular Dose (AGD) measurement is a very important part. In reality, it is difficult to measure AGD directly, Monte Carlo simulation was used to analyze the correlation between the AGD and breast thickness. As a result, AGDs calculated through the Monte Carlo simulation were 1.64, 1.41 and 0.88 mGy. The simulated AGDs mainly depend on the glandular ratio of the breast. With the increase of glandular breast tissue, absorption of low photon-energy increased so that the AGDs increased, too. In addition, the thicker the breast was, the more the AGD became. Consequently, this study will be used as basic data for establishing the diagnostic reference levels of mammography.

  6. GLABROUS INFLORESCENCE STEMS3 (GIS3) regulates trichome initiation and development in Arabidopsis.

    PubMed

    Sun, Lili; Zhang, Aidong; Zhou, Zhongjing; Zhao, Yongqin; Yan, An; Bao, Shengjie; Yu, Hao; Gan, Yinbo

    2015-04-01

    Arabidopsis trichome formation is an excellent model for studying various aspects of plant cell development and cell differentiation. Our previous works have demonstrated that several C2H2 zinc finger proteins, including GIS, GIS2, ZFP5, ZFP6 and ZFP8, control trichome cell development through GA and cytokinin signalling in Arabidopsis. We identified a novel C2H2 zinc finger protein, GLABROUS INFLORESCENCE STEMS 3 (GIS3), which is a key factor in regulating trichome development in Arabidopsis. In comparison with wild-type plants, loss-of-function of GIS3 mutants exhibited a significantly decreased number of trichomes in cauline leaves, lateral branches, sepals of flowers, and main stems. Overexpression of GIS3 resulted in increased trichome densities in sepal, cauline leaves, lateral branches, main inflorescence stems and in the appearance of ectopic trichomes on carpels. The molecular and genetic analyses show that GIS3 acts upstream of GIS, GIS2, ZFP8 and the key trichome initiation factors, GL1 and GL3. Steroid-inducible gene expression analyses and chromatin immunoprecipitation (ChIP) experiments suggest that GIS and GIS2 are the direct target genes of GIS3.

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

    PubMed

    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).

  8. Effects of three AM fungi on growth, distribution of glandular hairs, and essential oil production in Ocimum basilicum L. var. Genovese.

    PubMed

    Copetta, Andrea; Lingua, Guido; Berta, Graziella

    2006-10-01

    The essential oils of basil are widely used in the cosmetic, pharmaceutical, food, and flavoring industries. Little is known about the potential of arbuscular mycorrhizal (AM) fungi to affect their production in this aromatic plant. The effects of colonization by three AM fungi, Glomus mosseae BEG 12, Gigaspora margarita BEG 34, and Gigaspora rosea BEG 9 on shoot and root biomass, abundance of glandular hairs, and essential oil yield of Ocimum basilicum L. var. Genovese were studied. Plant P content was analyzed in the various treatments and no differences were observed. The AM fungi induced various modifications in the considered parameters, but only Gi. rosea significantly affected all of them in comparison to control plants or the other fungal treatments. It significantly increased biomass, root branching and length, and the total amount of essential oil (especially alpha-terpineol). Increased oil yield was associated to a significantly larger number of peltate glandular trichomes (main sites of essential oil synthesis) in the basal and central leaf zones. Furthermore, Gi. margarita and Gi. rosea increased the percentage of eugenol and reduced linalool yield. Results showed that different fungi can induce different effects in the same plant and that the essential oil yield can be modulated according to the colonizing AM fungus.

  9. Endometriosis mimicking glandular atypia in a cervical cytology

    PubMed Central

    Rodriguez–Urrego, Paula A; Dulcey–Hormiga, Isabel C; Barrera–Herrera, Luis E; Suarez–Zamora, David A; Palau–Lazaro, Mauricio A; Buritica–Cifuentes, Catalina

    2017-01-01

    Endometriosis involving the uterine cervix is a rare condition that can lead to diagnostic errors in the interpretation of Pap smear. We report the case of a 41-year-old patient in whom the initial Pap smear revealed three-dimensional clusters of glandular cells with elongated nuclei, occasional mitosis, and atypia, which was interpreted as atypical glandular cells, not otherwise specified (NOS). The patient was taken to colposcopy and endocervical biopsy. Colposcopy was normal and the biopsy presented glands with elongated nuclei and surrounded by endometrial stroma admixed with normal endocervical glands. Immunohistochemical studies were reactive for CD10 in the stromal cells and vimentin in endometrioid glands. The findings were consistent with cervical endometriosis. Endometriosis in the cervix is an uncommon pathology that mimics malignancy and may be interpreted as atypical or glandular neoplasia in the cytology. PMID:28182083

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

    PubMed

    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.

  11. Herbivore handling of a Plants trichome: the case of Heliconius charithonia (L.) (Lepidoptera: Nymphalidae) and Passiflora lobata (Killip) Hutch. (Passifloraceae).

    PubMed

    Cardoso, Márcio 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 plants 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.

  12. Modeling Filamentous Cyanobacteria Reveals the Advantages of Long and Fast Trichomes for Optimizing Light Exposure

    PubMed Central

    Tamulonis, Carlos; Postma, Marten; Kaandorp, Jaap

    2011-01-01

    Cyanobacteria form a very large and diverse phylum of prokaryotes that perform oxygenic photosynthesis. Many species of cyanobacteria live colonially in long trichomes of hundreds to thousands of cells. Of the filamentous species, many are also motile, gliding along their long axis, and display photomovement, by which a trichome modulates its gliding according to the incident light. The latter has been found to play an important role in guiding the trichomes to optimal lighting conditions, which can either inhibit the cells if the incident light is too weak, or damage the cells if too strong. We have developed a computational model for gliding filamentous photophobic cyanobacteria that allows us to perform simulations on the scale of a Petri dish using over 105 individual trichomes. Using the model, we quantify the effectiveness of one commonly observed photomovement strategy—photophobic responses—in distributing large populations of trichomes optimally over a light field. The model predicts that the typical observed length and gliding speeds of filamentous cyanobacteria are optimal for the photophobic strategy. Therefore, our results suggest that not just photomovement but also the trichome shape itself improves the ability of the cyanobacteria to optimize their light exposure. PMID:21789215

  13. Semi-automated 3D leaf reconstruction and analysis of trichome patterning from light microscopic images.

    PubMed

    Failmezger, Henrik; Jaegle, Benjamin; Schrader, Andrea; Hülskamp, Martin; Tresch, Achim

    2013-04-01

    Trichomes are leaf hairs that are formed by single cells on the leaf surface. They are known to be involved in pathogen resistance. Their patterning is considered to emerge from a field of initially equivalent cells through the action of a gene regulatory network involving trichome fate promoting and inhibiting factors. For a quantitative analysis of single and double mutants or the phenotypic variation of patterns in different ecotypes, it is imperative to statistically evaluate the pattern reliably on a large number of leaves. Here we present a method that enables the analysis of trichome patterns at early developmental leaf stages and the automatic analysis of various spatial parameters. We focus on the most challenging young leaf stages that require the analysis in three dimensions, as the leaves are typically not flat. Our software TrichEratops reconstructs 3D surface models from 2D stacks of conventional light-microscope pictures. It allows the GUI-based annotation of different stages of trichome development, which can be analyzed with respect to their spatial distribution to capture trichome patterning events. We show that 3D modeling removes biases of simpler 2D models and that novel trichome patterning features increase the sensitivity for inter-accession comparisons.

  14. Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images

    PubMed Central

    Schrader, Andrea; Hülskamp, Martin; Tresch, Achim

    2013-01-01

    Trichomes are leaf hairs that are formed by single cells on the leaf surface. They are known to be involved in pathogen resistance. Their patterning is considered to emerge from a field of initially equivalent cells through the action of a gene regulatory network involving trichome fate promoting and inhibiting factors. For a quantitative analysis of single and double mutants or the phenotypic variation of patterns in different ecotypes, it is imperative to statistically evaluate the pattern reliably on a large number of leaves. Here we present a method that enables the analysis of trichome patterns at early developmental leaf stages and the automatic analysis of various spatial parameters. We focus on the most challenging young leaf stages that require the analysis in three dimensions, as the leaves are typically not flat. Our software TrichEratops reconstructs 3D surface models from 2D stacks of conventional light-microscope pictures. It allows the GUI-based annotation of different stages of trichome development, which can be analyzed with respect to their spatial distribution to capture trichome patterning events. We show that 3D modeling removes biases of simpler 2D models and that novel trichome patterning features increase the sensitivity for inter-accession comparisons. PMID:23637587

  15. Gibberellins Promote Trichome Formation by Up-Regulating GLABROUS1 in Arabidopsis1

    PubMed Central

    Perazza, Daniel; Vachon, Gilles; Herzog, Michel

    1998-01-01

    Trichome development is dependent on gibberellin (GA) signaling in Arabidopsis thaliana. Using the GA-deficient mutant ga1–3, the GA-response mutant spy-5, and uniconazol (a GA-biosynthesis inhibitor), we show that the GA level response correlates positively with both trichome number and trichome branch number. Two genes, GL1 and TTG, are required for trichome initiation. In ga1–3, coexpression of GL1 and R, the maize TTG functional homolog, under control of the constitutive 35S promoter, restored trichome development, whereas overexpression of neither GL1 nor R alone was sufficient to significantly suppress the glabrous phenotype. We next focused on GL1 regulation by GAs. In the double mutant the gl1–1 glabrous phenotype is epistatic to the spy-5 phenotype, suggesting that GL1 acts downstream of the GA signal transduction pathway. The activity of a β-glucuronidase reporter gene driven by the GL1 promoter was decreased in the wild type grown on uniconazol and showed a clear GA-dependent activation in ga1–3. Finally, quantification of GL1 transcript levels by reverse transcriptase-polymerase chain reaction demonstrated that relative to wild type, ga1–3 plants contained less transcript. These data support the hypothesis that GAs induce trichome development through up-regulation of GL1 and possibly TTG genes. PMID:9625690

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

    PubMed Central

    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

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

    PubMed

    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.

  18. Glandular dose in breast computed tomography with synchrotron radiation.

    PubMed

    Mettivier, G; Fedon, C; Di Lillo, F; Longo, R; Sarno, A; Tromba, G; Russo, P

    2016-01-21

    The purpose of this work is to provide an evaluation of the mean glandular dose (MGD) for breast computed tomography (CT) with synchrotron radiation in an axial scanning configuration with a partial or total organ volume irradiation, for the in vivo program of breast CT ongoing at the ELETTRA facility (Trieste, Italy). A Geant4 Monte Carlo code was implemented, simulating the photon irradiation from a synchrotron radiation source in the energetic range from 8 to 50 keV with 1 keV intervals, to evaluate the MGD. The code was validated with literature data, in terms of mammographic normalized glandular dose coefficients (DgN) and with ad hoc experimental data, in terms of computed tomography dose index (CTDI). Simulated cylindrical phantoms of different sizes (diameter at phantom base 8, 10, 12, 14 or 16 cm, axial length 1.5 times the radius) and glandular fraction by weight (0%, 14.3%, 25%, 50%, 75% and 100%) were implemented into the code. The validation of the code shows an excellent agreement both with previously published work and in terms of DgN and CDTI measurements. The implemented simulations show a dependence of the glandular dose estimate on the vertical dimension of the irradiated zone when a partial organ irradiation was implemented. Specific normalized coefficients for calculating the MGD to the whole breast or to the single irradiated slice were reported.

  19. Clinical considerations of the glandular branch of the lacrimal artery.

    PubMed

    Kluckman, Matthew; Fan, Jerry; Balsiger, Heather; Scott, Gabriel; Gest, Thomas

    2015-10-01

    The lacrimal artery is classically described as a branch of the ophthalmic artery supplied by the internal carotid. In this study, 25 orbits were dissected to identify variations in glandular branching and to compare them to previously published accounts. The glandular branching patterns of the lacrimal artery fall into two categories, those that branch (56%) and those that do not branch (44%). We found the medial and lateral glandular branches to be equal in diameter with a divergence of 2.67-40.58 mm proximal to the gland parenchyma. The long glandular branches run alongside the superolateral aspect of the orbit. The lateral branch runs lateral to the lateral rectus muscle. The medial branch runs superomedial to the lateral rectus muscle and lateral to the superior rectus muscle. In relation to the lacrimal gland, the medial branch enters the superior aspect of the gland parenchyma and the lateral branch enters its inferior aspect. The average branch lengths were 17.88 mm (medial) and 13.51 mm (lateral) as measured with a Mitutoyo Absolute 1/100 mm caliper. We could not confirm the existence of a third branch supplying the lacrimal gland, as posited by other authors. The key finding in this study is that the lacrimal gland is predominantly supplied by two significant arterial branches, both of which must be identified during procedures involving the lateral orbit.

  20. Metabolic engineering of terpene biosynthesis in plants using a trichome-specific transcription factor MsYABBY5 from spearmint (Mentha spicata).

    PubMed

    Wang, Qian; Reddy, Vaishnavi Amarr; Panicker, Deepa; Mao, Hui-Zhu; Kumar, Nadimuthu; Rajan, Chakravarthy; Venkatesh, Prasanna Nori; Chua, Nam-Hai; Sarojam, Rajani

    2016-07-01

    In many aromatic plants including spearmint (Mentha spicata), the sites of secondary metabolite production are tiny specialized structures called peltate glandular trichomes (PGT). Having high commercial values, these secondary metabolites are exploited largely as flavours, fragrances and pharmaceuticals. But, knowledge about transcription factors (TFs) that regulate secondary metabolism in PGT remains elusive. Understanding the role of TFs in secondary metabolism pathway will aid in metabolic engineering for increased yield of secondary metabolites and also the development of new production techniques for valuable metabolites. Here, we isolated and functionally characterized a novel MsYABBY5 gene that is preferentially expressed in PGT of spearmint. We generated transgenic plants in which MsYABBY5 was either overexpressed or silenced using RNA interference (RNAi). Analysis of the transgenic lines showed that the reduced expression of MsYABBY5 led to increased levels of terpenes and that overexpression decreased terpene levels. Additionally, ectopic expression of MsYABBY5 in Ocimum basilicum and Nicotiana sylvestris decreased secondary metabolite production in them, suggesting that the encoded transcription factor is probably a repressor of secondary metabolism.

  1. Fine-mapping of the woolly gene controlling multicellular trichome formation and embryonic development in tomato.

    PubMed

    Yang, Changxian; Li, Hanxia; Zhang, Junhong; Wang, Taotao; Ye, Zhibiao

    2011-08-01

    Trichomes are small hairs that originate from the epidermal cells of nearly all land plants, and they exist in unicellular and multicellular forms. The regulatory pathway of unicellular trichomes in Arabidopsis is well characterized. However, little is known about the multicellular trichome formation in tomato (Solanum lycopersicum). The woolly (Wo) gene controls multicellular trichome initiation and leads to embryonic lethality when homozygous in tomato. To clone and characterize Wo, the gene was fine-mapped to a DNA fragment of ~200 kb using the map-based cloning strategy. A series of sequence-based molecular markers, including simple sequence repeat, sequence characterized amplified region, and cleaved amplified polymorphic sequence were utilized in this study. Analysis of the sequence indicated that this region carries 19 putative open reading frames. These results will provide not only the important information for the isolation and characterization of Wo but also the starting point for studying the regulatory pathway responsible for trichome formation and embryonic lethality in tomato.

  2. Intercellular transfer along the trichomes of the invasive terminal heterocyst forming cyanobacterium Cylindrospermopsis raciborskii CS-505.

    PubMed

    Plominsky, Álvaro M; Delherbe, Nathalie; Mandakovic, Dinka; Riquelme, Brenda; González, Karen; Bergman, Birgitta; Mariscal, Vicente; Vásquez, Mónica

    2015-03-01

    Cylindrospermopsis raciborskii CS-505 is an invasive freshwater filamentous cyanobacterium that when grown diazotrophically may develop trichomes of up to 100 vegetative cells while differentiating only two end heterocysts, the sole sites for their N2-fixation process. We examined the diazotrophic growth and intercellular transfer mechanisms in C. raciborskii CS-505. Subjecting cultures to a combined-nitrogen-free medium to elicit N2 fixation, the trichome length remained unaffected while growth rates decreased. The structures and proteins for intercellular communication showed that while a continuous periplasmic space was apparent along the trichomes, the putative septal junction sepJ gene is divided into two open reading frames and lacks several transmembrane domains unlike the situation in Anabaena, differentiating a 5-fold higher frequency of heterocysts. FRAP analyses also showed that the dyes calcein and 5-CFDA were taken up by heterocysts and vegetative cells, and that the transfer from heterocysts and 'terminal' vegetative cells showed considerably higher transfer rates than that from vegetative cells located in the middle of the trichomes. The data suggest that C. raciborskii CS-505 compensates its low-frequency heterocyst phenotype by a highly efficient transfer of the fixed nitrogen towards cells in distal parts of the trichomes (growing rapidly) while cells in central parts suffers (slow growth).

  3. Entrapment of bed bugs by leaf trichomes inspires microfabrication of biomimetic surfaces.

    PubMed

    Szyndler, Megan W; Haynes, Kenneth F; Potter, Michael F; Corn, Robert M; Loudon, Catherine

    2013-06-06

    Resurgence in bed bug infestations and widespread pesticide resistance have greatly renewed interest in the development of more sustainable, environmentally friendly methods to manage bed bugs. Historically, in Eastern Europe, bed bugs were entrapped by leaves from bean plants, which were then destroyed; this purely physical entrapment was related to microscopic hooked hairs (trichomes) on the leaf surfaces. Using scanning electron microscopy and videography, we documented the capture mechanism: the physical impaling of bed bug feet (tarsi) by these trichomes. This is distinct from a Velcro-like mechanism of non-piercing entanglement, which only momentarily holds the bug without sustained capture. Struggling, trapped bed bugs are impaled by trichomes on several legs and are unable to free themselves. Only specific, mechanically vulnerable locations on the bug tarsi are pierced by the trichomes, which are located at effective heights and orientations for bed bug entrapment despite a lack of any evolutionary association. Using bean leaves as templates, we microfabricated surfaces indistinguishable in geometry from the real leaves, including the trichomes, using polymers with material properties similar to plant cell walls. These synthetic surfaces snag the bed bugs temporarily but do not hinder their locomotion as effectively as real leaves.

  4. Effect of trichome density on soybean pod feeding by adult bean leaf beetles (Coleoptera: Chrysomelidae).

    PubMed

    Lam, W K; Pedigo, L P

    2001-12-01

    The role of soybean, Glycine max (L.) Merrill, pod trichomes on feeding by adult bean leaf beetles. Cerotoma trifurcata (Forster), was evaluated under laboratory and field conditions during 1997 and 1998. Three Clark isolines and 'Corsoy 79' were used to compare the feeding preference of the beetle on pods with different trichome densities. The three Clark isolines, including densely pubescent, sparsely pubescent, and glabrous, were isogenic except for trichome density. The trichome densities on the pods of Clark densely pubescent, Clark sparsely pubescent, and Corsoy 79 were significantly different. In no-choice tests, under both laboratory and field conditions, the feeding on pods of Clark densely pubescent was significantly lower than that on the other isolines. In the choice test of Corsoy 79 conducted in the laboratory and field, when the trichomes on one of the two pods were shaven off, the feeding on the shaven pods was significantly higher than that of the intact ones. In the choice test among Clark isolines under laboratory condition, the result was significant, with the lowest feeding on the densely pubescent pods. This study demonstrates that densely pubescent soybean has the potential to resist bean leaf beetle feeding on pods.

  5. A novel texture descriptor for detection of glandular structures in colon histology images

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

    The first step prior to most analyses on most histopathology images is the detection of area of interest. In this work, we present a superpixel-based approach for glandular structure detection in colon histology images. An image is first segmented into superpixels with the constraint on the presence of glandular boundaries. Texture and color information is then extracted from each superpixel to calculate the probability of that superpixel belonging to glandular regions, resulting in a glandular probability map. In addition, we present a novel texture descriptor derived from a region covariance matrix of scattering coefficients. Our approach shows encouraging results for the detection of glandular structures in colon tissue samples.

  6. Evidence for estrogen-dependent uterine serpin (SERPINA14) expression during estrus in the bovine endometrial glandular epithelium and lumen.

    PubMed

    Ulbrich, Susanne E; Frohlich, Thomas; Schulke, Katy; Englberger, Eva; Waldschmitt, Nadine; Arnold, Georg J; Reichenbach, Horst-Dieter; Reichenbach, Myriam; Wolf, Eckhard; Meyer, Heinrich H D; Bauersachs, Stefan

    2009-10-01

    Uterine secretions have a dominant impact on the environment in which embryo development takes place. The uterine serpins (SERPINA14, previously known as UTMP) are found most abundantly during pregnancy in the uterus of ruminants. Although progesterone is currently assumed to be the major regulator of SERPINA14 expression, our recent study of transcriptome changes in bovine endometrium during the estrous cycle unexpectedly detected a marked upregulation of SERPINA14 mRNA levels at estrus. The present study describes the full-length mRNA sequence, genomic organization, and putative promoter elements of the SERPINA14 gene. The SERPINA14 mRNA abundance was quantified by real-time RT-PCR in intercaruncular endometrium at several time points during the estrous cycle and early pregnancy. Highest levels were found at estrus, followed by a dramatic decrease and a moderate expression during the luteal phase. Transcript levels were higher in pregnant endometrium compared with controls at Day 18. At estrus, immunoreactive protein was localized in deep glandular epithelium, and Western blotting concomitantly showed the 52-kDa form in uterine flushings. SERPINA14 mRNA was significantly upregulated in glandular endometrial cells in vitro after stimulation with estradiol-17beta and progesterone, but not after interferon-tau treatment. Our results clearly demonstrate that SERPINA14 appears distinctly in bovine endometrium during the estrus phase. A supporting role toward providing a well-prepared endometrial environment for passing gametes, especially sperm, is assumed.

  7. Mean glandular dose in a breast screening programme

    SciTech Connect

    Galvan, H. A.; Perez-Badillo, M. P.; Villasenor, Y.

    2012-10-23

    Breast density has an important role in early detection of breast cancer, because has been reported the strong association between breast density and invasive breast cancer risk. Mammography is the gold standard to early detection of breast cancer, despite of this require ionizing radiation that may increase radio-induced cancer risk. This maybe limited with a quality control programme of mammographic units, with the main goal of achieving high quality images with low radiation dose. International Atomic Energy Agency (IAEA) published in 2011 the {sup Q}uality assurance programme for digital mammography{sup ,} where glandular tissue quantity is an important parameter to compute mean glandular dose (MGD), which is necessary to reduce its associated risk. In this work we show the first results in our country applying this protocol and studying breast density in a small group. MGD complies with national and IAEA dose limits.

  8. Glandular Odontogenic Cyst: The Value of Intraepithelial Hemosiderin.

    PubMed

    AbdullGaffar, Badr; Koilelat, Mohamed

    2017-05-01

    Glandular odontogenic cyst (GOC) is a relatively rare but well-described clinicopathologic entity. Its rarity and unpredictable clinical behavior are challenging to managing clinicians. Its variable and overlapping histomorphologic features are also diagnostically challenging for pathologists. Other odontogenic cysts and oral cystic neoplasms can simulate GOC. There are specific histologic criteria that help distinguish GOC from other mimickers. To our knowledge, the phenomenon of hemosiderin pigments deposition within the lining glandular epithelium of GOC has not been covered in detail or specifically reported so far in the literature. We report a case of nontraumatized anterior mandibular GOC in a middle-aged male, which histologically showed hemosiderin pigments within the lining epithelium without stromal siderophages. This finding might reflect a nonspecific spontaneous intraluminal hemorrhage. However, intraepithelial hemosiderin in GOC may be an additional helpful diagnostic clue of GOC in challenging cases since this phenomenon has not been reported in other mimicker cystic lesions.

  9. Pseudoneoplastic glandular lesions of the uterine cervix: a selective review.

    PubMed

    Nucci, Marisa R

    2014-07-01

    Pseudoneoplastic glandular lesions of the cervix continue to be diagnostically challenging for the surgical pathologist. This review covers a select number of these lesions that may be misinterpreted as premalignant or malignant, with an emphasis on those about which Dr Scully has advanced our knowledge. The topics covered include microglandular hyperplasia, mesonephric hyperplasia, diffuse laminar endocervical glandular hyperplasia, lobular endocervical glandular hyperplasia, and endocervical adenomyoma. The first listed entity has a greater diversity of morphology than the name might imply including, but not limited to solid growth and prominent hyaline stroma. The second entity may be remarkably diffuse within the cervical wall and reasonably result in consideration of diagnoses such as minimal deviation adenocarcinoma (adenoma malignum), but has nonmucinous epithelium and bland cytology. The third entity, one of the least common of those considered, represents a peculiar form of reactive hyperplasia of the endocervical epithelium. The fourth entity is the one about which knowledge is still fast advancing. In pure form with no atypia it is almost certainly a clinically benign process, but a subset of cases show cytologic atypia and an occasional association with adenocarcinoma is seen. Finally, adenomyomas of the uterus in general have received much attention in recent years, mostly in the corpus, but the less common endocervical variant may be particularly problematic because mucinous epithelium in abundant myogenic stroma may be potentially confused with an infiltrating differentiated mucinous adenocarcinoma. Although immunohistochemistry may play a role on occasion in evaluating benign endocervical glandular proliferations the mainstay of their interpretation remains conventional morphologic analysis of routinely stained slides.

  10. Bone metastasis of glandular cardiac myxoma mimicking a metastatic carcinoma.

    PubMed

    Uppin, Shantveer G; Jambhekar, Nirmala; Puri, Ajay; Kumar, Rajiv; Agarwal, Manish; Sanghvi, Darshana

    2011-01-01

    Skeletal metastasis from a cardiac myxoma is rare. We describe an extremely unusual case of a cardiac myxoma metastasing to the femur in a 46-year-old female presenting with pain in the right hip. Radiographs showed an expansile lytic lesion with pathological fracture involving the neck and proximal shaft of the right femur. Histology revealed features of cardiac myxoma with heterologous glandular elements, which was initially mistaken for a metastatic mucin-secreting adenocarcinoma.

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

    PubMed

    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.

  12. Cell wall maturation of Arabidopsis trichomes is dependent on exocyst subunit EXO70H4 and involves callose deposition.

    PubMed

    Kulich, Ivan; Vojtíková, Zdeňka; Glanc, Matouš; Ortmannová, Jitka; Rasmann, Sergio; Žárský, Viktor

    2015-05-01

    Arabidopsis (Arabidopsis thaliana) leaf trichomes are single-cell structures with a well-studied development, but little is understood about their function. Developmental studies focused mainly on the early shaping stages, and little attention has been paid to the maturation stage. We focused on the EXO70H4 exocyst subunit, one of the most up-regulated genes in the mature trichome. We uncovered EXO70H4-dependent development of the secondary cell wall layer, highly autofluorescent and callose rich, deposited only in the upper part of the trichome. The boundary is formed between the apical and the basal parts of mature trichome by a callose ring that is also deposited in an EXO70H4-dependent manner. We call this structure the Ortmannian ring (OR). Both the secondary cell wall layer and the OR are absent in the exo70H4 mutants. Ecophysiological aspects of the trichome cell wall thickening include interference with antiherbivore defense and heavy metal accumulation. Ultraviolet B light induces EXO70H4 transcription in a CONSTITUTIVE PHOTOMORPHOGENIC1-dependent way, resulting in stimulation of trichome cell wall thickening and the OR biogenesis. EXO70H4-dependent trichome cell wall hardening is a unique phenomenon, which may be conserved among a variety of the land plants. Our analyses support a concept that Arabidopsis trichome is an excellent model to study molecular mechanisms of secondary cell wall deposition.

  13. Clearance and metabolism of glandular kallikrein in the rat

    SciTech Connect

    Rabito, S.F.; Seto, M.; Maitra, S.R.; Carretero, O.A.

    1985-06-01

    This study was undertaken to characterize the clearance of circulating rat glandular kallikrein and to determine the contribution of various organs and the urinary excretion to the removal of glandular kallikrein from the bloodstream. The authors injected either active /sup 125/I-kallikrein or kallikrein inactivated with phenylmethylsulfonyl fluoride (/sup 125/I-PMSF-kallikrein) intravenously into intact or nephrectomized rats and then studied the disappearance rate of trichloroacetic acid (TCA)-precipitable radioactivity from the circulation. Inactivation by PMSF markedly reduced the binding of kallikrein to plasma protease inhibitors. The removal rate of the acid-precipitable radioactivity fit a biexponential curve for both active and inactive kallikrein. In the intact rats approximately 50% of the radioactivity was removed from the circulation 30 min after the injection of active /sup 125/I-kallikrein. Removal of the kidneys did not significantly affect the clearance of active kallikrein. On the other hand, inactive /sup 125/I-PMSF-kallikrein was removed from blood faster than active /sup 125/I-kallikrein in normal animals. Approximately 50% of the radioactivity was removed from the circulation 8 min after the injection, and the half-life of inactive /sup 125/I-PMSF-kallikrein was markedly prolonged by bilateral nephrectomy. Active /sup 125/I-kallikrein was taken up by tissues, particularly the liver and the kidney. In urine, less than 2% of the radioactivity was excreted in 60 min as TCA-precipitable material. The authors concluded that glandular kallikrein is cleared rapidly from the circulation of the rat, probably in the form of a complex with a plasma protease inhibitor.

  14. Differential regulation of a MYB transcription factor is correlated with transgenerational epigenetic inheritance of trichome density in Mimulus guttatus

    PubMed Central

    Scoville, Alison G.; Barnett, Laryssa L.; Bodbyl-Roels, Sarah; Kelly, John K.; Hileman, Lena C.

    2011-01-01

    Summary Epigenetic inheritance, transgenerational transmission of traits not proximally determined by DNA sequence, has been linked to transmission of chromatin modifications and gene regulation, which are known to be sensitive to environmental factors. Mimulus guttatus increases trichome (plant hair) density in response to simulated herbivore damage. Increased density is expressed in progeny even if progeny do not experience damage. To better understand epigenetic inheritance of trichome production, we tested the hypothesis that candidate gene expression states are inherited in response to parental damage.Using M. guttatus recombinant inbred lines, offspring of leaf-damaged and control plants were raised without damage. Relative expression of candidate trichome development genes was measured in offspring. Line and parental damage effects on trichome density were measured. Associations between gene expression, trichome density, and response to parental damage were determined.We identified M. guttatus MYB MIXTA-like 8 as a possible negative regulator of trichome development. We found that parental leaf damage induces down-regulation of MYB MIXTA-like 8 in progeny, which is associated with epigenetically inherited increased trichome density.Our results link epigenetic transmission of an ecologically important trait with differential gene expression states – providing insight into a mechanism underlying environmentally induced ‘soft inheritance’. PMID:21352232

  15. Genome-Wide Survey Reveals Transcriptional Differences Underlying the Contrasting Trichome Phenotypes of Two Sister Desert Poplars

    PubMed Central

    Ma, Jianchao; He, Xiaodong; Bai, Xiaotao; Niu, Zhimin; Duan, Bingbing; Chen, Ningning; Shao, Xuemin; Wan, Dongshi

    2016-01-01

    Trichomes, which are widely used as an important diagnostic characteristic in plant species delimitation, play important roles in plant defense and adaptation to adverse environments. In this study, we used two sister poplar species, Populus pruinosa and Populus euphratica—which have, respectively, dense and sparse trichomes—to examine the genetic differences associated with these contrasting phenotypes. The results showed that 42 and 45 genes could be identified as candidate genes related to trichomes in P. pruinosa and P. euphratica, respectively; most of these genes possessed high degrees of diversification in their coding sequences, but they were similar in intron/exon structure in the two species. We also found that most of the candidate trichome genes were expressed at higher levels in P. pruinosa, which has dense trichomes, than in P. euphratica, where there are few trichomes. Based on analyses of transcriptional profiles, a total of 195 genes, including many transcription factors, were found to show distinct differences in expression. The results of gene function annotation suggested that the genes identified as having contrasting levels of expression level are mainly associated with trichome elongation, ATPase activity, and hormone transduction. Changes in the expression of these and other related genes with high sequence diversification may have contributed to the contrast in the pattern of trichome phenotypes between the two species. PMID:27916935

  16. Comparison of TRY and the closely related At1g01380 gene in controlling Arabidopsis trichome patterning.

    PubMed

    Esch, Jeffrey J; Chen, Margaret A; Hillestad, Matthew; Marks, M David

    2004-12-01

    A screen of activation-tagged Arabidopsis lines resulted in the identification of At1g01380, which encodes a small R3 single repeat MYB gene, as a negative regulator of trichome initiation. Plants that overexpress this gene have fewer trichomes. The gene is closely related to the previously identified negative regulator TRY, and has a similar pattern of expression as TRY in developing leaves. As previously shown for TRY, At1g01380 protein can inhibit the interaction between the positive trichome regulators GL1 and GL3, and likely limits trichome initiation via this inhibition. While TRY and At1g01380 are closely related, they are not completely functionally equivalent. When placed under the transcriptional control of the TRY promoter, At1g01380 can only partially rescue the try mutant. Interestingly, Atg01380 is highly expressed in gl3-sst trichomes, while TRY expression is greatly reduced. The mutation in gl3-sst causes a reduced interaction between the GL1 and GL3 proteins and results in fewer leaf trichomes that develop in clusters. The differential expression of TRY and At1g01380 in this mutant can be used to explain how its altered trichome pattern in gl3-sst [corrected] is generated.

  17. Natural allelic variation defines a role for ATMYC1: trichome cell fate determination.

    PubMed

    Symonds, V Vaughan; Hatlestad, Greg; Lloyd, Alan M

    2011-06-01

    The molecular nature of biological variation is not well understood. Indeed, many questions persist regarding the types of molecular changes and the classes of genes that underlie morphological variation within and among species. Here we have taken a candidate gene approach based on previous mapping results to identify the gene and ultimately a polymorphism that underlies a trichome density QTL in Arabidopsis thaliana. Our results show that natural allelic variation in the transcription factor ATMYC1 alters trichome density in A. thaliana; this is the first reported function for ATMYC1. Using site-directed mutagenesis and yeast two-hybrid experiments, we demonstrate that a single amino acid replacement in ATMYC1, discovered in four ecotypes, eliminates known protein-protein interactions in the trichome initiation pathway. Additionally, in a broad screen for molecular variation at ATMYC1, including 72 A. thaliana ecotypes, a high-frequency block of variation was detected that results in >10% amino acid replacement within one of the eight exons of the gene. This sequence variation harbors a strong signal of divergent selection but has no measurable effect on trichome density. Homologs of ATMYC1 are pleiotropic, however, so this block of variation may be the result of natural selection having acted on another trait, while maintaining the trichome density role of the gene. These results show that ATMYC1 is an important source of variation for epidermal traits in A. thaliana and indicate that the transcription factors that make up the TTG1 genetic pathway generally may be important sources of epidermal variation in plants.

  18. New method for generating breast models featuring glandular tissue spatial distribution

    NASA Astrophysics Data System (ADS)

    Paixão, L.; Oliveira, B. B.; Oliveira, M. A.; Teixeira, M. H. A.; Fonseca, T. C. F.; Nogueira, M. S.

    2016-02-01

    Mammography is the main radiographic technique used for breast imaging. A major concern with mammographic imaging is the risk of radiation-induced breast cancer due to the high sensitivity of breast tissue. The mean glandular dose (DG) is the dosimetric quantity widely accepted to characterize the risk of radiation induced cancer. Previous studies have concluded that DG depends not only on the breast glandular content but also on the spatial distribution of glandular tissue within the breast. In this work, a new method for generating computational breast models featuring skin composition and glandular tissue distribution from patients undergoing digital mammography is proposed. Such models allow a more accurate way of calculating individualized breast glandular doses taking into consideration the glandular tissue fraction. Sixteen breast models of four patients with different glandularity breasts were simulated and the results were compared with those obtained from recommended DG conversion factors. The results show that the internationally recommended conversion factors may be overestimating the mean glandular dose to less dense breasts and underestimating the mean glandular dose for denser breasts. The methodology described in this work constitutes a powerful tool for breast dosimetry, especially for risk studies.

  19. Mixed squamous cell and glandular papilloma of the lung in a 64-year-old woman.

    PubMed

    Yun, Ju Sik; Kim, Do Wan; Choi, Yoo Duk; Na, Kook Joo; Song, Sang Yun

    2014-02-01

    Mixed squamous cell and glandular papilloma of the lung is an extremely rare benign epithelial tumor showing a mixture of squamous and glandular epithelium. Here, we report a case of mixed squamous cell and glandular papilloma that presented as a solitary nodule in the left lower lobe of a 64-year-old woman. Chest computed tomography demonstrated a lobulated mass in the basal segment of the left lower lobe. The patient underwent a lobectomy under the suspicion of lung malignancy. The histopathological diagnosis was mixed squamous cell and glandular papilloma.

  20. The costs of anti-herbivore defense traits in agricultural crop plants: a case study involving leafhoppers and trichomes.

    PubMed

    Kaplan, Ian; Dively, Galen P; Denno, Robert F

    2009-06-01

    The expression of plant defenses is thought to entail costs (e.g., the allocation of resources away from growth or reproduction) that constrain the evolution of plant genotypes maximally defended against herbivores. Although central to the ecological theory underlying plant-insect interactions at large, the concept of defense costs is particularly evident in agricultural crops where plants may be under simultaneous selection for enhanced growth and/or reproduction (i.e., yield) and anti-herbivore resistance traits that deter pests. In this study we investigate the role of trichomes as a resistance mechanism against a sap-feeding insect (the leafhopper, Empoasca fabae) on potato. Natural variation in trichome density among 17 potato cultivars was used to test for the role of trichomes as a putative defense against leafhoppers, and evidence of costs in trichome expression. Two different types of costs were explored: (1) allocation costs (i.e., the relationship between trichomes and yield), and (2) costs involving trade-offs with alternative defense strategies (e.g., tolerance). Although leafhopper abundance did not decrease as trichome density increased, leafhopper injury to potato plants (foliar necrosis) was negatively correlated with trichome density. As a result, the per capita effect of leafhopper adults and nymphs on foliar damage was lower on plants with high trichome densities. We found no evidence, however, for costs of expressing this resistance trait; trichomes were not correlated with either potato yield or tolerance to herbivory. Thus, selection for multiple plant defenses to alleviate the impact of pests in agronomic crops may indeed be possible without inherent losses in plant yield.

  1. Population Responses of Potato Leafhopper (Hemiptera: Cicadellidae) to Insecticide in Glandular-Haired and Non-glandular-Haired Alfalfa Cultivars.

    PubMed

    Sulc, R Mark; McCormick, John S; Hammond, Ronald B; Miller, David J

    2014-12-01

    Conflicting results have been reported on the ability of glandular-haired alfalfa (Medicago sativa L.) cultivars to reduce potato leafhopper, Empoasca fabae Harris, population abundance in field environments. We measured potato leafhopper adult and nymph abundance and yield responses in a cultivar selected for high potato leafhopper resistance ('54H91') and in a non-glandular-haired susceptible cultivar ('54V54') with and without insecticide treatment across 3 yr. Treatments included no insecticide and insecticide applied either early or late in each summer growth cycle. Date × cultivar × treatment interactions were found for potato leafhopper population abundance. In the absence of insecticides, total potato leafhopper abundance (adults + nymphs per sweep) was lower in 54H91 than in 54V54 on 85% of sampling dates; cultivar differences were especially evident as potato leafhopper abundance peaked. Insecticide treatment reduced potato leafhopper populations in both cultivars, but populations recovered and often exceeded the normal action threshold in both cultivars within 2-3 wk of insecticide application. Yield gain from early insecticide treatment of 54V54 was >400 kg/ha in 11 of 14 summer harvests, whereas in 54H91 the yield gain was <250 kg/ha in 10 of 14 summer harvests. We conclude that glandular-haired alfalfa cultivars with high levels of potato leafhopper resistance significantly suppress potato leafhopper adult and nymph abundance, reduce yield losses in the absence of insecticides, and have potential within an integrated pest management strategy to reduce insecticide use in alfalfa production systems.

  2. Flat urothelial carcinoma in situ of the bladder with glandular differentiation.

    PubMed

    Lopez-Beltran, Antonio; Jimenez, Rafael E; Montironi, Rodolfo; Patriarca, Carlo; Blanca, Ana; Menendez, Carmen L; Algaba, Ferran; Cheng, Liang

    2011-11-01

    We present the clinicopathologic and immunonohistochemical features of 25 cases of flat urothelial carcinoma in situ with glandular differentiation. Previously, cases on this category have been reported as in situ adenocarcinoma (a term not currently preferred). Fourteen of 25 cases had concurrent conventional urothelial carcinoma in situ. Five of the cases were primary carcinoma in situ with glandular differentiation; twenty cases of secondary carcinoma in situ with glandular differentiation were associated with urothelial carcinoma alone (n = 11) or with glandular differentiation (n = 7), discohesive (n = 1) or micropapillary carcinoma (n = 1). The individual tumor cells were columnar. The architectural pattern of the carcinoma in situ with glandular differentiation consisted of 1 or more papillary, flat or cribriform glandular patterns. Univariate statistical analysis showed no survival differences between urothelial carcinoma in situ with glandular differentiation and conventional urothelial carcinoma in situ (log-rank 0.810; P = .368). Carcinoma in situ with glandular differentiation showed high ki-67 index and p53 accumulation, high nuclear and cytoplasmic p16 expression and diffuse PTEN expression, a phenotype that also characterized concurrent conventional carcinoma in situ. MUC5A, MUC2, CK20, and c-erbB2 were positive in all 25 cases of urothelial carcinoma in situ with glandular differentiation, and CDX-2 was present in 19 cases; MUC1, CK7, or 34βE12 was focally present in 21, 19, and 18 cases, respectively. MUC1core was negative in all cases. We concluded that urothelial carcinoma in situ with glandular differentiation is a variant of carcinoma in situ that follows the natural history of conventional urothelial carcinoma in situ. The immunophenotype suggests urothelial origin with the expression of MUC5A and CDX2 as signature for glandular differentiation.

  3. Biosynthesis of a new tobacco alkaloid, hydroxy-N-acylnornicotine in the trichomes of Nicotiana stocktonii. [Manduca sexta

    SciTech Connect

    Zador, E.; Jones, D.

    1986-04-01

    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/sup 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.

  4. Effect of plant trichomes on the vertical migration of Haemonchus contortus infective larvae on five tropical forages.

    PubMed

    Oliveira, Aruaque L F; Costa, Ciniro; Rodella, Roberto A; Silva, Bruna F; Amarante, Alessandro F T

    2009-06-01

    The influence of trichomes on vertical migration and survival of Haemonchus contortus infective larvae (L3) on different forages was investigated. Four different forages showing different distributions of trichomes (Brachiaria brizantha cv. Marandu, Brachiaria brizantha cv. Xaraes, Andropogon gayanus, and Stylosanthes spp.), and one forage species without trichomes (Panicum maximum cv. Tanzania), were used. Forages cut at the post-grazing height were contaminated with faeces containing L3. Samples of different grass strata (0-10, 10-20, >20 cm) and faeces were collected for L3 quantification once per week over four weeks. In all forages studied, the highest L3 recovery occurred seven days after contamination, with the lowest recovery on A. gayanus. In general, larvae were found on all forages' strata. However, most of the larvae were at the lower stratum. There was no influence of trichomes on migration and survival of H. contortus L3 on the forages.

  5. Human bronchial epithelial cells differentiate to 3D glandular acini on basement membrane matrix.

    PubMed

    Wu, Xiaofang; Peters-Hall, Jennifer R; Bose, Sumit; Peña, Maria T; Rose, Mary C

    2011-06-01

    To create a model system that investigates mechanisms resulting in hyperplasia and hypertrophy of respiratory tract submucosal glands, we developed an in vitro three-dimensional (3D) system wherein normal human bronchial epithelial (HBE) cells differentiated into glandular acini when grown on a basement membrane matrix. The differentiation of primary HBE cells into glandular acini was monitored temporally by light microscopy. Apoptosis-induced lumen formation was observed by immunofluorescence analysis. The acinar cells expressed and secreted MUC5B mucin (marker for glandular mucous cells) and lysozyme, lactoferrin, and zinc-α2-glycoprotein (markers for glandular serous cells) at Day 22. β-Tubulin IV, a marker for ciliated cells, was not detected. Expression of mucous and serous cell markers in HBE glandular acini demonstrated that HBE cells grown on a basement membrane matrix differentiated into acini that exhibit molecular characteristics of respiratory tract glandular acinar cells. Inhibition studies with neutralizing antibodies resulted in a marked decrease in size of the spheroids at Day 7, demonstrating that laminin (a major component of the basement membrane matrix), the cell surface receptor integrin α6, and the cell junction marker E-cadherin have functional roles in HBE acinar morphogenesis. No significant variability was detected in the average size of glandular acini formed by HBE cells from two normal individuals. These results demonstrated that this in vitro model system is reproducible, stable, and potentially useful for studies of glandular differentiation and hyperplasia.

  6. Glandular odontogenic cyst: report of an unusual bilateral occurrence.

    PubMed

    Amberkar, Vikram S; Jahagirdar, Abhishek; Ahmed Mujib, B R

    2011-01-01

    Glandular odontogenic cyst (GOC) is a recently recognized rare developmental odontogenic cyst having an aggressive behavior and accounting for 0.012% to 1.3% of all jaw cysts. GOC usually presents as a painless, slow-growing swelling that tends to affect the anterior part of the jaws. It chiefly occurs in the fourth and fifth decades of life and presents as an expansion of jaws with or without pain or paresthesia. Aggressive nature of the lesion has been reported, as supported by the fact that 25 to 55% of cases recur following curettage. So far only just over 113 cases of GOC have been reported in the literature. Here, we report a case of bilateral GOC in the posterior region of the maxilla, in a 29-year-old male patient, which is unique, being the first case of bilateral GOC to be reported in the literature.

  7. Glandular odontogenic cyst: absence of PTCH gene mutation.

    PubMed

    Barreto, D C; De Marco, L; Castro, W H; Gomez, R S

    2001-02-01

    Glandular odontogenic cyst (GOC) is a rare jawbone cyst of odontogenic origin. Human patched (PTCH) is a tumour suppressor gene that has been recently associated with signalling pathways during odontogenesis. Recently alterations of this gene were found on sporadic odontogenic keratocysts. This evidence, together with the biological behaviour similarities of both lesions, and the absence of reports on molecular analysis of GOC, led us to hypothesize that PTCH gene mutations may underlie the tumorigenesis of GOC. Therefore the aim of this study was to report one additional case of GOC and investigate the PTCH gene of the cyst. No mutations were found in the splicing and coding regions of the PTCH gene. In conclusion, the PTCH gene does not seem to be involved in GOC pathogenesis.

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

    PubMed Central

    Tian, Juan; Wang, Xiaohong; Mao, Tonglin; Yuan, Ming; Li, Yunhai

    2016-01-01

    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. PMID:27768706

  9. Structure and biomechanics of trapping flower trichomes and their role in the pollination biology of Aristolochia plants (Aristolochiaceae).

    PubMed

    Oelschlägel, Birgit; Gorb, Stanislav; Wanke, Stefan; Neinhuis, Christoph

    2009-12-01

    *Catching insects to ensure pollination is one of the most elaborate and specialized mechanisms of insect-plant interactions. Phylogenetically, Aristolochiaceae represent the first angiosperm lineage that developed trap flowers. Here we report the structure and function of specific trichomes contributing to the highly specialized trapping devices. *Investigations were carried out on six Mediterranean Aristolochia species. The morphology and arrangement of the trapping trichomes were investigated by scanning electron microscopy (SEM) and cryo-SEM. To demonstrate frictional anisotropy of the trapping trichome array, a microtribological approach was used. *The results of our experiments support a hypothesis long proposed, but never tested, regarding the trapping mechanism in proterogynous Aristolochia flowers: that an array of highly specialized trichomes arranged eccentrically to the underlying surface is responsible for the easy entrance of insects into flowers but impedes their escape. As they enter the male stage of anthesis, flowers significantly modify their inner surface characteristics, allowing insects to leave. *We have demonstrated the substantial contribution of trapping trichomes to the capture, retention and release of pollinators, an important prerequisite for making cross-pollination possible in most Aristolochia species. Finally, we compare trapping trichomes of Aristolochia with similar structures found in other trapping flowers as well as in pitchers of carnivorous plants not optimized for insect release.

  10. Glandular odontogenic cyst of the maxilla: a case report and literature review.

    PubMed

    Figueiredo, Nigel Roque; Dinkar, Ajit Dattatray; Khorate, Manisha Maruti

    2016-01-01

    Glandular Odontogenic Cyst is a relatively rare cyst of odontogenic origin, which shows glandular or salivary features that are thought to indicate the pluripotentiality of odontogenic epithelium. It is seen in middle-aged adults, and commonly involves the anterior region of the jaws, especially the mandible. It shows non-specific clinico-radiographic findings which may resemble other lesions, but has characteristic histopathologic features which help in its diagnosis. This paper reports an unusual presentation of a glandular odontogenic cyst which was diagnosed in a 64-year old female in the posterior maxilla, along with a literature review of this cyst, especially the cases reported in India in the past.

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

    PubMed Central

    Hernandez, Andrew M.; Seibert, J. Anthony; Boone, John M.

    2015-01-01

    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 (pDgNhetero) and homogeneous (pDgNhomo) 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 pDgNhetero coefficients were on average 35.3% (SD, 4.1) and 24.2% (SD, 3.0) lower than the pDgNhomo 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 pDgNhetero relative to pDgNhomo of 23.6%–27.4% for a W–Rh spectrum. Displacement of the glandular distribution, at a distance equal to 10% of the compressed breast width in the superior and

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

    SciTech Connect

    Hernandez, Andrew M.; Seibert, J. Anthony; Boone, John M.

    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

  13. Dosimetry in Mammography: Average Glandular Dose Based on Homogeneous Phantom

    NASA Astrophysics Data System (ADS)

    Benevides, Luis A.; Hintenlang, David E.

    2011-05-01

    The objective of this study was to demonstrate that a clinical dosimetry protocol that utilizes a dosimetric breast phantom series based on population anthropometric measurements can reliably predict the average glandular dose (AGD) imparted to the patient during a routine screening mammogram. AGD was calculated using entrance skin exposure and dose conversion factors based on fibroglandular content, compressed breast thickness, mammography unit parameters and modifying parameters for homogeneous phantom (phantom factor), compressed breast lateral dimensions (volume factor) and anatomical features (anatomical factor). The patient fibroglandular content was evaluated using a calibrated modified breast tissue equivalent homogeneous phantom series (BRTES-MOD) designed from anthropomorphic measurements of a screening mammography population and whose elemental composition was referenced to International Commission on Radiation Units and Measurements Report 44 and 46 tissues. The patient fibroglandular content, compressed breast thickness along with unit parameters and spectrum half-value layer were used to derive the currently used dose conversion factor (DgN). The study showed that the use of a homogeneous phantom, patient compressed breast lateral dimensions and patient anatomical features can affect AGD by as much as 12%, 3% and 1%, respectively. The protocol was found to be superior to existing methodologies. The clinical dosimetry protocol developed in this study can reliably predict the AGD imparted to an individual patient during a routine screening mammogram.

  14. Dosimetry in Mammography: Average Glandular Dose Based on Homogeneous Phantom

    SciTech Connect

    Benevides, Luis A.; Hintenlang, David E.

    2011-05-05

    The objective of this study was to demonstrate that a clinical dosimetry protocol that utilizes a dosimetric breast phantom series based on population anthropometric measurements can reliably predict the average glandular dose (AGD) imparted to the patient during a routine screening mammogram. AGD was calculated using entrance skin exposure and dose conversion factors based on fibroglandular content, compressed breast thickness, mammography unit parameters and modifying parameters for homogeneous phantom (phantom factor), compressed breast lateral dimensions (volume factor) and anatomical features (anatomical factor). The patient fibroglandular content was evaluated using a calibrated modified breast tissue equivalent homogeneous phantom series (BRTES-MOD) designed from anthropomorphic measurements of a screening mammography population and whose elemental composition was referenced to International Commission on Radiation Units and Measurements Report 44 and 46 tissues. The patient fibroglandular content, compressed breast thickness along with unit parameters and spectrum half-value layer were used to derive the currently used dose conversion factor (DgN). The study showed that the use of a homogeneous phantom, patient compressed breast lateral dimensions and patient anatomical features can affect AGD by as much as 12%, 3% and 1%, respectively. The protocol was found to be superior to existing methodologies. The clinical dosimetry protocol developed in this study can reliably predict the AGD imparted to an individual patient during a routine screening mammogram.

  15. Pulmonary mixed squamous cell and glandular papilloma mimicking adenocarcinoma: a case study and literature review.

    PubMed

    Lin, Dongliang; Jiang, Yanxia; Wang, Jigang; Ding, Li; Xin, Fangjie; Zhao, Han; Li, Yujun

    2013-08-01

    Mixed squamous cell and glandular papilloma of the lung is an extremely rare benign neoplasm. Here we present another case of mixed squamous cell and glandular papilloma in a 64-year-old female nonsmoker. Histologically, the tumor was composed of mainly papillary structures covered with squamous, glandular and transitional epithelium. Some glandular structures extending into adjacent bronchiolar and alveolar spaces with mucus were similar to adenocarcinoma. Immunohistochemical analysis showed the different kinds of epithelia had similar immunophenotype. The different components were positive for cytokeratin (CK)7, CK19, CAM5.2, CK5/6, CK34βE12, and TTF-1, but negative for CK20. The transitional morphology and immunohistochemistry indicate the different components likely come from a same kind of progenitor in the bronchiolar wall.

  16. [Study on characteristics of non-glandular hairs of cultivated Lonicera japonica].

    PubMed

    Zhang, Shan-shan; Yuan, Yuan; Huang, Lu-qi; Chen, Ping

    2015-02-01

    We collected 22 cultivated population of Lonicera japonica from 17 areas. The characteristics of non-glandular hairs were observed and measured by the scanning electron microscopy. The principal components analysis and correlation analysis were conduct based on length and density of L. japonica. The results showed a significant negative correlation between length and density of non-glandular hairs, and the characteristics of non-glandular was not corrrelated significantly with latitude. The correlation results indicated that the density was a key to separate "Damaohua" and "Jizhuahua". The contribution of climate and soil was important to the cultivated population. This reminded that the characteristics of non-glandular hairs were affected by environmental and genetic interaction.

  17. Filamentous Trichomic Prokaryotes in Carbonaceous Meteorites: Indigenous Microfossils, Minerals, or Modern Bio-Contaminants?

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.; Rozanov, Alexei Yu.

    2011-01-01

    Large complex filaments have been detected in freshly fractured interior surfaces of a variety of carbonaceous meteorites. Many exhibit the detailed morphological and morphometric characteristics of known filamentous trichomic prokaryotic microorganisms. In this paper we review prior studies of filamentous microstructures encountered in the meteorites along with the elemental compositions and characteristics of the, fibrous evaporite minerals and filamentous cyanobacteria and homologous trichomic sulfur bacteria. The meteorite images and elemental compositions will compared with data obtained with the same instruments for abiotic microstructures and living and fossil microorganisms in order to evaluate the relative merits of the alternate hypotheses that have been advanced to explain the nature and characteristics of the meteorite filaments. The possibiility that the filaments found in the meteorites may be comprise modern bio-contaminants will be evaluated in light of their observed elemental compositions and data by other researchers on the detection of indigenous complex organic biosignatures, and extraterrestrial amino acids and nucleobases found in the Murchison CM2 and the Orgueil CI1 carbonaceous meteorites.

  18. Leaf trichome responses to herbivory in willows: induction, relaxation and costs.

    PubMed

    Björkman, Christer; Dalin, Peter; Ahrné, Karin

    2008-01-01

    To circumvent the inherent problem of discriminating between the cost of losing photosynthetic tissue and the cost of producing an inducible defence, the growth response of herbivore-damaged plants was compared with plants damaged mechanically to the same extent but without eliciting the defence. Two experiments were conducted, studying the response of willows (Salix cinerea) to damage by adult leaf beetles (Phratora vulgatissima). In the first experiment, willows produced new leaves with an enhanced leaf trichome density 10-20 d after damage, coinciding in time with the feeding of beetle offspring. The response was relaxed in foliage produced 30-40 d after damage. In the second experiment, which also included mechanical damage, willows exposed to beetle feeding showed an increase in leaf trichome density of the same magnitude (> 70%) as in the first experiment. The cost of producing the defence was a 20% reduction in shoot length growth and biomass production. Willows exposed to mechanical damage had an 8% reduction in shoot length growth compared with control plants, that is, a cost of leaf area removal. The results are the first quantitative estimates of the cost of a plant defence induced by natural and low amounts (3.3%) of herbivory.

  19. Glandular epithelial AR inactivation enhances PTEN deletion-induced uterine pathology.

    PubMed

    Choi, Jaesung Peter; Zheng, Yu; Handelsman, David J; Simanainen, Ulla

    2016-05-01

    Phosphatase and tensin homolog (PTEN) deletion induces uterine pathology, whereas androgen actions via androgen receptor (AR) support uterine growth and therefore may modify uterine cancer risk. We hypothesized that the androgen actions mediated via uterine glandular epithelial AR could modify PTEN deletion-induced uterine pathology. To test our hypothesis, we developed uterine glandular epithelium-specific PTEN and/or AR knockout mouse models comparing the uterine pathology among wild-type (WT), glandular epithelium-specific AR inactivation (ugeARKO), PTEN deletion (ugePTENKO), and the combined PTEN and AR knockout (ugePTENARKO) female mice. The double knockout restricted to glandular epithelium showed that AR inactivation enhanced PTEN deletion-induced uterine pathology with development of intraepithelial neoplasia by 20 weeks of age. In ugePTENARKO, 6/10 (60%) developed intraepithelial neoplasia, whereas 3/10 (30%) developed only glandular hyperplasia in ugePTENKO uterus. No uterine pathology was observed in WT (n=8) and ugeARKO (n=7) uteri. Uterine weight was significantly (P=0.002) increased in ugePTENARKO (374±97 mg (mean±s.e.)) compared with WT (97±6 mg), ugeARKO (94±12 mg), and ugePTENKO (205±33 mg). Estrogen receptor alpha (ERα) and P-AKT expression was modified by uterine pathology but did not differ between ugePTENKO and ugePTENARKO, suggesting that its expressions are not directly affected by androgens. However, progesterone receptor (PR) expression was reduced in ugePTENARKO compared to ugePTENKO uterus, suggesting that PR expression could be regulated by glandular epithelial AR inactivation. In conclusion, glandular epithelial AR inactivation (with persistent stromal AR action) enhanced PTEN deletion-induced uterine pathology possibly by downregulating PR expression in the uterus.

  20. Establishing epithelial glandular polarity: interlinked roles for ARF6, Rac1, and the matrix microenvironment.

    PubMed

    Monteleon, Christine L; Sedgwick, Alanna; Hartsell, Alyssa; Dai, Michael; Whittington, Catherine; Voytik-Harbin, Sherry; D'Souza-Schorey, Crislyn

    2012-12-01

    Epithelial cysts comprise the structural units of the glandular epithelium. Although glandular inversion in epithelial tumors is thought to be a potential mechanism for the establishment of metastatic disease, little is known about the morphogenic cues and signaling pathways that govern glandular polarity and organization. Using organotypic cultures of Madin-Darby canine kidney cells in reconstituted basement membrane, we show that cellular depletion of the small GTP-binding protein ARF6 promotes the formation of inverted cysts, wherein the apical cell membrane faces the cyst exterior, and the basal domain faces the central lumen, while individual cell polarity is maintained. These cysts are also defective in interactions with laminin at the cyst-matrix interface. This inversion of glandular orientation is accompanied by Rac1 inactivation during early cystogenesis, and temporal activation of Rac1 is sufficient to recover the normal cyst phenotype. In an unnatural collagen I microenvironment, ARF6-depleted, inverted epithelial cysts exhibit some loss of cell polarity, a marked increase in Rho activation and Rac1 inactivation, and striking rearrangement of the surrounding collagen I matrix. These studies demonstrate the importance of ARF6 as a critical determinant of glandular orientation and the matrix environment in dictating structural organization of epithelial cysts.

  1. Aquaporins are upregulated in glandular epithelium at the time of implantation in the rat.

    PubMed

    Lindsay, Laura A; Murphy, Christopher R

    2007-03-01

    Regulation of luminal fluid is essential for blastocyst implantation. While it has been known for quite some time that there is a reduction in the amount of luminal fluid at the time of implantation, the mechanisms regulating this process are only just emerging. Previous studies have shown an upregulation of aquaporin (AQP) 5 channels in luminal epithelial cells at the time of implantation providing a mechanism for fluid reabsorption across the surface epithelium. However to date the contribution of fluid reabsorption by glandular epithelial cells has not been established. This study using reverse transcriptase polymerase chain reaction demonstrates the presence of several AQP isoforms in the rat uterus at the time of implantation while immunofluorescence data demonstrates an apical distribution of AQPs5 and 9 in the glandular epithelium at the time of implantation. The presence of AQPs5 and 9 in the apical plasma membrane of the glandular epithelium seen in this study provides a mechanism for transcellular fluid transport across these glandular epithelial cells similar to that seen in luminal epithelial cells. The reabsorption of glandular fluid via AQP channels may also regulate luminal fluid volume and be involved in the reduction in luminal fluid seen at the time of implantation.

  2. Terrific Trichomes (and Other Specialised Cells) in African Violets: How to Get a Lot from One Plant in the Classroom

    ERIC Educational Resources Information Center

    Cottrell, Vicki M.

    2013-01-01

    African violet (genus "Saintpaulia") was identified as a particularly suitable genus for the study of specialised plant cells in the classroom using microscopes. The techniques described here involve simple preparation without staining. The cells and structures that can be investigated include: trichomes (hairs); stomata; guard cells and…

  3. A New Glabrous Gene (csgl3) Identified in Trichome Development in Cucumber (Cucumis sativus L.)

    PubMed Central

    Ding, Li-Hong; Wehner, Todd C.; Liu, Pan-Na; Wang, Ye; Zhang, Sheng-Ping; Gu, Xing-Fang

    2016-01-01

    Spines or trichomes on the fruit of cucumbers enhance their commercial value in China. In addition, glabrous mutants exhibit resistance to aphids and therefore their use by growers can reduce pesticide residues. Previous studies have reported two glabrous mutant plants containing the genes, csgl1 and csgl2. In the present study, a new glabrous mutant, NCG157, was identified showing a gene interaction effect with csgl1 and csgl2. This mutant showed the glabrous character on stems, leaves, tendrils, receptacles and ovaries, and there were no spines or tumors on the fruit surface. Inheritance analysis showed that a single recessive gene, named csgl3, determined the glabrous trait. An F2 population derived from the cross of two inbred lines 9930 (a fresh market type from Northern China that exhibits trichomes) and NCG157 (an American processing type with glabrous surfaces) was used for genetic mapping of the csgl3 gene. By combining bulked segregant analysis (BAS) with molecular markers, 18 markers, including two simple sequence repeats (SSR), nine insertion deletions (InDel) and seven derived cleaved amplified polymorphism sequences (dCAPs), were identified to link to the csgl3 gene. All of the linked markers were used as anchor loci to locate the csgl3 gene on cucumber chromosome 6. The csgl3 gene was mapped between the dCAPs markers dCAPs-21 and dCAPs-19, at genetic distances of 0.05 cM and 0.15 cM, respectively. The physical distance of this region was 19.6 kb. Three markers, InDel-19, dCAPs-2 and dCAPs-11, co-segregated with csgl3. There were two candidate genes in the region, Csa6M514860 and Csa6M514870. Quantitative real-time PCR showed that the expression of Csa6M514870 was higher in the tissues of 9930 than that of NCG157, and this was consistent with their phenotypic characters. Csa6M514870 is therefore postulated to be the candidate gene for the development of trichomes in cucumber. This study will facilitate marker-assisted selection (MAS) of the smooth

  4. A New Glabrous Gene (csgl3) Identified in Trichome Development in Cucumber (Cucumis sativus L.).

    PubMed

    Cui, Jin-Ying; Miao, Han; Ding, Li-Hong; Wehner, Todd C; Liu, Pan-Na; Wang, Ye; Zhang, Sheng-Ping; Gu, Xing-Fang

    2016-01-01

    Spines or trichomes on the fruit of cucumbers enhance their commercial value in China. In addition, glabrous mutants exhibit resistance to aphids and therefore their use by growers can reduce pesticide residues. Previous studies have reported two glabrous mutant plants containing the genes, csgl1 and csgl2. In the present study, a new glabrous mutant, NCG157, was identified showing a gene interaction effect with csgl1 and csgl2. This mutant showed the glabrous character on stems, leaves, tendrils, receptacles and ovaries, and there were no spines or tumors on the fruit surface. Inheritance analysis showed that a single recessive gene, named csgl3, determined the glabrous trait. An F2 population derived from the cross of two inbred lines 9930 (a fresh market type from Northern China that exhibits trichomes) and NCG157 (an American processing type with glabrous surfaces) was used for genetic mapping of the csgl3 gene. By combining bulked segregant analysis (BAS) with molecular markers, 18 markers, including two simple sequence repeats (SSR), nine insertion deletions (InDel) and seven derived cleaved amplified polymorphism sequences (dCAPs), were identified to link to the csgl3 gene. All of the linked markers were used as anchor loci to locate the csgl3 gene on cucumber chromosome 6. The csgl3 gene was mapped between the dCAPs markers dCAPs-21 and dCAPs-19, at genetic distances of 0.05 cM and 0.15 cM, respectively. The physical distance of this region was 19.6 kb. Three markers, InDel-19, dCAPs-2 and dCAPs-11, co-segregated with csgl3. There were two candidate genes in the region, Csa6M514860 and Csa6M514870. Quantitative real-time PCR showed that the expression of Csa6M514870 was higher in the tissues of 9930 than that of NCG157, and this was consistent with their phenotypic characters. Csa6M514870 is therefore postulated to be the candidate gene for the development of trichomes in cucumber. This study will facilitate marker-assisted selection (MAS) of the smooth

  5. Zinc Finger Protein5 Is Required for the Control of Trichome Initiation by Acting Upstream of Zinc Finger Protein8 in Arabidopsis1[C][W][OA

    PubMed Central

    Zhou, Zhongjing; An, Lijun; Sun, Lili; Zhu, Shuijin; Xi, Wanyan; Broun, Pierre; Yu, Hao; Gan, Yinbo

    2011-01-01

    Arabidopsis (Arabidopsis thaliana) trichome development is a model system for studying cell development, cell differentiation, and the cell cycle. Our previous studies have shown that the GLABROUS INFLORESCENCE STEMS (GIS) family genes, GIS, GIS2, and ZINC FINGER PROTEIN8 (ZFP8), control shoot maturation and epidermal cell fate by integrating gibberellins (GAs) and cytokinin signaling in Arabidopsis. Here, we show that a new C2H2 zinc finger protein, ZFP5, plays an important role in controlling trichome cell development through GA signaling. Overexpression of ZFP5 results in the formation of ectopic trichomes on carpels and other inflorescence organs. zfp5 loss-of-function mutants exhibit a reduced number of trichomes on sepals, cauline leaves, paraclades, and main inflorescence stems in comparison with wild-type plants. More importantly, it is found that ZFP5 mediates the regulation of trichome initiation by GAs. These results are consistent with ZFP5 expression patterns and the regional influence of GA on trichome initiation. The molecular analyses suggest that ZFP5 functions upstream of GIS, GIS2, ZFP8, and the key trichome initiation regulators GLABROUS1 (GL1) and GL3. Using a steroid-inducible activation of ZFP5 and chromatin immunoprecipitation experiments, we further demonstrate that ZFP8 is the direct target of ZFP5 in controlling epidermal cell differentiation. PMID:21803862

  6. Glandular odontogenic cyst of the maxilla: a case report and literature review

    PubMed Central

    Figueiredo, Nigel Roque; Dinkar, Ajit Dattatray; Khorate, Manisha Maruti

    2016-01-01

    Glandular Odontogenic Cyst is a relatively rare cyst of odontogenic origin, which shows glandular or salivary features that are thought to indicate the pluripotentiality of odontogenic epithelium. It is seen in middle-aged adults, and commonly involves the anterior region of the jaws, especially the mandible. It shows non-specific clinico-radiographic findings which may resemble other lesions, but has characteristic histopathologic features which help in its diagnosis. This paper reports an unusual presentation of a glandular odontogenic cyst which was diagnosed in a 64-year old female in the posterior maxilla, along with a literature review of this cyst, especially the cases reported in India in the past. PMID:28292079

  7. Mesothelial glandular structures within pseudosarcomatous proliferative funiculitis--a diagnostic pitfall: report of 17 cases.

    PubMed

    Michal, Michal; Hes, Ondrej; Kazakov, Dmitry V

    2008-01-01

    We describe 17 cases of distinct benign pseudomalignant mesothelial proliferations, involving the spermatic cord. All cases revealed necrosis. The areas adjacent to the necrotic tissue comprised a cellular spindle cell proliferation with a haphazard arrangement of the myofibroblasts that in many areas revealed transitions into plump oval epithelioid cells and into cells with genuine epithelial appearances arranged in linear cords and often luminized into small microcysts. These epithelial cells formed isolated groups with glandular structures arising on the myofibroblastic background. Glandular structures were often situated deeply in the stroma of the spermatic cords. All cellular elements were strongly positive with AE1/AE3 antibody. All myofibroblasts stained with SM-actin antibody. Ultrastructurally, the spindle cells displayed features of myofibroblasts including actin microfilaments, as did the plump epithelioid cells that, additionally, had desmosomes, and the cords of the epithelial cells including those forming glandular structures had characteristics of mesothelias including the characteristic microvilli.

  8. Immunoreactive glandular kallikrein in rat plasma: a radioimmunoassay for its determination

    SciTech Connect

    Rabito, S.F.; Scicli, A.G.; Kher, V.; Carretero, O.A.

    1982-04-01

    A radioimmunoassay (RIA) has been developed to measure immunoreactive glandular kallikrein in rat plasma. To prevent the binding of radioactive kallikrein to plasma inhibitors, /sup 125/I-kallikrein was inactivated with phenylmethylsulfonyl fluoride (PMSF), a procedure that maintained /sup 125/I-kallikrein immunoreactivity. Different volumes of plasma displaced /sup 125/I-PMSF-kallikrein in a parallel fashion to the kallikrein standard curve. The sensitivity of the RIA was 200 pg, and the recovery of nonradioactive active kallikrein added to plasma was 58.7%. The concentration of immunoreactive glandular kallikrein in normal rat plasma averaged 47.1 +/- 1.7 (SE) ng/ml. Bilateral nephrectomy caused a threefold increase in circulating glandular kallikrein (50 +/- 2.7 to 167 +/- 7 ng/ml; P < 0.001). Removal of the submandibular and sublingual glands signficantly decreased its concentration from 52 +/- 2.3 to 34 +/- 1.6 ng/ml (P < 0.001). Immunoreactive glandular kallikrein was higher in the submandibular gland vein than in arterial blood (venous; 94 +/- 10.5; arterial: 64 +/- 6.3 ng/ml; P < 0.05) and was lower in the renal venous blood (venous: 44 +/- 2.2; arterial: 53 +/- 2.6 ng/ml; P < 0.05). In conclusion, this study shows that the use of /sup 125/I-PMSF-kallikrein as tracer prevents the interference in the RIA caused by plasma protease inhibitors. It also indicates that the submandibular gland is an important source of the immunoreactive glandular kallikrein in rat plasma and that the kidney probably participates in its metabolism. Glandular kallikrein released by the submandibular gland into the circulation may participate in regulating local blood flow before it is inactivated by plasma inhibitors.

  9. Cardiac myxoma with glandular elements: a clinicopathological and immunohistochemical study of five new cases with an emphasis on differential diagnosis.

    PubMed

    Zhang, Minghui; Ding, Li; Liu, Yanhui; Xue, Ling

    2014-01-01

    This paper reported five new cases of cardiac myxoma with glandular components, known as glandular cardiac myxoma. The goals of this study were to analyze the clinicopathological features of this disease and to explore new features for differential diagnosis. The patient series included three women and two men. All tumors were located in the left atrium without invasion of the adjacent myocardium. Patients presented with cardiac-related or embolization symptoms. Histologically, neoplasms consisted of well-formed glandular structures and typical myxoma areas. No nuclear atypia, mitosis, or necrosis was identified in the glandular structures. Glandular lining cells were strongly positive for pan-cytokeratin, epithelial membrane antigen, CAM5.2 and cytokeratin 7, but were negative for some organ-specific markers, such as thyroid transcription factor-1, calretinin, estrogen receptor, progesterone receptor, gross cystic disease fluid protein, prostate-specific antigen, prostate-specific acid phosphatase, cytokeratin 20 and caudal type homeobox 2. In conclusion, glandular cardiac myxoma is a rare disease which shows characteristics similar to those of classical cardiac myxoma. Because of its rarity, glandular cardiac myxoma must be distinguished from adenocarcinoma metastatic to the heart. The combination of histopathological features and immunohistochemical profiles should improve the diagnostic accuracy of glandular cardiac myxoma.

  10. 21 CFR 201.300 - Notice to manufacturers, packers, and distributors of glandular preparations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 4 2010-04-01 2010-04-01 false Notice to manufacturers, packers, and distributors of glandular preparations. 201.300 Section 201.300 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING Specific Labeling...

  11. 21 CFR 201.300 - Notice to manufacturers, packers, and distributors of glandular preparations.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 4 2012-04-01 2012-04-01 false Notice to manufacturers, packers, and distributors of glandular preparations. 201.300 Section 201.300 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING Specific Labeling...

  12. 21 CFR 201.300 - Notice to manufacturers, packers, and distributors of glandular preparations.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 4 2014-04-01 2014-04-01 false Notice to manufacturers, packers, and distributors of glandular preparations. 201.300 Section 201.300 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING Specific Labeling...

  13. 21 CFR 201.300 - Notice to manufacturers, packers, and distributors of glandular preparations.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 4 2011-04-01 2011-04-01 false Notice to manufacturers, packers, and distributors of glandular preparations. 201.300 Section 201.300 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL LABELING Specific Labeling...

  14. [Computerized estimation of a percent glandular tissue composition in computed radiography mammography].

    PubMed

    Tsujita, Naoko; Goto, Sachiko; Azuma, Yoshiharu; Shiraishi, Junji

    2011-01-01

    Measurement of a percent glandular tissue composition (%GTC) is important in terms of the estimation of individual patient exposure dose and the prediction of malignancy, and thus a number of reports for estimating %GTC by use of a mammogram have been published. In this study, we propose a method for estimating individual %GTC by use of computed radiography (CR) mammograms. By employing breast-equivalent phantoms that are able to create breast phantom images with various combinations of fat and glandular tissue, as well as the thickness of whole breast, we determined a reference table for converting an each pixel value on CR mammography to the glandular tissue ratio. Therefore, the %GTC for individual breast was estimated by averaging glandular tissue ratio for a whole region. The clinical image data set that consisted of 49 CR mammograms were used for estimating %GTC. A paired comparison method for determining subjective ranking of the degree of breast density was employed in order to demonstrate the validity of our method. The results indicate that the average estimated %GTC was 35.0% (ranged from 12.0% to 67.0%) and they had a increased correlation with the ranking of those obtained by observer test. Therefore, it was suggested that our proposed method would be utilized for estimating the %GTC in objective manner.

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

    SciTech Connect

    Okunade, Akintunde Akangbe

    2006-04-15

    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.

  16. Transcriptome 2002 Conference

    SciTech Connect

    Quackenbush, John

    2002-01-01

    The Transcriptome 2002 meeting was held March 11-13, 2002 in Seattle, Washington with attendance by more than 300 scientists representing the international community. The scientific program was developed by an international organizing committee. In association with the main meeting, an Image Consortium invitational meeting was organized by Charles Auffray of CNRS and held with approximately 40 participants immediately following the conclusion of the Transcriptome meeting.

  17. Next-generation transcriptome assembly

    SciTech Connect

    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.

  18. Fine mapping and candidate gene analysis of Brtri1, a gene controlling trichome development in Chinese cabbage (Brassica rapa L. ssp pekinensis).

    PubMed

    Ye, X L; Hu, F Y; Ren, J; Huang, S N; Liu, W J; Feng, H; Liu, Z Y

    2016-12-02

    Trichomes are derived from the epidermis and constitute an ideal system for studying cell division in plants. Here, a Chinese cabbage doubled haploid (DH) line (FT) without trichomes was crossed with another DH line (PurDH-1) with trichomes to develop an F2 population for fine mapping of trichome control genes. Genetic analysis showed that the trichome phenotype was controlled by a single dominant gene, Brtri1. Using 1226 glabrous individuals in the F2 segregation population, Brtri1 was localized to a 16.84 kb region between markers Pur6-31 and Pur6-39 on chromosome A06. One of the four complete open reading frames within the mapping region, Bra025311, encodes a MYB transcription factor and is highly homologous to the trichome regulatory gene GL1 in Arabidopsis thaliana. It was thus regarded as a candidate gene for Brtri1. Comparative sequencing showed a 5-bp deletion in the third exon of Bra025311 in FT, resulting in a frame-shift mutation. No expression of Bra025311 was detected in FT. A co-dominant indel marker close to this mutation site was developed for marker-assisted selection in Chinese cabbage breeding.

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

    PubMed

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

    2015-12-01

    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° angular range (from -7.5° to +7.5°). 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 44.35 % between

  20. Transcriptomics in ecotoxicology.

    PubMed

    Schirmer, Kristin; Fischer, Beat B; Madureira, Danielle J; Pillai, Smitha

    2010-06-01

    The emergence of analytical tools for high-throughput screening of biomolecules has revolutionized the way in which toxicologists explore the impact of chemicals or other stressors on organisms. One of the most developed and routinely applied high-throughput analysis approaches is transcriptomics, also often referred to as gene expression profiling. The transcriptome represents all RNA molecules, including the messenger RNA (mRNA), which constitutes the building blocks for translating DNA into amino acids to form proteins. The entirety of mRNA is a mirror of the genes that are actively expressed in a cell or an organism at a given time. This in turn allows one to deduce how organisms respond to changes in the external environment. In this article we explore how transcriptomics is currently applied in ecotoxicology and highlight challenges and trends.

  1. Mayolenes: labile defensive lipids from the glandular hairs of a caterpillar (Pieris rapae).

    PubMed

    Smedley, Scott R; Schroeder, Frank C; Weibel, Douglas B; Meinwald, Jerrold; Lafleur, Katie A; Renwick, J Alan; Rutowski, Ronald; Eisner, Thomas

    2002-05-14

    Larvae of the European cabbage butterfly, Pieris rapae (Pieridae), are beset with glandular hairs, bearing droplets of a clear oily secretion at their tip. The fluid consists primarily of a series of chemically labile, unsaturated lipids, the mayolenes, which are derived from 11-hydroxylinolenic acid. In bioassays with the ant Crematogaster lineolata, the secretion was shown to be potently deterrent, indicating that the fluid plays a defensive role in nature.

  2. Adhesion protein VSIG1 is required for the proper differentiation of glandular gastric epithelia.

    PubMed

    Oidovsambuu, Odgerel; Nyamsuren, Gunsmaa; Liu, Shuai; Göring, Wolfgang; Engel, Wolfgang; Adham, Ibrahim M

    2011-01-01

    VSIG1, a cell adhesion protein of the immunoglobulin superfamily, is preferentially expressed in stomach, testis, and certain gastric, esophageal and ovarian cancers. Here, we describe the expression patterns of three alternatively spliced isoforms of mouse Vsig1 during pre- and postnatal development of stomach and potential function of Vsig1 in differentiation of gastric epithelia. We show that isoforms Vsig1A and Vsig1B, which differ in the 3'untranslated region, are expressed in the early stages of stomach development. Immunohistochemical analysis revealed that VSIG1 is restricted to the adherens junction of the glandular epithelium. The shorter transcript Vsig1C is restricted to the testis, encodes an N-terminal truncated protein and is presumably regulated by an internal promoter, which is located upstream of exon 1b. To determine whether the 5' flanking region of exon 1a specifically targets the expression of Vsig1 to stomach epithelia, we generated and analyzed transgenic mice. The 4.8-kb fragment located upstream of exon 1a was sufficient to direct the expression of the reporter gene to the glandular epithelia of transgenic stomach. To determine the role of VSIG1 during the development of stomach epithelia, an X-linked Vsig1 was inactivated in embryonic stem cells (ESCs). Although Vsig1(-/Y) ESCs were only able to generate low coat color chimeric mice, no male chimeras transmitted the targeted allele to their progeny suggesting that the high contribution of Vsig1(-/Y) cells leads to the lethality of chimeric embryos. Analysis of chimeric stomachs revealed the differentiation of VSIG1-null cells into squamous epithelia inside the glandular region. These results suggest that VSIG1 is required for the establishment of glandular versus squamous epithelia in the stomach.

  3. Comparison of mean glandular dose values provided by a digital breast tomosynthesis system in Brazil.

    PubMed

    Beraldo Oliveira, Bruno; Paixão, Lucas; Donato da Silva, Sabrina; Teixeira, Maria Helena Araújo; Nogueira, Maria do Socorro

    2015-06-01

    Studies are needed to determine the radiation dose of patients that are undergoing Digital breast tomosynthesis (DBT) procedures. Mean glandular dose (DG) values were derived from the incident air kerma (Ki) measurements and tabulated conversion coefficients. Ki values were obtained through an ionization chamber positioned in a Hologic Selenia Dimensions system using appropriate exposure parameters. This work contributes to determine the reliable radiation dose received by the patients and compare DG values provided by this DBT system images.

  4. Thymomas with prominent glandular differentiation: a clinicopathologic and immunohistochemical study of 12 cases.

    PubMed

    Weissferdt, Annikka; Moran, Cesar A

    2013-08-01

    Twelve cases of thymomas with prominent glandular differentiation are presented. The patients were 7 men and 5 women aged between 45 and 68 years (average, 56.5 years). Clinically, the patients presented with nonspecific symptoms of chest pain, cough, and fatigue. None of the patients had a history of myasthenia gravis or other autoimmune syndrome. Thymectomy was performed in all patients. The tumor size ranged from 4 to 7 cm in greatest diameter. Macroscopically, the tumors were described as firm and light tan without areas of necrosis, hemorrhage, or cystic change. Histologically, 7 tumors were classified as spindle cell (World Health Organization type A), 2 as mixed spindle cell and conventional (A+B1), 2 as conventional (B1), and 1 as atypical thymoma (B3). In 4 cases, the tumors showed invasion into periadipose thymic tissue. All cases showed the typical growth patterns of their particular subtypes. In addition, a distinct glandular component was present in all cases showing mucinous differentiation in 4 of them. Immunohistochemical studies showed tumor cells positive for CAM5.2, cytokeratin 5/6, and Pax8 and negative for carcinoembryonic antigen, thyroid transcription factor 1, and epithelial membrane antigen. Calretinin showed focal weak staining in the nonmucinous glandular components in 3 cases. Follow-up information obtained in 8 patients showed that all were alive and well in a period ranging from 2 to 5 years. The possibility of a glandular component in thymomas should be kept in mind in the assessment of mediastinoscopic biopsies to avoid misdiagnosis for other neoplasms that may require different treatment modalities.

  5. Identification of glandular (preputial and clitoral) proteins in house rat (Rattus rattus) involved in pheromonal communication.

    PubMed

    Archunan, G; Kamalakkannan, S; Achiraman, S; Rajkumar, R

    2004-10-01

    Proteins (18-20 kDa) belonging to lipocalin family have been reported to act as carriers for ligands binding to pheromones in mouse urine, pig saliva, hamster vaginal fluid and human sweat, that are involved in pheromonal communication. As the preputial gland is a major pheromonal source, the present study was aimed to detect the specific protein bands (around 18-20 kDa) in the preputial and clitoral glands of the house rat, R. rattus. The amount of protein was higher in preputial gland of the male than that of female (clitoral) gland. A 20 kDa protein was noted in male and female glands; however, the intensity of the band was much higher in male than in female. In addition, 70, 60, 35 kDa bands, identified in male preputial gland, were absent in females. The presence of higher concentration of glandular proteins in the male preputial gland suggests that male rats may depend more on these glandular proteins for the maintenance of reproductive and dominance behaviours. The results further suggest that these glandular proteins (20 kDa) may act as a carrier for ligand binding.

  6. Benign müllerian glandular inclusions in men undergoing pelvic lymph node dissection.

    PubMed

    Gallan, Alexander J; Antic, Tatjana

    2016-11-01

    Benign müllerian-type glandular inclusions in lymph nodes are commonly seen in women, but to our knowledge, there have only been 4 reported cases in men. Distinction of these glandular structures from metastatic adenocarcinoma is crucial for proper staging, prognosis, and treatment of the patient. We report 3 cases of benign müllerian-type glandular inclusions in men undergoing either prostatectomy or cystoprostatectomy with lymph node dissection for treatment of prostatic adenocarcinoma and/or urothelial carcinoma. None of the patients were receiving hormonal therapy. All 3 cases showed benign glands with ciliated cuboidal to columnar cells and rare secretory cells, morphologically comparable with endosalpingiosis in women. These glands were diffusely positive for PAX-8, WT-1, estrogen receptor, and progesteron receptor consistent with müllerian origin. Our study is the first to confirm müllerian origin of these glands by PAX-8 and WT-1 positivity. This finding of müllerian glands in men identical to endosalpingiosis in women supports the theory that this entity can result from müllerian metaplasia of the peritoneal mesothelium rather than displacement of tubal-type epithelium. Pathologists should also be aware that müllerian-type glands can rarely occur in men to prevent the incorrect diagnosis of metastatic adenocarcinoma involving a lymph node.

  7. [Estimation of the Average Glandular Dose Using the Mammary Gland Image Analysis in Mammography].

    PubMed

    Otsuka, Tomoko; Teramoto, Atsushi; Asada, Yasuki; Suzuki, Shoichi; Fujita, Hiroshi; Kamiya, Satoru; Anno, Hirofumi

    2016-05-01

    Currently, the glandular dose is evaluated quantitatively on the basis of the measured data using phantom, and not in a dose based on the mammary gland structure of an individual patient. However, mammary gland structures of the patients are different from each other and mammary gland dose of an individual patient cannot be obtained by the existing methods. In this study, we present an automated estimation method of mammary gland dose by means of mammary structure which is measured automatically using mammogram. In this method, mammary gland structure is extracted by Gabor filter; mammary region is segmented by the automated thresholding. For the evaluation, mammograms of 100 patients diagnosed with category 1 were collected. Using these mammograms we compared the mammary gland ratio measured by proposed method and visual evaluation. As a result, 78% of the total cases were matched. Furthermore, the mammary gland ratio and average glandular dose among the patients with same breast thickness was matched well. These results show that the proposed method may be useful for the estimation of average glandular dose for the individual patients.

  8. Is lobular endocervical glandular hyperplasia a cancerous precursor of minimal deviation adenocarcinoma?: a comparative molecular-genetic and immunohistochemical study.

    PubMed

    Kawauchi, Shigeto; Kusuda, Tomoko; Liu, Xu-Ping; Suehiro, Yutaka; Kaku, Tsunehisa; Mikami, Yoshiki; Takeshita, Morishige; Nakao, Motonao; Chochi, Yasuyo; Sasaki, Kohsuke

    2008-12-01

    Although lobular endocervical glandular hyperplasia (LEGH) was originally described as a distinct hyperplastic glandular lesion of the uterine cervix, recent studies have raised a question that LEGH may be a cancerous precursor of minimal deviation adenocarcinoma (MDA) and other mucinous adenocarcinomas (MACs) of the uterine cervix. In the present study, we studied LEGH, MDA, and MAC by using molecular-genetic and immunohistochemical methods for chromosomal imbalance, microsatellite instability, human papillomavirus (HPV) infection, and gastric pyloric-type mucin secretion to clarify their relationship. Comparative genomic hybridization revealed recurrent chromosomal imbalances, that is, gains of chromosome 3q and a loss of 1p, which were common to MDA and MAC, in 3 of 14 LEGHs analyzed (21%). LEGHs with chromosomal imbalances showed a degree of cellular atypia in the hyperplastic glandular epithelium. Dual-color fluorescence in situ hybridization confirmed a gain of chromosome 3 fragment in these cervical glandular lesions. HPV in situ hybridization revealed that high-risk HPV (types 16 and 18) was positive in over 80% of MACs, but negative in all LEGHs and MDAs examined. Microsatellite instability was rarely detected in these cervical glandular lesions. Our present study results demonstrated a molecular-genetic link between LEGH and cervical mucinous glandular malignancies including MDA and MAC, and are thought to support the hypothesis that a proportion of LEGHs are cancerous precursors of MDA and/or MAC.

  9. The ENHANCER OF TRY AND CPC1 gene acts redundantly with TRIPTYCHON and CAPRICE in trichome and root hair cell patterning in Arabidopsis.

    PubMed

    Kirik, Victor; Simon, Marissa; Huelskamp, Martin; Schiefelbein, John

    2004-04-15

    The development of trichomes and root hairs in Arabidopsis provide useful models for the study of cell fate determination in plants. A common network of putative transcriptional regulators, including the small MYB proteins TRIPTYCHON (TRY) and CAPRICE (CPC), is known to influence the patterning of both cell types. Here, we used an activation tagging strategy to identify a new regulator, ENHANCER OF TRY AND CPC 1 (ETC1). The ETC1 sequence is similar to TRY and CPC, and ETC1 overexpression causes a reduction in trichome formation and excessive root hair production. The etc1 single mutant has no significant phenotype, but it enhances the effect of cpc and try on trichome and root hair development, which shows that ETC1 function is partially redundant with TRY and CPC. In addition, the etc1 try cpc triple mutant has novel phenotypes, revealing previously unrecognized roles for these regulators in epidermis development. An ETC1 promoter-reporter gene fusion is expressed in the developing trichome and non-hair cells, similar to the expression of TRY and CPC. These results suggest that ETC1, TRY, and CPC act in concert to repress the trichome cell fate in the shoot epidermis and the non-hair cell fate in the root epidermis.

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

    PubMed

    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. Rescue of glandular dysmorphogenesis in PTEN-deficient colorectal cancer epithelium by PPARγ-targeted therapy.

    PubMed

    Jagan, I; Fatehullah, A; Deevi, R K; Bingham, V; Campbell, F C

    2013-03-07

    Disruption of glandular architecture associates with poor clinical outcome in high-grade colorectal cancer (CRC). Phosphatase and tensin homolog deleted on chromosome ten (PTEN) regulates morphogenic growth of benign MDCK (Madin Darby Canine Kidney) cells through effects on the Rho-like GTPase cdc42 (cell division cycle 42). This study investigates PTEN-dependent morphogenesis in a CRC model. Stable short hairpin RNA knockdown of PTEN in Caco-2 cells influenced expression or localization of cdc42 guanine nucleotide exchange factors and inhibited cdc42 activation. Parental Caco-2 cells formed regular hollow gland-like structures (glands) with a single central lumen, in three-dimensional (3D) cultures. Conversely, PTEN-deficient Caco-2 ShPTEN cells formed irregular glands with multiple abnormal lumens as well as intra- and/or intercellular vacuoles evocative of the high-grade CRC phenotype. Effects of targeted treatment were investigated. Phosphatidinylinositol 3-kinase (PI3K) modulating treatment did not affect gland morphogenesis but did influence gland number, gland size and/or cell size within glands. As PTEN may be regulated by the nuclear receptor peroxisome proliferator-activated receptor-γ (PPARγ), cultures were treated with the PPARγ ligand rosiglitazone. This treatment enhanced PTEN expression, cdc42 activation and rescued dysmorphogenesis by restoring single lumen formation in Caco-2 ShPTEN glands. Rosiglitazone effects on cdc42 activation and Caco-2 ShPTEN gland development were attenuated by cotreatment with GW9662, a PPARγ antagonist. Taken together, these studies show PTEN-cdc42 regulation of lumen formation in a 3D model of human CRC glandular morphogenesis. Treatment by the PPARγ ligand rosiglitazone, but not PI3K modulators, rescued colorectal glandular dysmorphogenesis of PTEN deficiency.

  12. Uncertainties involved in the estimation of mean glandular dose for women in the Norwegian Breast Cancer Screening Program (NBCSP).

    PubMed

    Hauge, I H R; Olerud, H M

    2013-06-01

    The aim of this study was to reflect on the estimation of the mean glandular dose for women in Norway aged 50-69 y. Estimation of mean glandular dose (MGD) has been conducted by applying the method of Dance et al. (1990, 2000, 2009). Uncertainties in the thickness of approximately ±10 mm adds uncertainties in the MGD of approximately ±10 %, and uncertainty in the glandularity of ±0 % will lead to an uncertainty in the MGD of ±4 %. However, the inherent uncertainty in the air kerma, given by the European protocol on dosimetry, will add an uncertainty of 12 %. The total uncertainty in the MGD is estimated to be ∼20 %, taking into consideration uncertainties in compressed breast thickness (±10 %), the air kerma (12 %), change in HVL by -0.05 mm (-9.0 %), uncertainty in the s-factor of ±2.1 % and changing the glandularity to an age-dependent glandularity distribution (+8.4 %).

  13. Immunohistochemical evidence: testicular and scented glandular androgen synthesis in muskrats (Ondatra zibethicus) during the breeding season.

    PubMed

    Li, Q; Weng, J; Zhang, H; Lu, L; Ma, X; Wang, Q; Cao, H; Liu, S; Xu, M; Weng, Q; Watanabe, G; Taya, K

    2011-10-19

    In order to elucidate the relationship between androgens and the function of the muskrat (Ondatra zibethicus) scented glands during the breeding season, we investigated immunolocalization of steroidogenic enzymes P450scc, 3βHSD and P450c17 in the muskrat testes and scented glands. Nine adult muskrats were obtained in March (n=3), May (n=3) and July (n=3) 2010. Steroidogenic enzymes were immunolocalized using polyclonal antisera raised against bovine adrenal P450scc, human placental 3βHSD and porcine testicular P450c17. Histologically, all types of spermatogenic cells including mature-phase spermatozoa in seminiferous tubules were observed in all testes. Glandular cells, interstitial cells, epithelial cells and excretory tubules were identified in scented glands during the breeding season. P450scc, 3βHSD and P450c17 were only identified in Leydig cells during the breeding season; P450scc and P450c17 were observed in glandular cells of scented glands, however, 3βHSD was not found in scented glands during the breeding season. These novel findings provide the first evidence showing that scented glands of the muskrats are capable of locally synthesizing androgens and androgens acting via an endocrine, autocrine or paracrine manner may play an important role in scented gland function during the breeding season.

  14. Glandular Epithelium as a Possible Source of a Fertility Signal in Ectatomma tuberculatum (Hymenoptera: Formicidae) Queens

    PubMed Central

    da Hora, Riviane Rodigues; Delabie, Jacques Hubert Charles; dos Santos, Carolina Gonçalves; Serrão, José Eduardo

    2010-01-01

    The wax layer covering the insect's cuticle plays an important protective role, as for example, uncontrolled water loss. In social insects, wax production is well-known in some bees that use it for nest building. Curiously, mated-fertile queens of the ant Ectatomma tuberculatum produce an uncommon extra-wax coat and, consequently queens (mated-fertile females) are matte due to such extra cuticular hydrocarbon (CHC) coat that covers the cuticle and masks the brightness of the queens' cuticle while gynes (virgin-infertile queens) are shiny. In this study, histological analysis showed differences in the epidermis between fertile (i.e., queens or gynes with highly ovarian activity) and infertile females (gynes or workers with non developed ovaries). In fertile females the epidermis is a single layer of cubic cells found in all body segments whereas in infertile females it is a thin layer of flattened cells. Ultrastructural features showed active secretory tissue from fertile females similar to the glandular epithelium of wax-producing bees (type I gland). Different hypotheses related to the functions of the glandular epithelium exclusive to the E. tuberculatum fertile queens are discussed. PMID:20419093

  15. Glandular epithelium as a possible source of a fertility signal in Ectatomma tuberculatum (Hymenoptera: Formicidae) queens.

    PubMed

    da Hora, Riviane Rodigues; Delabie, Jacques Hubert Charles; dos Santos, Carolina Gonçalves; Serrão, José Eduardo

    2010-04-19

    The wax layer covering the insect's cuticle plays an important protective role, as for example, uncontrolled water loss. In social insects, wax production is well-known in some bees that use it for nest building. Curiously, mated-fertile queens of the ant Ectatomma tuberculatum produce an uncommon extra-wax coat and, consequently queens (mated-fertile females) are matte due to such extra cuticular hydrocarbon (CHC) coat that covers the cuticle and masks the brightness of the queens' cuticle while gynes (virgin-infertile queens) are shiny. In this study, histological analysis showed differences in the epidermis between fertile (i.e., queens or gynes with highly ovarian activity) and infertile females (gynes or workers with non developed ovaries). In fertile females the epidermis is a single layer of cubic cells found in all body segments whereas in infertile females it is a thin layer of flattened cells. Ultrastructural features showed active secretory tissue from fertile females similar to the glandular epithelium of wax-producing bees (type I gland). Different hypotheses related to the functions of the glandular epithelium exclusive to the E. tuberculatum fertile queens are discussed.

  16. Cancerous versus noncancerous breasts. A comparative morphological analysis of the entire glandular tree of the breast.

    PubMed

    Sarnelli, R; Squartini, F

    1989-01-01

    Cancerous and clinically normal autopsy obtained breasts were collected in order to compare the physiopathological profile of both types of glandular tree. Each breast was visualized by whole thin sections and observed under a stereomicroscope with removal of the more interesting changes for histology. The comparison was made between 67 atrophic cancerous breasts and 88 atrophic control breasts. The results were as follows: 25% of the cancerous breasts versus 47% of control breasts showed no changes, atypical lobules, microfoci of "in situ" and/or infiltrating cancer were present in 46% of cancerous breasts and in 16% of control breasts, showing a significant correlation with clinical cancer. All other types of functional and proliferative changes, variously associated each other, were found in 29% of cancerous and in 37% of control breasts. Our morphological data agree completely with the statements in follow-up studies carried out on benign breast biopsies. The significant differences in the physiopathological profile of the glandular tree between "normal" and cancerous breasts, confirms that some changes are causally related to clinical cancer.

  17. Endocervical glandular involvement, multicentricity, and extent of the disease are features of high-grade cervical intraepithelial neoplasia.

    PubMed

    Güdücü, Nilgün; Sidar, Güliz; Başsüllü, Nuray; Türkmen, Ilknur; Dünder, Ilkkan

    2013-08-01

    This study aimed to evaluate the rate of endocervical glandular involvement, positive surgical margins, multicentricity, and disease extent between low-grade and high-grade cervical intraepithelial lesions after loop electrosurgical excision procedure (LEEP). Pathology medical records of patients who underwent LEEP were reviewed retrospectively. Patients with negative LEEP results were excluded. Loop electrosurgical excision procedure reports of patients with cervical intraepithelial neoplasia (CIN) 1, 2, and 3 were compared. There was no statistically significant difference between patients with CIN 1 (n=24), CIN 2 (n=27), and CIN 3 (n=64) when age and surgical margin positivity were considered. Endocervical glandular involvement, multicentricity, and disease extent were higher in patients with CIN 3 (P=.001, P=.002, and P=.001, respectively). In conclusion, we recommend that patients with endocervical glandular involvement, lesions involving more than two-thirds of the LEEP specimen, and multicentricity be followed up more closely.

  18. Structural differentiation of human uterine luminal and glandular epithelium during early pregnancy: an ultrastructural and immunohistochemical study.

    PubMed

    Demir, R; Kayisli, U A; Celik-Ozenci, C; Korgun, E T; Demir-Weusten, A Y; Arici, A

    2002-01-01

    The differentiation of human endometrial epithelium is a dynamic event that occurs throughout the menstrual cycle and early pregnancy. The structural transformation and differentiation of human uterine luminal and glandular epithelium of early human pregnancy (n=14) was investigated ultrastructurally and immunohistochemically using antibodies against cytokeratin (CT), endothelial marker CD31, Fas, and proliferating cell nuclear antigen (PCNA). Ultrastructurally, luminal epithelial cells showed distinctive euchromatic nuclei with prominent nucleoli and relatively loose cell membranes in all poles (apical to basal). Subcellular components were easily recognized in luminal epithelium except in degenerating cells. Mainly two cell types, dark and clear cells, formed the glandular epithelium. In the early gestation period, microvilli were abundant on the apical and apico-lateral poles of these cells. Only a few cytoplasmic projections were observed in dark cells. Numerous cilia were observed on the apical pole of some clear cells, located at the adluminal segment. In contrast, dark cells lacked cilia, nuclear channels, or giant mitochondrial profiles. Glycogen synthesis and apocrine secretion were recognizable for several days during early gestation. The apocrine secretory activity differed among dark cells of the glandular epithelium. The immunoreactivity of PCNA and Fas, and ultrastructural observations in the glandular epithelium suggest that, even in different segments of the same gland, epithelial cells do not regress during early gestation, but proliferate, perhaps representing a resistance against trophoblastic invasion. These morphological and molecular changes suggest that both luminal and glandular epithelium may play an important role in cellular defense and limitation for trophoblastic invasion during early pregnancy since plasma membrane alterations of the surface epithelium take place at the apical, basal and lateral poles compared to early secretory phase

  19. Changes in mammary histology and transcriptome profiles by low-dose exposure to environmental phenols at critical windows of development.

    PubMed

    Gopalakrishnan, Kalpana; Teitelbaum, Susan L; Lambertini, Luca; Wetmur, James; Manservisi, Fabiana; Falcioni, Laura; Panzacchi, Simona; Belpoggi, Fiorella; Chen, Jia

    2017-01-01

    Exposure to environmental chemicals has been linked to altered mammary development and cancer risk at high doses using animal models. Effects at low doses comparable to human exposure remain poorly understood, especially during critical developmental windows. We investigated the effects of two environmental phenols commonly used in personal care products - methyl paraben (MPB) and triclosan (TCS) - on the histology and transcriptome of normal mammary glands at low doses mimicking human exposure during critical windows of development. Sprague-Dawley rats were exposed during perinatal, prepubertal and pubertal windows, as well as from birth to lactation. Low-dose exposure to MPB and TCS induced measurable changes in both mammary histology (by Masson's Trichrome Stain) and transcriptome (by microarrays) in a window-specific fashion. Puberty represented a window of heightened sensitivity to MPB, with increased glandular tissue and changes of expression in 295 genes with significant enrichment in functions such as DNA replication and cell cycle regulation. Long-term exposure to TCS from birth to lactation was associated with increased adipose and reduced glandular and secretory tissue, with expression alterations in 993 genes enriched in pathways such as cholesterol synthesis and adipogenesis. Finally, enrichment analyses revealed that genes modified by MPB and TCS were over-represented in human breast cancer gene signatures, suggesting possible links with breast carcinogenesis. These findings highlight the issues of critical windows of susceptibility that may confer heightened sensitivity to environmental insults and implicate the potential health effects of these ubiquitous environmental chemicals in breast cancer.

  20. The genetics of extreme microgeographic adaptation: an integrated approach identifies a major gene underlying leaf trichome divergence in Yellowstone Mimulus guttatus.

    PubMed

    Hendrick, Margaret F; Finseth, Findley R; Mathiasson, Minna E; Palmer, Kristen A; Broder, Emma M; Breigenzer, Peter; Fishman, Lila

    2016-11-01

    Microgeographic adaptation provides a particularly interesting context for understanding the genetic basis of phenotypic divergence and may also present unique empirical challenges. In particular, plant adaptation to extreme soil mosaics may generate barriers to gene flow or shifts in mating system that confound simple genomic scans for adaptive loci. Here, we combine three approaches - quantitative trait locus (QTL) mapping of candidate intervals in controlled crosses, population resequencing (PoolSeq) and analyses of wild recombinant individuals - to investigate one trait associated with Mimulus guttatus (yellow monkeyflower) adaptation to geothermal soils in Yellowstone National Park. We mapped a major QTL causing dense leaf trichomes in thermally adapted plants to a <50-kb region of linkage Group 14 (Tr14) previously implicated in trichome divergence between independent M. guttatus populations. A PoolSeq scan of Tr14 region revealed a cluster of six genes, coincident with the inferred QTL peak, with high allele frequency differences sufficient to explain observed phenotypic differentiation. One of these, the R2R3 MYB transcription factor Migut.N02661, is a plausible functional candidate and was also strongly associated (r(2)  = 0.27) with trichome phenotype in analyses of wild-collected admixed individuals. Although functional analyses will be necessary to definitively link molecular variants in Tr14 with trichome divergence, our analyses are a major step in that direction. They point to a simple, and parallel, genetic basis for one axis of Mimulus guttatus adaptation to an extreme habitat, suggest a broadly conserved genetic basis for trichome variation across flowering plants and pave the way for further investigations of this challenging case of microgeographic incipient speciation.

  1. Inside the granulosa transcriptome.

    PubMed

    D'Aurora, Marco; Sperduti, Samantha; Di Emidio, Giovanna; Stuppia, Liborio; Artini, Paolo Giovanni; Gatta, Valentina

    2016-12-01

    The somatic component of follicular structure is a mixture of different cell types, represented by Granulosa cells (GCs) that are the paracrine regulators of the oocyte growth. GCs finely support this process by a continuous bidirectional talk with oocyte, which ensure oocyte quality and competence. Specific pathways are involved in the cross-talk and in both GCs and oocyte development. This review summarizes data from GCs gene expression analysis concerning both their physiological role and their interaction with oocyte. We also explore the CGs transcriptome modifications induced by controlled ovarian stimulation (COS) or pathological conditions and their impact in reproduction. The transcriptome analysis of GCs could be a powerful tool to improve our knowledge about the pathways involved in oocyte development. This approach, associated with new technologies as RNA-seq could allow the identifications of new noninvasive biological markers of oocyte quality to increase the efficiency of clinical IVF. Moreover, GCs expression analysis could be useful to shed light on new therapeutic targets by providing new options for the treatment of infertility.

  2. Chemistry of fruit flies: Glandular secretion ofBactrocera (Polistomimetes) visenda (Hardy).

    PubMed

    Krohn, S; Fletcher, M T; Kitching, W; Moore, C J; Drew, R A; Francke, W

    1992-12-01

    The major component (>90% of volatiles) of the male rectal glandular extract of the nonpest speciesBactrocera visenda (Hardy) is 3-methyl2-butenyl acetate, with minor components being the isomeric 3-methyl-3-butenyl acetate, the homologous esters, 3-methyl-2-butenyl propanoate and 3-methyl-2-butenyl formate, along with 3-methyl-2-buten-1-ol, 3-methyl-2-butenal, and 3-methylbutyl acetate. None of these compounds has been identified previously from aBactrocera species, supporting the view thatBactrocera visenda is taxonomically distant from otherBactrocera species identified from the Australian mainland. This collection of compounds adds to the known types utilized by dipteran species and emphasizes their extensive biosynthetic capability.

  3. An integrin-ILK-microtubule network orients cell polarity and lumen formation in glandular epithelium.

    PubMed

    Akhtar, Nasreen; Streuli, Charles H

    2013-01-01

    The extracellular matrix has a crucial role in determining the spatial orientation of epithelial polarity and the formation of lumens in glandular tissues; however, the underlying mechanisms remain elusive. By using Cre–Lox deletion we show that β1 integrins are required for normal mammary gland morphogenesis and lumen formation, both in vivo and in a three-dimensional primary culture model in which epithelial cells directly contact a basement membrane. Downstream of basement membrane β1 integrins, Rac1 is not involved; however, ILK is needed to polarize microtubule plus ends at the basolateral membrane and disrupting each of these components prevents lumen formation. The integrin–microtubule axis is necessary for the endocytic removal of apical proteins from the basement-membrane–cell interface and for internal Golgi positioning. We propose that this integrin signalling network controls the delivery of apical components to the correct surface and thereby governs the orientation of polarity and development of lumens.

  4. Endometrial stromal sarcoma with smooth muscle and glandular differentiation of the feline uterus.

    PubMed

    Sato, T; Maeda, H; Suzuki, A; Shibuya, H; Sakata, A; Shirai, W

    2007-05-01

    The intra-abdominal tumor developing in the uterus and lung of a domestic Shorthair cat was examined histopathologically and immunohistochemically. The tumor showed a proliferation of both endometrial stromal and smooth muscle cells accompanied by prominent vasculature. There were well-differentiated endometrial glands, and tubuli made up a monolayer of eosinophilic cuboidal epithelium. Immunohistochemically, the spindle-shaped cells and half of the stromal-like cells reacted to caldesmon and desmin antibodies. The neoplastic epithelium expressed AE1/AE3 cytokeratin. Feline endometrial stromal tumor has, to the best of our knowledge, not been reported previously and has smooth muscle and glandular components that are a unique variant to the human counterpart.

  5. Conformance of mean glandular dose from phantom and patient data in mammography.

    PubMed

    Kelaranta, A; Toroi, P; Timonen, M; Komssi, S; Kortesniemi, M

    2015-04-01

    In mammography dosimetry, phantoms are often used to represent breast tissue. The conformance of phantom- and patient-based mean glandular dose (MGD) estimates was evaluated mainly from the aspect of diagnostic reference levels. Patient and phantom exposure data were collected for eight diagnostic and three screening mammography devices. More extensive assessments were performed for two devices. The average breast thickness was close to the nationally used reference of 50 mm in diagnostic (50 mm, SD = 13 mm, n = 5342) and screening (47 mm, SD = 13 mm, n = 395) examinations. The average MGD for all breasts differed by 2% from the MGD determined for breasts in the limited compressed thickness range of 40-60 mm. The difference between phantom- and patient-based MGD estimations was up to 30%. Therefore, phantom measurements cannot replace patient dose data in MGD determination.

  6. Effect of filter on average glandular dose and image quality in digital mammography

    NASA Astrophysics Data System (ADS)

    Songsaeng, C.; Krisanachinda, A.; Theerakul, K.

    2016-03-01

    To determine the average glandular dose and entrance surface air kerma in both phantoms and patients to assess image quality for different target-filters (W/Rh and W/Ag) in digital mammography system. The compressed breast thickness, compression force, average glandular dose, entrance surface air kerma, peak kilovoltage and tube current time were recorded and compared between W/Rh and W/Ag target filter. The CNR and the figure of merit were used to determine the effect of target filter on image quality. The mean AGD of the W/Rh target filter was 1.75 mGy, the mean ESAK was 6.67 mGy, the mean CBT was 54.1 mm, the mean CF was 14 1bs. The mean AGD of W/Ag target filter was 2.7 mGy, the mean ESAK was 12.6 mGy, the mean CBT was 75.5 mm, the mean CF was 15 1bs. In phantom study, the AGD was 1.2 mGy at 4 cm, 3.3 mGy at 6 cm and 3.83 mGy at 7 cm thickness. The FOM was 24.6, CNR was 9.02 at thickness 6 cm. The FOM was 18.4, CNR was 8.6 at thickness 7 cm. The AGD from Digital Mammogram system with W/Rh of thinner CBT was lower than the AGD from W/Ag target filter.

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

    PubMed

    Kappadath, S Cheenu; Shaw, Chris C

    2003-06-01

    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 approximately 50 microm for the aluminum thickness and approximately 0.05 for the glandular ratio.

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

    SciTech Connect

    Baconnais, S.; Delavoie, F. |; Zahm, J.M.; Milliot, M.; Castillon, N.; Terryn, C.; Banchet, V.; Michel, J.; Danos, O.; Merten, M.; Chinet, T.; Zierold, K.; Bonnet, N.; Puchelle, E. , E-Mail: edith.puchelle@univ-reims.fr; Balossier, G.

    2005-10-01

    The absence or decreased expression of cystic fibrosis transmembrane conductance regulator (CFTR) induces increased Na{sup +} 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{sup +}, Mg{sup 2+}, P, S and Cl{sup -}) 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{sub 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.

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

    PubMed Central

    Kamal, Izdihar; Chelliah, Kanaga K.; Mustafa, Nawal

    2015-01-01

    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. PMID:26052465

  10. Establishing Substantial Equivalence: Transcriptomics

    NASA Astrophysics Data System (ADS)

    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.

  11. Chondrocyte channel transcriptomics

    PubMed Central

    Lewis, Rebecca; May, Hannah; Mobasheri, Ali; Barrett-Jolley, Richard

    2013-01-01

    To date, a range of ion channels have been identified in chondrocytes using a number of different techniques, predominantly electrophysiological and/or biomolecular; each of these has its advantages and disadvantages. Here we aim to compare and contrast the data available from biophysical and microarray experiments. This letter analyses recent transcriptomics datasets from chondrocytes, accessible from the European Bioinformatics Institute (EBI). We discuss whether such bioinformatic analysis of microarray datasets can potentially accelerate identification and discovery of ion channels in chondrocytes. The ion channels which appear most frequently across these microarray datasets are discussed, along with their possible functions. We discuss whether functional or protein data exist which support the microarray data. A microarray experiment comparing gene expression in osteoarthritis and healthy cartilage is also discussed and we verify the differential expression of 2 of these genes, namely the genes encoding large calcium-activated potassium (BK) and aquaporin channels. PMID:23995703

  12. Anguillid Herpesvirus 1 Transcriptome

    PubMed Central

    van Beurden, Steven J.; Gatherer, Derek; Kerr, Karen; Galbraith, Julie; Herzyk, Pawel; Peeters, Ben P. H.; Rottier, Peter J. M.; Engelsma, Marc Y.

    2012-01-01

    We used deep sequencing of poly(A) RNA to characterize the transcriptome of an economically important eel virus, anguillid herpesvirus 1 (AngHV1), at a stage during the lytic life cycle when infectious virus was being produced. In contrast to the transcription of mammalian herpesviruses, the overall level of antisense transcription from the 248,526-bp genome was low, amounting to only 1.5% of transcription in predicted protein-coding regions, and no abundant, nonoverlapping, noncoding RNAs were identified. RNA splicing was found to be more common than had been anticipated previously. Counting the 10,634-bp terminal direct repeat once, 100 splice junctions were identified, of which 58 were considered likely to be involved in the expression of functional proteins because they represent splicing between protein-coding exons or between 5′ untranslated regions and protein-coding exons. Each of the 30 most highly represented of these 58 splice junctions was confirmed by RT-PCR. We also used deep sequencing to identify numerous putative 5′ and 3′ ends of AngHV1 transcripts, confirming some and adding others by rapid amplification of cDNA ends (RACE). The findings prompted a revision of the AngHV1 genome map to include a total of 129 protein-coding genes, 5 of which are duplicated in the terminal direct repeat. Not counting duplicates, 11 genes contain integral, spliced protein-coding exons, and 9 contain 5′ untranslated exons or, because of alternative splicing, 5′ untranslated and 5′ translated exons. The results of this study sharpen our understanding of AngHV1 genomics and provide the first detailed view of a fish herpesvirus transcriptome. PMID:22787220

  13. Advances in Swine Transcriptomics

    PubMed Central

    Tuggle, Christopher K.; Wang, Yanfang; Couture, Oliver

    2007-01-01

    The past five years have seen a tremendous rise in porcine transcriptomic data. Available porcine Expressed Sequence Tags (ESTs) have expanded greatly, with over 623,000 ESTs deposited in Genbank. ESTs have been used to expand the pig-human comparative maps, but such data has also been used in many ways to understand pig gene expression. Several methods have been used to identify genes differentially expressed (DE) in specific tissues or cell types under different treatments. These include open screening methods such as suppression subtractive hybridization, differential display, serial analysis of gene expression, and EST sequence frequency, as well as closed methods that measure expression of a defined set of sequences such as hybridization to membrane arrays and microarrays. The use of microarrays to begin large-scale transcriptome analysis has been recently reported, using either specialized or broad-coverage arrays. This review covers published results using the above techniques in the pig, as well as unpublished data provided by the research community, and reports on unpublished Affymetrix data from our group. Published and unpublished bioinformatics efforts are discussed, including recent work by our group to integrate two broad-coverage microarray platforms. We conclude by predicting experiments that will become possible with new anticipated tools and data, including the porcine genome sequence. We emphasize that the need for bioinformatics infrastructure to efficiently store and analyze the expanding amounts of gene expression data is critical, and that this deficit has emerged as a limiting factor for acceleration of genomic understanding in the pig. PMID:17384733

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

    PubMed Central

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

    2016-01-01

    Background 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. Objectives 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. Materials and Methods 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%. Results 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. Conclusion 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. PMID:27895876

  15. ‘And then there were three’: highly efficient uptake of potassium by foliar trichomes of epiphytic bromeliads

    PubMed Central

    Winkler, Uwe; Zotz, Gerhard

    2010-01-01

    Background and Aims Vascular epiphytes have to acquire nutrients from atmospheric wash out, stem-flow, canopy soils and trapped litter. Physiological studies on the adaptations to nutrient acquisition and plant utilization of nutrients have focused on phosphorus and nitrogen; potassium, as a third highly abundant nutrient element, has received minor attention. In the present study, potassium uptake kinetics by leaves, within-plant distribution and nutrient accumulation were analysed to gain an improved understanding of physiological adaptations to non-terrestrial nutrient supply of plants. Methods Radioactively labelled 86RbCl was used as an analogue to study uptake kinetics of potassium absorbed from tanks of epiphytes, its plant distribution and the correlation between uptake efficiency and abundance of trichomes, functioning as uptake organs of leaves. Potassium in leaves was additionally analysed by atomic absorption spectroscopy to assess plant responses to potassium deficiency. Key Results Labelled rubidium was taken up from tanks over a wide range of concentrations, 0·01–90 mm, which was achieved by two uptake systems. In four tank epiphytes, the high-affinity transporters had average Km values of 41·2 µm, and the low-affinity transporters average Km values of 44·8 mm. Further analysis in Vriesea splenriet showed that high-affinity uptake of rubidium was an ATP-dependent process, while low-affinity uptake was mediated by a K+-channel. The kinetic properties of both types of transporters are comparable with those of potassium transporters in roots of terrestrial plants. Specific differences in uptake velocities of epiphytes are correlated with the abundance of trichomes on their leaf surfaces. The main sinks for potassium were fully grown leaves. These leaves thus function as internal potassium sources, which allow growth to be maintained during periods of low external potassium availability. Conclusions Vascular epiphytes possess effective mechanisms

  16. TRICHOME BIREFRINGENCE and Its Homolog AT5G01360 Encode Plant-Specific DUF231 Proteins Required for Cellulose Biosynthesis in Arabidopsis1[W][OA

    PubMed Central

    Bischoff, Volker; Nita, Silvia; Neumetzler, Lutz; Schindelasch, Dana; Urbain, Aurélie; Eshed, Ravit; Persson, Staffan; Delmer, Deborah; Scheible, Wolf-Rüdiger

    2010-01-01

    The Arabidopsis (Arabidopsis thaliana) trichome birefringence (tbr) mutant has severely reduced crystalline cellulose in trichomes, but the molecular nature of TBR was unknown. We determined TBR to belong to the plant-specific DUF231 domain gene family comprising 46 members of unknown function in Arabidopsis. The genes harbor another plant-specific domain, called the TBL domain, which contains a conserved GDSL motif known from some esterases/lipases. TBR and TBR-like3 (TBL3) are transcriptionally coordinated with primary and secondary CELLULOSE SYNTHASE (CESA) genes, respectively. The tbr and tbl3 mutants hold lower levels of crystalline cellulose and have altered pectin composition in trichomes and stems, respectively, tissues generally thought to contain mainly secondary wall crystalline cellulose. In contrast, primary wall cellulose levels remain unchanged in both mutants as measured in etiolated tbr and tbl3 hypocotyls, while the amount of esterified pectins is reduced and pectin methylesterase activity is increased in this tissue. Furthermore, etiolated tbr hypocotyls have reduced length with swollen epidermal cells, a phenotype characteristic for primary cesa mutants or the wild type treated with cellulose synthesis inhibitors. Taken together, we show that two TBL genes contribute to the synthesis and deposition of secondary wall cellulose, presumably by influencing the esterification state of pectic polymers. PMID:20388664

  17. Weeding atypical glandular cell look-alikes from the true atypical lesions in liquid-based Pap tests: a review.

    PubMed

    Wood, Moira D; Horst, Julie A; Bibbo, Marluce

    2007-01-01

    The purpose of this review is to identify features that separate atypical glandular cells (AGC) associated with glandular neoplasia from its mimickers, both benign and neoplastic. We reviewed cases of AGC diagnosed on liquid-based Pap tests (LBP) for which corresponding histological follow-up was available. A review of the literature for similar studies in LBP tests was also conducted. We find that certain benign mimics can be reliably separated from AGC, but recommend caution in attempting to increase specificity at the risk of losing sensitivity. Although accounting for only a small percentage of diagnoses AGC require a thorough clinical evaluation, including colposcopy. Most cases are ultimately found to be benign. When evaluating smears suspicious for AGC, it is important to examine the subtle features which make truly atypical cells discernible from their numerous benign mimickers.

  18. GEOPHYSICS, ASTRONOMY AND ASTROPHYSICS: Second-harmonic generation as a DNA malignancy indicator of prostate glandular epithelial cells

    NASA Astrophysics Data System (ADS)

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

    2010-04-01

    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.

  19. Mean glandular dose in six digital mammography services in Santiago, Chile: preliminary reference levels.

    PubMed

    Leyton, Fernando; Nogueira, Maria Do Socorro; Dantas, Marcelino; Duran, Maria Paz; Ubeda, Carlos

    2015-07-01

    The purpose of this paper was to estimate mean glandular dose levels (DG) in six digital mammography systems in Santiago, Chile, and to propose preliminary reference levels to execute mammography in Chile. The study was carried out assessing two direct digital systems and four computer-based radiography (CR) systems. Estimates of DG were calculated for different thicknesses of polymethyl methacrylate according to the quality control protocol in digital mammography of the Spanish Society of Medical Physics and NHSBSP Equipment Report 0604 Version 3. DG values ranged between 0.64 and 7.26 mGy for a range of 20- to 70-mm thickness, respectively. Thirty-six per cent of DG was higher than the acceptable dose level and 100 % of DG was higher than the desirable level. It is therefore necessary to optimise doses. The initial proposal to establish dose reference levels for DG would range between 0.90 and 6.40 mGy for a thickness range of 20 to 70 mm.

  20. Coherent angular motion in the establishment of multicellular architecture of glandular tissues

    PubMed Central

    Tanner, Kandice; Mori, Hidetoshi; Mroue, Rana; Bruni-Cardoso, Alexandre; Bissell, Mina J.

    2012-01-01

    Glandular tissues form ducts (tubes) and acini (spheres) in multicellular organisms. This process is best demonstrated in the organization of the ductal tree of the mammary gland and in 3D models of morphogenesis in culture. Here, we asked a fundamental question: How do single adult epithelial cells generate polarized acini when placed in a surrogate basement membrane 3D gel? Using human breast epithelial cells from either reduction mammoplasty or nonmalignant breast cell lines, we observed a unique cellular movement where single cells undergo multiple rotations and then maintain it cohesively as they divide to assemble into acini. This coherent angular motion (CAMo) was observed in both primary cells and breast cell lines. If CAMo was disrupted, the final geometry was not a sphere. The malignant counterparts of the human breast cell lines in 3D were randomly motile, did not display CAMo, and did not form spheres. Upon “phenotypic reversion” of malignant cells, both CAMo and spherical architecture were restored. We show that cell-cell adhesion and tissue polarity are essential for the formation of acini and link the functional relevance of CAMo to the establishment of spherical architecture rather than to multicellular aggregation or growth. We propose that CAMo is an integral step in the formation of the tissue architecture and that its disruption is involved in malignant transformation. PMID:22308439

  1. Development and Characterization of Uterine Glandular Epithelium Specific Androgen Receptor Knockout Mouse Model.

    PubMed

    Choi, Jaesung Peter; Zheng, Yu; Skulte, Katherine A; Handelsman, David J; Simanainen, Ulla

    2015-11-01

    While estrogen action is the major driver of uterine development, androgens acting via the androgen receptor (AR) may also promote uterine growth as suggested by uterine phenotypes in global AR knockout (ARKO) female mice. Because AR is expressed in uterine endometrial glands, we generated (Cre/loxP) uterine gland epithelium-specific ARKO (ugeARKO) to determine the role of endometrial gland-specific androgen actions. However, AR in uterine gland epithelium may not be required for normal uterine development and function because ugeARKO females had normal uterine development and fertility. To determine if exogenous androgens acting via AR can fully support uterine growth in the absence of estrogens, the ARKO and ugeARKO females were ovariectomized and treated with supraphysiological doses of testosterone or dihydrotestosterone (nonaromatizable androgen). Both dihydrotestosterone and testosterone supported full uterine regrowth in wild-type females while ARKO females had no regrowth (comparable to ovariectomized only). These findings suggest that androgens acting via AR can promote full uterine regrowth in the absence of estrogens. The ugeARKO had 50% regrowth when compared to intact uterine glands, and histomorphologically, both the endometrial and myometrial areas were significantly (P < 0.05) reduced, suggesting glandular epithelial AR located in the endometrium may indirectly modify myometrial development. Additionally, to confirm Cre function in endometrial glands, we generated uge-specific PTEN knockout mouse model. The ugePTEN knockout females developed severe endometrial hyperplasia and therefore present a novel model for future research.

  2. A solitary mixed squamous cell and glandular papilloma of the lung.

    PubMed

    Kozu, Yoshiki; Maniwa, Tomohiro; Ohde, Yasuhisa; Nakajima, Takashi

    2014-01-01

    Mixed squamous cell and glandular papilloma (mixed papilloma) of the lung is exceedingly rare, with only 18 cases reported in the literature. Herein, we report a case of mixed papilloma and its associated immunohistochemical and positron emission tomographic (PET) findings. A 60-year-old Japanese male with a smoking history of 40 pack-years presented with a smooth-edged pulmonary lesion in the right S5 segment on computed tomography (CT). F18-fluorodeoxyglucose (FDG) PET revealed abnormally increased FDG uptake in the mass (maximum standardized uptake value, 3.4). We performed right middle lobectomy and combined partial resection of the S8 segment. The 1.8-cm tumor that filled the enlarged lumen of the B5b was histologically diagnosed as mixed papilloma. Immunohistochemically, the pseudostratified columnar epithelium was positive for cytokeratin (CK) 5/6 and CK7. p40 positivity was predominant in the basal and squamous cells. Thyroid transcription factor-1 and carcinoembryonic antigen were negative on immunostaining. Malignant features were absent. The postoperative course has been uneventful for 3 months after the surgery. No recurrences were reported after the surgical resection of the mixed papilloma. Therefore, surgical resection may be considered the mainstay of curative treatment.

  3. Glandular odontogenic cyst: review of literature and report of a new case with cytokeratin-19 expression.

    PubMed

    Mascitti, Marco; Santarelli, Andrea; Sabatucci, Antonio; Procaccini, Maurizio; Lo Muzio, Lorenzo; Zizzi, Antonio; Rubini, Corrado

    2014-01-01

    The glandular odontogenic cyst (GOC) was a rare jawbone cyst described in 1988 as a distinct entity. This lesion can involve either jaw, and the anterior region of the mandible was the most commonly affected area. Clinical and radiographic findings were not specific, and the diagnosis of GOC can be extremely difficult due to the rarity of this lesion. The cyst presented a wall constituted by fibrous connective tissue and was lined by a non-keratinized stratified squamous epithelium of variable thickness. Large areas of the lining epithelium presented cylinder cells, sometimes ciliated. A variable amount of mucina was occasionally noted. Due to the strong similarities, this cyst can be easily misdiag-nosed as a central mucoepidermoid carcinoma (CMEC). Immunohistochemistry may be an aid in diagnosis; in fact has been demonstrated that there were differences in the expression of cytokeratins (CK) in GOC and CMEC. In this study, we reported a new case of GOC in a 38 year female patient. In addition, we carried out a review of 110 previous cases reported in literature.

  4. Single-cell analysis of glandular T cell receptors in Sjögren’s syndrome

    PubMed Central

    Lawrence, Christina; Pelikan, Richard C.; Moore, Jacen S.; Pan, Zijian; Radfar, Lida; Lewis, David M.; Grundahl, Kiely M.; Kelly, Jennifer A.; Wiley, Graham B.; Chudakov, Dmitriy M.; Lessard, Christopher J.; Stone, Donald U.; Scofield, R. Hal; Montgomery, Courtney G.; Sivils, Kathy L.; Thompson, Linda F.; Farris, A. Darise

    2016-01-01

    CD4+ T cells predominate in salivary gland (SG) inflammatory lesions in Sjögren’s syndrome (SS). However, their antigen specificity, degree of clonal expansion, and relationship to clinical disease features remain unknown. We used multiplex reverse-transcriptase PCR to amplify paired T cell receptor α (TCRα) and β transcripts of single CD4+CD45RA– T cells from SG and peripheral blood (PB) of 10 individuals with primary SS, 9 of whom shared the HLA DR3/DQ2 risk haplotype. TCRα and β sequences were obtained from a median of 91 SG and 107 PB cells per subject. The degree of clonal expansion and frequency of cells expressing two productively rearranged α genes were increased in SG versus PB. Expanded clones from SG exhibited complementary-determining region 3 (CDR3) sequence similarity both within and among subjects, suggesting antigenic selection and shared antigen recognition. CDR3 similarities were shared among expanded clones from individuals discordant for canonical Ro and La autoantibodies, suggesting recognition of alternative SG antigen(s). The extent of SG clonal expansion correlated with reduced saliva production and increased SG fibrosis, linking expanded SG T cells with glandular dysfunction. Knowledge of paired TCRα and β sequences enables further work toward identification of target antigens and development of novel therapies. PMID:27358913

  5. Clinical picture of primary HIV infection presenting as a glandular-fever-like illness.

    PubMed Central

    Gaines, H.; von Sydow, M.; Pehrson, P. O.; Lundbegh, P.

    1988-01-01

    The clinical symptoms and signs were assessed in 20 consecutive patients developing infection with the human immunodeficiency virus (HIV). All were male homosexuals and all presented with a glandular-fever-like illness. Changes in laboratory values were compared with findings in 40 HIV negative male homosexual controls. In the 10 patients for whom date of exposure to the virus could be established the incubation period was 11-28 days (median 14). One or two days after the sudden onset of fever patients developed sore throat, lymphadenopathy, rash, lethargy, coated tongue, tonsillar hypertrophy, dry cough, headache, myalgia, conjunctivitis, vomiting, night sweats, nausea, diarrhoea, and palatal enanthema. Twelve patients had painful, shallow ulcers in the mouth or on the genitals or anus or as manifested by oesophageal symptoms; these ulcers may have been the site of entry of the virus. During the first week after the onset of symptoms mild leucopenia, thrombocytopenia, and increased numbers of banded neutrophils were detected (p less than 0.0005). The mean duration of acute illness was 12.7 days (range 5-44). All patients remained healthy during a mean follow up period of 2.5 years. Heightened awareness of the typical clinical picture in patients developing primary HIV infection will alert the physician at an early stage and so aid prompt diagnosis and help contain the epidemic spread of AIDS. PMID:3146367

  6. Identification of cholinergic chemosensory cells in mouse tracheal and laryngeal glandular ducts.

    PubMed

    Krasteva-Christ, G; Soultanova, A; Schütz, B; Papadakis, T; Weiss, C; Deckmann, K; Chubanov, V; Gudermann, T; Voigt, A; Meyerhof, W; Boehm, U; Weihe, E; Kummer, W

    2015-11-01

    Specialized epithelial cells in the respiratory tract such as solitary chemosensory cells and brush cells sense the luminal content and initiate protective reflexes in response to the detection of potentially harmful substances. The majority of these cells are cholinergic and utilize the canonical taste signal transduction cascade to detect "bitter" substances such as bacterial quorum sensing molecules. Utilizing two different mouse strains reporting expression of choline acetyltransferase (ChAT), the synthesizing enzyme of acetylcholine (ACh), we detected cholinergic cells in the submucosal glands of the murine larynx and trachea. These cells were localized in the ciliated glandular ducts and were neither found in the collecting ducts nor in alveolar or tubular segments of the glands. ChAT expression in tracheal gland ducts was confirmed by in situ hybridization. The cholinergic duct cells expressed the brush cell marker proteins, villin and cytokeratin-18, and were immunoreactive for components of the taste signal transduction cascade (Gα-gustducin, transient receptor potential melastatin-like subtype 5 channel = TRPM5, phospholipase C(β2)), but not for carbonic anhydrase IV. Furthermore, these cells expressed the bitter taste receptor Tas2r131, as demonstrated utilizing an appropriate reporter mouse strain. Our study identified a previously unrecognized presumptive chemosensory cell type in the duct of the airway submucosal glands that likely utilizes ACh for paracrine signaling. We propose that these cells participate in infection-sensing mechanisms and initiate responses assisting bacterial clearance from the lower airways.

  7. Trichomes as dangerous lollipops: do lizards also use caterpillar body and frass odor to optimize their foraging?

    PubMed

    Stork, William F J; Weinhold, Alexander; Baldwin, Ian T

    2011-12-01

    When attacked by herbivores, plants produce toxic secondary metabolites that function as direct defenses, as well as indirect defenses that attract and reward predators of the offending herbivores. These indirect defenses include both nutritive rewards such as extra floral nectar, as well as informational rewards, such as the production and release of volatile compounds that betray the location of feeding herbivores to predators. Herbivory of Nicotiana attenuata by the tobacco hornworm (Manduca larvae) alters the volatile profiles of both the plant and larval headspace. Herbivory-elicited specific changes in the volatile profiles are detected by arthropod predators of Manduca larvae. The known predators that perceive volatile cues induced by Manduca herbivory of N. attenuata are insects that target Manduca at early developmental stages, when the larvae are still small; large, late-instar larvae may have outgrown these predation risks. However, here we offer evidence that branched chain aliphatic acids derived from the digestion of plant O-acyl sugars from trichomes may betray Manduca larvae to lizard predators during late developmental stages as well.

  8. The characterization of SaPIN2b, a plant trichome-localized proteinase inhibitor from Solanum americanum.

    PubMed

    Luo, Ming; Ding, Ling-Wen; Ge, Zhi-Juan; Wang, Zhen-Yu; Hu, Bo-Lun; Yang, Xiao-Bei; Sun, Qiao-Yang; Xu, Zeng-Fu

    2012-11-16

    Proteinase inhibitors play an important role in plant resistance of insects and pathogens. In this study, we characterized the serine proteinase inhibitor SaPIN2b, which is constitutively expressed in Solanum americanum trichomes and contains two conserved motifs of the proteinase inhibitor II (PIN2) family. The recombinant SaPIN2b (rSaPIN2b), which was expressed in Escherichia coli, was demonstrated to be a potent proteinase inhibitor against a panel of serine proteinases, including subtilisin A, chymotrypsin and trypsin. Moreover, rSaPIN2b also effectively inhibited the proteinase activities of midgut trypsin-like proteinases that were extracted from the devastating pest Helicoverpa armigera. Furthermore, the overexpression of SaPIN2b in transgenic tobacco plants resulted in enhanced resistance against H. armigera. Taken together, our results demonstrated that SaPIN2b is a potent serine proteinase inhibitor that may act as a protective protein in plant defense against insect attacks.

  9. Dense white trichome production by plants as possible mimicry of arthropod silk or fungal hyphae that deter herbivory.

    PubMed

    Yamazaki, Kazuo; Lev-Yadun, Simcha

    2015-01-07

    Some spiders are well-known to mimic flowers or other plant surfaces in order to be cryptic to both their prey and their predators. We propose that dense, thread-like white trichomes of some plants from Estonia, Greece, Israel and Japan visually mimic spider webs, lepidopteran and spider-mite web nests and plant-pathogenic fungi, and that it may result in reduced herbivory, since various herbivores avoid spider- or other arthropod webs to circumvent predation or toxic attacks, or refrain from colonizing plants that have already been occupied by other herbivores and pathogens. Spiders and other web-forming arthropods are also the prey of certain vertebrate predators and wasps, and therefore such predators may be attracted to these web-like plant structures and prey on the invertebrate herbivores occupying them. We do not dismiss the possibility that these web-like structures may also have other defensive or physiological functions or that they are not classic mimics but rather exploit the herbivore׳s perceptual state concerning the avoidance of potentially risky objects.

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

    PubMed

    Speer, Allison L; Al Alam, Denise; Sala, Frederic G; Ford, Henri R; Bellusci, Saverio; Grikscheit, Tracy C

    2012-01-01

    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.

  11. Notch signaling functions as a binary switch for the determination of glandular and luminal fates of endodermal epithelium during chicken stomach development.

    PubMed

    Matsuda, Yoshimasa; Wakamatsu, Yoshio; Kohyama, Jun; Okano, Hideyuki; Fukuda, Kimiko; Yasugi, Sadao

    2005-06-01

    During development of the chicken proventriculus (glandular stomach), gut endoderm differentiates into glandular and luminal epithelium. We found that Delta1-expressing cells, undifferentiated cells and Notch-activated cells colocalize within the endodermal epithelium during early gland formation. Inhibition of Notch signaling using Numb or dominant-negative form of Su(H) resulted in a luminal differentiation, while forced activation of Notch signaling promoted the specification of immature glandular cells, but prevented the subsequent differentiation and the invagination of the glands. These results suggest that Delta1-mediated Notch signaling among endodermal cells functions as a binary switch for determination of glandular and luminal fates, and regulates patterned differentiation of glands in the chicken proventriculus.

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

    PubMed

    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.

  13. Transcriptomic Approaches to Neural Repair

    PubMed Central

    Antunes-Martins, Ana; Chandran, Vijayendran; Costigan, Michael; Lerch, Jessica K.; Willis, Dianna E.; Tuszynski, Mark H.

    2015-01-01

    Understanding why adult CNS neurons fail to regenerate their axons following injury remains a central challenge of neuroscience research. A more complete appreciation of the biological mechanisms shaping the injured nervous system is a crucial prerequisite for the development of robust therapies to promote neural repair. Historically, the identification of regeneration associated signaling pathways has been impeded by the limitations of available genetic and molecular tools. As we progress into an era in which the high-throughput interrogation of gene expression is commonplace and our knowledge base of interactome data is rapidly expanding, we can now begin to assemble a more comprehensive view of the complex biology governing axon regeneration. Here, we highlight current and ongoing work featuring transcriptomic approaches toward the discovery of novel molecular mechanisms that can be manipulated to promote neural repair. SIGNIFICANCE STATEMENT Transcriptional profiling is a powerful technique with broad applications in the field of neuroscience. Recent advances such as single-cell transcriptomics, CNS cell type-specific and developmental stage-specific expression libraries are rapidly enhancing the power of transcriptomics for neuroscience applications. However, extracting biologically meaningful information from large transcriptomic datasets remains a formidable challenge. This mini-symposium will highlight current work using transcriptomic approaches to identify regulatory networks in the injured nervous system. We will discuss analytical strategies for transcriptomics data, the significance of noncoding RNA networks, and the utility of multiomic data integration. Though the studies featured here specifically focus on neural repair, the approaches highlighted in this mini-symposium will be of broad interest and utility to neuroscientists working in diverse areas of the field. PMID:26468186

  14. Rat retinal transcriptome

    PubMed Central

    Kozhevnikova, Oyuna S.; Korbolina, Elena E.; Ershov, Nikita I.; Kolosova, Natalia G.

    2013-01-01

    Pathogenesis of age-related macular degeneration (AMD), the leading cause of vision loss in the elderly, remains poorly understood due to the paucity of animal models that fully replicate the human disease. Recently, we showed that senescence-accelerated OXYS rats develop a retinopathy similar to human AMD. To identify alterations in response to normal aging and progression of AMD-like retinopathy, we compared gene expression profiles of retina from 3- and 18-mo-old OXYS and control Wistar rats by means of high-throughput RNA sequencing (RNA-Seq). We identified 160 and 146 age-regulated genes in Wistar and OXYS retinas, respectively. The majority of them are related to the immune system and extracellular matrix turnover. Only 24 age-regulated genes were common for the two strains, suggestive of different rates and mechanisms of aging. Over 600 genes showed significant differences in expression between the two strains. These genes are involved in disease-associated pathways such as immune response, inflammation, apoptosis, Ca2+ homeostasis and oxidative stress. The altered expression for selected genes was confirmed by qRT-PCR analysis. To our knowledge, this study represents the first analysis of retinal transcriptome from young and old rats with biologic replicates generated by RNA-Seq technology. We can conclude that the development of AMD-like retinopathy in OXYS rats is associated with an imbalance in immune and inflammatory responses. Aging alters the expression profile of numerous genes in the retina, and the genetic background of OXYS rats has a profound impact on the development of AMD-like retinopathy. PMID:23656783

  15. Annual changes in the number, testosterone content and ultrastructure of glandular tissue cells of the testis in the marbled newt Triturus marmoratus.

    PubMed Central

    Fraile, B; Paniagua, R; Rodríguez, M C; Sáez, F J; Jimenez, A

    1989-01-01

    The testes of 8 specimens of Triturus marmoratus were collected during each month of 1987 and processed for electron microscopy and light microscopy demonstration of testosterone (T) following the ABC (avidin-biotin peroxidase complex) method. According to their staining affinity for anti-T antibodies, the glandular tissue cells were classified as T-, T+, T++, and T and the annual changes in the numbers of these cell populations, as well as in the volume occupied by the glandular tissue, were calculated. The volume occupied by the glandular tissue increases from September to December; it begins to decrease in April and disappears from June to August. The glandular tissue is formed from the interstitial cells that surround the lobules containing differentiating germ cells. During the spermatogenic process, the interstitial cells do not show staining affinity for anti-T antibodies. In August-September, the interstitial cells around the lobules that have completed spermatogenesis become positively stained (T+) and form the glandular tissue when the spermatozoa leave the testis. The numbers of intensely stained cells in the glandular tissue (T++ and T ) increase from September to November; begin to decrease in December; disappear in January-February; increase again in March and decrease again in April until they disappear in June-September. The interstitial cells, before their transformation in glandular tissue, are ultrastructurally similar to fibroblasts. After their transformation these cells increase in size and develop abundant smooth endoplasmic reticulum, mitochondria with tubular cristae and lipid droplets. This morphological pattern is maintained in the glandular tissue from September to April in spite of the changes in staining affinity during this period. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 6 Fig. 7 Fig. 8 Fig. 9 Fig. 10 Fig. 11 Fig. 12 Fig. 13 PMID:2630543

  16. Human mast cell transcriptome project.

    PubMed

    Saito, H; Nakajima, T; Matsumoto, K

    2001-05-01

    After draft reading of the human genome sequence, systemic analysis of the transcriptome (the whole transcripts present in a cell) is progressing especially in commonly available cell types. Until recently, human mast cells were not commonly available. We have succeeded to generate a substantial number of human mast cells from umbilical cord blood and from adult peripheral blood progenitors. Then, we have examined messenger RNA selectively transcribed in these mast cells using high-density oligonucleotide probe arrays. Many unexpected but important transcripts were selectively expressed in human mast cells. We discuss the results obtained from transcriptome screening by introducing our data regarding mast-cell-specific genes.

  17. Risk of invasive cervical cancer after atypical glandular cells in cervical screening: nationwide cohort study

    PubMed Central

    Andrae, Bengt; Sundström, Karin; Ström, Peter; Ploner, Alexander; Elfström, K Miriam; Arnheim-Dahlström, Lisen; Dillner, Joakim; Sparén, Pär

    2016-01-01

    Objectives To investigate the risks of invasive cervical cancer after detection of atypical glandular cells (AGC) during cervical screening. Design Nationwide population based cohort study. Setting Cancer and population registries in Sweden. Participants 3 054 328 women living in Sweden at any time between 1 January 1980 and 1 July 2011 who had any record of cervical cytological testing at ages 23-59. Of these, 2 899 968 women had normal cytology results at the first screening record. The first recorded abnormal result was atypical glandular cells (AGC) in 14 625, high grade squamous intraepithelial lesion (HSIL) in 65 633, and low grade squamous intraepithelial lesions (LSIL) in 244 168. Main outcome measures Cumulative incidence of invasive cervical cancer over 15.5 years; proportion of invasive cervical cancer within six months of abnormality (prevalence); crude incidence rates for invasive cervical cancer over 0.5-15.5 years of follow-up; incidence rate ratios compared with women with normal cytology, estimated with Poisson regression adjusted for age and stratified by histopathology of cancer; distribution of clinical assessment within six months after the abnormality. Results The prevalence of cervical cancer was 1.4% for women with AGC, which was lower than for women with HSIL (2.5%) but higher than for women with LSIL (0.2%); adenocarcinoma accounted for 73.2% of the prevalent cases associated with AGC. The incidence rate of invasive cervical cancer after AGC was significantly higher than for women with normal results on cytology for up to 15.5 years and higher than HSIL and LSIL for up to 6.5 years. The incidence rate of adenocarcinoma was 61 times higher than for women with normal results on cytology in the first screening round after AGC, and remained nine times higher for up to 15.5 years. Incidence and prevalence of invasive cervical cancer was highest when AGC was found at ages 30-39. Only 54% of women with AGC underwent histology assessment

  18. Co-Relationships between Glandular Salivary Flow Rates and Dental Caries

    PubMed Central

    de Guillory, Carolina Diaz; Schoolfield, John D; Johnson, Dorthea; Yeh, Chih-Ko; Chen, Shuo; Cappelli, David P; Bober-Moken, Irene G; Dang, Howard

    2013-01-01

    Objective This study was designed to evaluate the relationship of age, gender, ethnicity and salivary flow rates on dental caries in an adult population using data collected from the Oral Health San Antonio Longitudinal Study of Aging (OH:SALSA). Background Saliva is essential to maintain a healthy oral environment and diminished output can result in dental caries. Although gender and age play a role in the quantity of saliva, little is known about the interaction of age, gender and ethnicity on dental caries and salivary flow rates. Materials and Methods Data from the 1,147 participants in the OH: SALSA was analyzed. The dependent variables were the number of teeth with untreated coronal caries, number of teeth with root caries, and the number of coronal and root surfaces with untreated caries. The independent variables were stimulated and unstimulated glandular salivary flow rates along with the age, sex, and ethnicity (e.g. European or Mexican ancestry) of the participants. Results Coronal caries experience was greater in younger participants while root surface caries experience was greater in the older participants. Coronal caries was lower in the older age groups while the root caries experience increased. Men had a statistically significant (p<0.02) higher experience of root caries than women. Values for unstimulated and stimulated parotid salivary flow rates showed no age difference and remained constant with age, whereas the age differences in the unstimulated and stimulated submandibular/sublingual salivary flow rates were significant. The mean number of teeth with coronal and root caries was higher in Mexican-Americans than in European-Americans. Conclusions Over one-fourth of the adults between the ages of 60 and 79 have untreated root caries over one-third having untreated coronal caries. Lower salivary flow rates play a significant role in the both the number of teeth and the number of surfaces developing caries in these adults. Women and individuals

  19. SU-E-I-04: A Mammography Phantom to Measure Mean Glandular Dose and Image Quality

    SciTech Connect

    Lopez-Pineda, E; Ruiz-Trejo, C; E, Brandan M

    2014-06-01

    Purpose: To evaluate mean glandular dose (MGD) and image quality in a selection of mammography systems using a novel phantom based on thermoluminescent dosemeters and the ACR wax insert. Methods: The phantom consists of two acrylic, 19 cm diameter, 4.5 cm thick, semicircular modules, used in sequence. The image quality module contains the ACR insert and is used to obtain a quality control image under automatic exposure conditions. The dosimetric module carries 15 TLD-100 chips, some under Al foils, to determine air kerma and half-value-layer. TL readings take place at our laboratory under controlled conditions. Calibration was performed using an ionization chamber and a Senographe 2000D unit for a variety of beam qualities, from 24 to 40 kV, Mo and Rh anodes and filters. Phantom MGD values agree, on the average, within 3% with ionization chamber data, and their precision is better than 10% (k=1). Results: MGD and image quality have been evaluated in a selection of mammography units currently used in Mexican health services. The sample includes analogic (screen/film), flexible digital (CR), and full-field digital image receptors. The highest MDG are associated to the CR technology. The most common image quality failure is due to artifacts (dust, intensifying screen scratches, and processor marks for film/screen, laser reader defects for CR). Conclusion: The developed phantom permits the MGD measurement without the need of a calibrated ionization chamber at the mammography site and can be used by a technician without the presence of a medical physicist. The results indicate the urgent need to establish quality control programs for mammography.

  20. Predominant Glandular Cholinergic Dysautonomia in Patients with Primary Sjögren’s Syndrome

    PubMed Central

    Imrich, Richard; Alevizos, Ilias; Bebris, Lolita; Goldstein, David S.; Holmes, Courtney S.; Illei, Gabor G.; Nikolov, Nikolay P.

    2015-01-01

    Objectives The autonomic nervous system (ANS) modulates exocrine gland function. Available data show poor correlation between the degree of exocrine gland function and destruction in primary Sjögren’s syndrome (pSS) suggesting other mechanisms, such as autonomic dysfunction may be important in these patients. We performed a comprehensive analysis of sympathoneural and sympathetic cholinergic function in well-characterized patients with pSS. Methods 21 pSS patients (mean±SE age 44±3 years) and in 13 healthy controls (51±2 years) were assessed during orthostasis and intravenous injection of edrophonium (10 mg). The postganglionic sympathetic cholinergic system was evaluated by assessing sweat production by the quantitative sudomotor axon reflex test (QSART). Gastric empting testing assessed the gastro-intestinal ANS in pSS patients. Results Velocity index and acceleration index were significantly higher (p<0.05) in pSS compared to controls before and during the orthostatic and edrophonium tests. Other hemodynamic and neurochemical parameters did not differ between pSS patients and controls during the orthostasis and edrophonium test, however, edrophonium-induced saliva increment was lower in pSS (p=0.002). Abnormally low sweat production was found in four (N=4) pSS patients but in none of the controls in the QSART. Gastric empting was delayed in 53 % of pSS patients. Conclusion We observed subtle differences in several ANS domains, including gastrointestinal and sympathocholinergic system suggesting a complex ANS dysfunction in pSS. The impact was the largest on the exocrine glands with subtle differences in the cardiac parasympathetic function independent of glandular inflammation and atrophy, suggesting an alternative pathogenesis mechanism of the disease in pSS. PMID:25622919

  1. Two Trichome Birefringence-Like Proteins Mediate Xylan Acetylation, Which Is Essential for Leaf Blight Resistance in Rice1[OPEN

    PubMed Central

    He, Congwu; Liu, Xiangling; Tian, Yanbao; Liu, Xue-Hui; Pauly, Markus

    2017-01-01

    Acetylation is a ubiquitous modification on cell wall polymers, which play a structural role in plant growth and stress defenses. However, the mechanisms for how crop plants accomplish cell wall polymer O-acetylation are largely unknown. Here, we report on the isolation and characterization of two trichome birefringence-like (tbl) mutants in rice (Oryza sativa), which are affected in xylan O-acetylation. ostbl1 and ostbl2 single mutant and the tbl1 tbl2 double mutant displayed a stunted growth phenotype with varied degree of dwarfism. As shown by chemical assays, the wall acetylation level is affected in the mutants and the knock-down and overexpression transgenic plants. Furthermore, NMR spectroscopy analyses showed that all those mutants have varied decreases in xylan monoacetylation. The divergent expression levels of OsTBL1 and OsTBL2 explained the chemotype difference and indicated that OsTBL1 is a functionally dominant gene. OsTBL1 was found to be Golgi-localized. The recombinant OsTBL1 protein incorporates acetyl groups onto xylan. By using xylopentaose, a preferred acceptor substrate, OsTBL1 can transfer up to four acetyl residues onto xylopentaose, and this activity showed saturable kinetics. 2D-NMR spectroscopy showed that OsTBL1 transfers acetate to both 2-O and 3-O sites of xylosyl residues. In addition, ostbl1 and tbl1 tbl2 displayed susceptibility to rice blight disease, indicating that this xylan modification is required for pathogen resistance. This study identifies the major genes responsible for xylan acetylation in rice plants. PMID:27864442

  2. Two Trichome Birefringence-Like Proteins Mediate Xylan Acetylation, Which Is Essential for Leaf Blight Resistance in Rice.

    PubMed

    Gao, Yaping; He, Congwu; Zhang, Dongmei; Liu, Xiangling; Xu, Zuopeng; Tian, Yanbao; Liu, Xue-Hui; Zang, Shanshan; Pauly, Markus; Zhou, Yihua; Zhang, Baocai

    2017-01-01

    Acetylation is a ubiquitous modification on cell wall polymers, which play a structural role in plant growth and stress defenses. However, the mechanisms for how crop plants accomplish cell wall polymer O-acetylation are largely unknown. Here, we report on the isolation and characterization of two trichome birefringence-like (tbl) mutants in rice (Oryza sativa), which are affected in xylan O-acetylation. ostbl1 and ostbl2 single mutant and the tbl1 tbl2 double mutant displayed a stunted growth phenotype with varied degree of dwarfism. As shown by chemical assays, the wall acetylation level is affected in the mutants and the knock-down and overexpression transgenic plants. Furthermore, NMR spectroscopy analyses showed that all those mutants have varied decreases in xylan monoacetylation. The divergent expression levels of OsTBL1 and OsTBL2 explained the chemotype difference and indicated that OsTBL1 is a functionally dominant gene. OsTBL1 was found to be Golgi-localized. The recombinant OsTBL1 protein incorporates acetyl groups onto xylan. By using xylopentaose, a preferred acceptor substrate, OsTBL1 can transfer up to four acetyl residues onto xylopentaose, and this activity showed saturable kinetics. 2D-NMR spectroscopy showed that OsTBL1 transfers acetate to both 2-O and 3-O sites of xylosyl residues. In addition, ostbl1 and tbl1 tbl2 displayed susceptibility to rice blight disease, indicating that this xylan modification is required for pathogen resistance. This study identifies the major genes responsible for xylan acetylation in rice plants.

  3. The human pancreas proteome defined by transcriptomics and antibody-based profiling.

    PubMed

    Danielsson, Angelika; Pontén, Fredrik; 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.

  4. Expression of Brassica napus TTG2, a regulator of trichome development, increases plant sensitivity to salt stress by suppressing the expression of auxin biosynthesis genes.

    PubMed

    Li, Qingyuan; Yin, Mei; Li, Yongpeng; Fan, Chuchuan; Yang, Qingyong; Wu, Jian; Zhang, Chunyu; Wang, Hong; Zhou, Yongming

    2015-09-01

    WRKY transcription factors (TFs) are plant specific and play important roles in regulating diverse biological processes. To identify TFs with broad-spectrum effects on various stress responses in Brassica napus, an important oil crop grown across diverse ecological regions worldwide, we functionally characterized Bna.TTG2 genes, which are homologous to the Arabidopsis AtTTG2 (WRKY44) gene. Four Bna.TTG2 genes were capable of rescuing the trichome phenotypes of Arabidopsis ttg2 mutants. Overexpressing one Bna.TTG2 family member, BnaA.TTG2.a.1, remarkably increased trichome numbers in Arabidopsis and B. napus plants. Interestingly, the BnaA.TTG2.a.1-overexpressing plants of both species exhibited increased sensitivity to salt stress. In BnaA.TTG2.a.1-overexpressing Arabidopsis under salt stress, the endogenous indole-3-acetic acid (IAA) content was reduced, and the expression of two auxin biosynthesis genes, TRYPTOPHAN BIOSYNTHESIS 5 (TRP5) and YUCCA2 (YUC2), was downregulated. The results from yeast one-hybrid, electrophoretic mobility shift, and dual-luciferase reporter assays revealed that BnaA.TTG2.a.1 is able to bind to the promoters of TRP5 and YUC2. These data indicated that BnaA.TTG2.a.1 confers salt sensitivity to overexpressing plants by suppressing the expression of IAA synthesis genes and thus lowering IAA levels. Transgenic Arabidopsis plants with an N-terminus-deleted BnaA.TTG2.a.1 no longer showed hypersensitivity to salt stress, suggesting that the N terminus of BnaA.TTG2.a.1 plays a critical role in salt stress responses. Therefore, in addition to its classical function in trichome development, our study reveals a novel role for Bna.TTG2 genes in salt stress responses.

  5. Auxin regulates first leaf development and promotes the formation of protocorm trichomes and rhizome-like structures in developing seedlings of Spathoglottis plicata (Orchidaceae)

    PubMed Central

    Novak, Stacey D.; Whitehouse, Grace A.

    2013-01-01

    Auxin flows in a polar manner to target tissues and exert its morphogenic effect. Preventing auxin movement, with polar auxin transport (PAT) inhibitors, or increasing auxin levels in tissues through exogenous application can provide a means for assessing the importance of appropriate tissue distribution and concentration of this hormone during development. The formulation of culture media for micropropagation has been the primary focus of most orchid tissue culture research, a goal that unveils seedling hormone responses at a single point in development. This study was unique because it evaluated the auxin response of orchids during three stages of seedling development. Seedlings were grown on standard culture media for 10, 35 and 85 days. Each group was sub-cultured onto auxin- and/or PAT inhibitor-containing media for an additional 10, 30 and 60 days, respectively. Data were collected on first leaf initiation, trichome formation and the appearance of propagative structures. In the 20-day seedlings, auxins and PAT inhibitors promoted precocious formation and random placement of protocorm hairs rather than in tufts, as seen in older, control seedlings. The 65-day seedlings formed protocorm-like bodies, rhizome-like growths from the stem, and fleshy leaves with trichomes. Seedlings cultured for 145 days developed microshoots or callus growth in the axils of older leaves and exhibited necrosis of original seedling roots and leaves. In general, exogenously applied auxin promoted the reversion of differentiated Spathoglottis plicata seedling tissue to a morphology that had propagative properties. Additionally, auxins commonly induced hair formation, which suggests that protocorm hairs may be root hair-like in nature. This work characterized three auxin growth responses in S. plicata seedlings that have not been reported in orchids: (i) the inhibition of first leaf initiation and abnormal first leaf morphology; (ii) the promotion of trichome formation; and (iii) the

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

    PubMed

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

    2013-09-21

    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

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

    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

  8. Gastric tumor development in Smad3-deficient mice initiates from forestomach/glandular transition zone along the lesser curvature.

    PubMed

    Nam, Ki Taek; O'Neal, Ryan; Lee, Yeo Song; Lee, Yong Chan; Coffey, Robert J; Goldenring, James R

    2012-06-01

    SMAD proteins are downstream effectors of the TGF-β signaling pathway. Smad3-null mice develop colorectal cancer by 6 months of age. In this study, we have examined whether the loss of Smad3 promotes gastric neoplasia in mice. The stomachs of Smad3⁻/⁻ mice were compared with age-matched Smad3 heterozygous and wild-type mice. E-cadherin, Ki-67, phosphoSTAT3, and TFF2/SP expression was analyzed by immunohistochemisty. The short hairpin RNA (ShRNA)-mediated knockdown of Smad3 in AGS and MKN28 cells was also performed. In addition, we examined alterations in DCLK1-expressing cells. Smad3⁻/⁻ mouse stomachs at 6 months of age revealed the presence of exophytic growths along the lesser curvature in the proximal fundus. Six-month-old Smad3⁻/⁻ mouse stomachs showed metaplastic columnar glands initiating from the transition zone junction between the forestomach and the glandular epithelium along the lesser curvature. Ten-month-old Smad3⁻/⁻ mice all exhibited invasive gastric neoplastic changes with increased Ki-67, phosphoSTAT3 expression, and aberrant cytosolic E-cadherin staining in papillary glands within the invading submucosal gland. The shRNA-mediated knockdown of Smad3 in AGS and MKN28 cells promoted the expression of phosphoSTAT3. DCLK1-expressing cells, which also stained for the tuft cell marker acetylated-α-tubulin, were observed in 10-month-old Smad3⁻/⁻ mice within tumors and in fundic invasive lesions. In conclusion, Smad3-null mice develop gastric tumors in the fundus, which arise from the junction between the forestomach and the glandular epithelium and progress to prominent invasive tumors over time. Smad3-null mice represent a novel model of fundic gastric tumor initiated from forestomach/glandular transition zone along the lesser curvature.

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

    PubMed

    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 (P<0.05). The calcium ion concentration was increased in low-intensity 2-h group but decreased in high-intensity 4-h group as compared with the normal control group (P<0.05). However, no significant difference was found in mitochondrial membrane potential of endometrial glandular cells between low- or mid-intensity groups and the normal control group, indicating stronger intensity of the electromagnetic 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

  10. Morphology of a novel glandular epithelium lining the infrabuccal cavity in the ant Monomorium pharaonis (Hymenoptera, Formicidae).

    PubMed

    Eelen, Dieter; Børgesen, Lisbeth W; Billen, Johan

    2004-10-01

    A novel glandular epithelium lining the infrabuccal cavity and anterior pharynx is described in both workers and queens of the pharaoh's ant Monomorium pharaonis. The infrabuccal cavity, connected with the buccal tube, forms a ventral outgrowth of the anterior pharynx, and as such displays the tegumental lining with a cuticle and an epithelial layer. In its dorsal region, the cavity's epithelium reaches a thickness of approx. 11-12mum in both workers and queens, which is considerably thicker than the epithelium lining the rest of the infrabuccal cavity. Also the possible role of the infrabuccal gland is discussed.

  11. Human saliva proteome and transcriptome.

    PubMed

    Hu, S; Li, Y; Wang, J; Xie, Y; Tjon, K; Wolinsky, L; Loo, R R O; Loo, J A; Wong, D T

    2006-12-01

    This paper tests the hypothesis that salivary proteins and their counterpart mRNAs co-exist in human whole saliva. Global profiling of human saliva proteomes and transcriptomes by mass spectrometry (MS) and expression microarray technologies, respectively, revealed many similarities between saliva proteins and mRNAs. Of the function-known proteins identified in saliva, from 61 to 70% were also found present as mRNA transcripts. For genes not detected at both protein and mRNA levels, we made further efforts to determine if the counterpart is present. Of 19 selected genes detected only at the protein level, the mRNAs of 13 (68%) genes were found in saliva by RT-PCR. In contrast, of many mRNAs detected only by microarrays, their protein products were found in saliva, as reported previously by other investigators. The saliva transcriptome may provide preliminary insights into the boundary of the saliva proteome.

  12. Ablation of beta1 integrin in mammary epithelium reveals a key role for integrin in glandular morphogenesis and differentiation.

    PubMed

    Naylor, Matthew J; Li, Na; Cheung, Julia; Lowe, Emma T; Lambert, Elise; Marlow, Rebecca; Wang, Pengbo; Schatzmann, Franziska; Wintermantel, Timothy; Schüetz, Günther; Clarke, Alan R; Mueller, Ulrich; Hynes, Nancy E; Streuli, Charles H

    2005-11-21

    Integrin-mediated adhesion regulates the development and function of a range of tissues; however, little is known about its role in glandular epithelium. To assess the contribution of beta1 integrin, we conditionally deleted its gene in luminal epithelia during different stages of mouse mammary gland development and in cultured primary mammary epithelia. Loss of beta1 integrin in vivo resulted in impaired alveologenesis and lactation. Cultured beta1 integrin-null cells displayed abnormal focal adhesion function and signal transduction and could not form or maintain polarized acini. In vivo, epithelial cells became detached from the extracellular matrix but remained associated with each other and did not undergo overt apoptosis. beta1 integrin-null mammary epithelial cells did not differentiate in response to prolactin stimulation because of defective Stat5 activation. In mice where beta1 integrin was deleted after the initiation of differentiation, fewer defects in alveolar morphology occurred, yet major deficiencies were also observed in milk protein and milk fat production and Stat5 activation, indicating a permissive role for beta1 integrins in prolactin signaling. This study demonstrates that beta1 integrin is critical for the alveolar morphogenesis of a glandular epithelium and for maintenance of its differentiated function. Moreover, it provides genetic evidence for the cooperation between integrin and cytokine signaling pathways.

  13. A Monte Carlo study of monoenergetic and polyenergetic normalized glandular dose (DgN) coefficients in mammography

    NASA Astrophysics Data System (ADS)

    Sarno, Antonio; Mettivier, Giovanni; Di Lillo, Francesca; Russo, Paolo

    2017-01-01

    We investigated the influence of model assumptions in GEANT4 Monte Carlo (MC) simulations for the calculation of monoenergetic and polyenergetic normalized glandular dose coefficients (DgN) in mammography, focussing on the effect of the skin thickness and composition, of the role of compression paddles and of the bremsstrahlung processes. We showed that selecting a skin thickness of 4 mm instead of 1.45 mm produced DgN values with deviations from 9% to 32% for x-ray spectra routinely adopted in mammography. Consideration of the bremsstrahlung radiation had a weak influence on monoenergetic DgN. Simulations (in the range 8-40 kVp) which included consideration of bremsstrahlung radiation, a skin thickness of 1.45 mm and a 2 mm thick compression paddles produced polyenergetic DgN coefficients up to 19% higher than corresponding literature data. Adding a 2 mm thick adipose layer between the skin layer and the radiosensitive portion of the breast produces polyenergetic DgN values up to 15% higher than those routinely adopted. These findings provide a quantitative estimate of the influence of model parameters on the calculation of the mean glandular dose in mammography.

  14. Mean glandular dose coefficients (D(g)N) for x-ray spectra used in contemporary breast imaging systems.

    PubMed

    Nosratieh, Anita; Hernandez, Andrew; Shen, Sam Z; Yaffe, Martin J; Seibert, J Anthony; Boone, John M

    2015-09-21

    To develop tables of normalized glandular dose coefficients D(g)N for a range of anode-filter combinations and tube voltages used in contemporary breast imaging systems. Previously published mono-energetic D(g)N values were used with various spectra to mathematically compute D(g)N coefficients. The tungsten anode spectra from TASMICS were used; molybdenum and rhodium anode-spectra were generated using MCNPX Monte Carlo code. The spectra were filtered with various thicknesses of Al, Rh, Mo or Cu. An initial half value layer (HVL) calculation was made using the anode and filter material. A range of the HVL values was produced with the addition of small thicknesses of polymethyl methacrylate (PMMA) as a surrogate for the breast compression paddle, to produce a range of HVL values at each tube voltage. Using a spectral weighting method, D(g)N coefficients for the generated spectra were calculated for breast glandular densities of 0%, 12.5%, 25%, 37.5%, 50% and 100% for a range of compressed breast thicknesses from 3 to 8 cm. Eleven tables of normalized glandular dose (D(g)N) coefficients were produced for the following anode/filter combinations: W + 50 μm Ag, W + 500 μm Al, W + 700 μm Al, W + 200 μm Cu, W + 300 μm Cu, W + 50 μm Rh, Mo + 400 μm Cu, Mo + 30 μm Mo, Mo + 25 μm Rh, Rh + 400 μm Cu and Rh + 25 μm Rh. Where possible, these results were compared to previously published D(g)N values and were found to be on average less than 2% different than previously reported values.Over 200 pages of D(g)N coefficients were computed for modeled x-ray system spectra that are used in a number of new breast imaging applications. The reported values were found to be in excellent agreement when compared to published values.

  15. Mean Glandular dose coefficients (DgN) for x-ray spectra used in contemporary breast imaging systems

    PubMed Central

    Nosratieh, Anita; Hernandez, Andrew; Shen, Sam Z.; Yaffe, Martin J.; Seibert, J. Anthony; Boone, John M.

    2015-01-01

    Purpose To develop tables of normalized glandular dose coefficients DgN for a range of anode–filter combinations and tube voltages used in contemporary breast imaging systems. Methods Previously published mono-energetic DgN values were used with various spectra to mathematically compute DgN coefficients. The tungsten anode spectra from TASMICS were used; Molybdenum and Rhodium anode-spectra were generated using MCNPx Monte Carlo code. The spectra were filtered with various thicknesses of Al, Rh, Mo or Cu. An initial HVL calculation was made using the anode and filter material. A range of the HVL values was produced with the addition of small thicknesses of polymethyl methacrylate (PMMA) as a surrogate for the breast compression paddle, to produce a range of HVL values at each tube voltage. Using a spectral weighting method, DgN coefficients for the generated spectra were calculated for breast glandular densities of 0%, 12.5%, 25%, 37.5%, 50% and 100% for a range of compressed breast thicknesses from 3 to 8 cm. Results Eleven tables of normalized glandular dose (DgN) coefficients were produced for the following anode/filter combinations: W + 50 μm Ag, W + 500 μm Al, W + 700 μm Al, W + 200 μm Cu, W + 300 μm Cu, W + 50 μm Rh, Mo + 400 μm Cu, Mo + 30 μm Mo, Mo + 25 μm Rh, Rh + 400 μm Cu and Rh + 25 μm Rh. Where possible, these results were compared to previously published DgN values and were found to be on average less than 2% different than previously reported values. Conclusion Over 200-pages of DgN coefficients were computed for modeled x-ray system spectra that are used in a number of new breast imaging applications. The reported values were found to be in excellent agreement when compared to published values. PMID:26348995

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

    NASA Astrophysics Data System (ADS)

    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

  17. Developmental transcriptome of Aplysia californica.

    PubMed

    Heyland, Andreas; Vue, Zer; Voolstra, Christian R; Medina, Mónica; Moroz, Leonid L

    2011-03-15

    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.

  18. Developmental Transcriptome of Aplysia californica

    PubMed Central

    HEYLAND, ANDREAS; VUE, ZER; VOOLSTRA, CHRISTIAN R.; MEDINA, MÓNICA; MOROZ, LEONID L.

    2014-01-01

    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. PMID:21328528

  19. Proteomics of the human endometrial glandular epithelium and stroma from the proliferative and secretory phases of the menstrual cycle.

    PubMed

    Hood, Brian L; Liu, Baoquan; Alkhas, Addie; Shoji, Yutaka; Challa, Rusheeswar; Wang, Guisong; Ferguson, Susan; Oliver, Julie; Mitchell, Dave; Bateman, Nicholas W; Zahn, Christopher M; Hamilton, Chad A; Payson, Mark; Lessey, Bruce; Fazleabas, Asgerally T; Maxwell, G Larry; Conrads, Thomas P; Risinger, John I

    2015-04-01

    Despite its importance in reproductive biology and women's health, a detailed molecular-level understanding of the human endometrium is lacking. Indeed, no comprehensive studies have been undertaken to elucidate the important protein expression differences between the endometrial glandular epithelium and surrounding stroma during the proliferative and midsecretory phases of the menstrual cycle. We utilized laser microdissection to harvest epithelial cells and stromal compartments from proliferative and secretory premenopausal endometrial tissue and performed a global, quantitative mass spectrometry-based proteomics analysis. This analysis identified 1224 total proteins from epithelial cells, among which 318 were differentially abundant between the proliferative and secretory phases (q < 0.05), and 1005 proteins from the stromal compartments, 19 of which were differentially abundant between the phases (q < 0.05). Several proteins were chosen for validation by immunohistochemistry in an independent set of uterine tissues, including carboxypeptidase M, tenascin C, neprilysin, and ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (ENPP3). ENPP3, which was elevated in epithelial glandular cells in the secretory phase, was confirmed to be elevated in midsecretory-phase baboon uterine lavage samples and also observed to have an N-linked glycosylated form that was not observed in the proliferative phase. This study provides a detailed view into the global proteomic alterations of the epithelial cells and stromal compartments of the cycling premenopausal endometrium. These proteomic alterations during endometrial remodeling provide a basis for numerous follow-up investigations on the function of these differentially regulated proteins and their role in reproductive biology and endometrial pathologies.

  20. Two IIIf Clade-bHLHs from Freesia hybrida Play Divergent Roles in Flavonoid Biosynthesis and Trichome Formation when Ectopically Expressed in Arabidopsis

    PubMed Central

    Li, Yueqing; Shan, Xiaotong; Gao, Ruifang; Yang, Song; Wang, Shucai; Gao, Xiang; Wang, Li

    2016-01-01

    The MBW complex, comprised by R2R3-MYB, basic helix-loop-helix (bHLH) and WD40, is a single regulatory protein complex that drives the evolution of multiple traits such as flavonoid biosynthesis and epidermal cell differentiation in plants. In this study, two IIIf Clade-bHLH regulator genes, FhGL3L and FhTT8L, were isolated and functionally characterized from Freesia hybrida. Different spatio-temporal transcription patterns were observed showing diverse correlation with anthocyanin and proanthocyanidin accumulation. When overexpressed in Arabidopsis, FhGL3L could enhance the anthocyanin accumulation through up-regulating endogenous regulators and late structural genes. Unexpectedly, trichome formation was inhibited associating with the down-regulation of AtGL2. Comparably, only the accumulation of anthocyanins and proanthocyanidins was strengthened in FhTT8L transgenic lines. Furthermore, transient expression assays demonstrated that FhGL3L interacted with AtPAP1, AtTT2 and AtGL1, while FhTT8L only showed interaction with AtPAP1 and AtTT2. In addition, similar activation of the AtDFR promoter was found between AtPAP1-FhGL3L/FhTT8L and AtPAP1- AtGL3/AtTT8 combinations. When FhGL3L was fused with a strong activation domain VP16, it could activate the AtGL2 promoter when co-transfected with AtGL1. Therefore, it can be concluded that the functionality of bHLH factors may have diverged, and a sophisticated interaction and hierarchical network might exist in the regulation of flavonoid biosynthesis and trichome formation. PMID:27465838

  1. Characterization of the Asian Citrus Psyllid Transcriptome

    PubMed Central

    Reese, Justin; Christenson, Matthew K.; Leng, Nan; Saha, Surya; Cantarel, Brandi; Lindeberg, Magdalen; Tamborindeguy, Cecilia; MacCarthy, Justin; Weaver, Daniel; Trease, Andrew J.; Ready, Steven V.; Davis, Vincent M.; McCormick, Courtney; Haudenschild, Christian; Han, Shunsheng; Johnson, Shannon L.; Shelby, Kent S.; Huang, Hong; Bextine, Blake R.; Shatters, Robert G.; Hall, David G.; Davis, Paul H.; Hunter, Wayne B.

    2014-01-01

    The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447]. PMID:24511328

  2. [Transcriptome platforms and applications to metabolic engineering].

    PubMed

    Shi, Shuobo; Chen, Tao; Zhao, Xueming

    2010-09-01

    Omics technologies have profoundly promoted development and applications of metabolic engineering by analysis of cell metabolism at a system level. Whole genome transcription profiles have provided researchers more rigorous evaluation of cell phenotype and an increased understanding of cellular metabolism. Furthermore, transcriptome analysis can conduce to identification of effective gene targets for strain improvement, and consequently accelerates rational design and construction of microbial cell factories for desired product. In this review, we briefly introduced the principle of three main platforms of transcriptome, and reviewed the recent applications of the transcriptome to metabolic engineering, finally provided conclusions and future prospects.

  3. Chemopreventive effects of curcumin on glandular stomach carcinogenesis induced by N-methyl-N'-nitro-N-nitrosoguanidine and sodium chloride in rats.

    PubMed

    Ikezaki, S; Nishikawa, A; Furukawa, F; Kudo, K; Nakamura, H; Tamura, K; Mori, H

    2001-01-01

    The modifying effects of pure curcumin on glandular stomach carcinogenesis were investigated during the post-initiation phase in male Wistar rats treated with N-methyl-N'-nitro-N-nitrosoguanisine (MNNG) and sodium chloride. A total of 110 male 6-week-old rats were divided into four groups. Groups 1-3 (consisting of 30 rats/group) were given MNNG in their drinking water at a concentration of 100 ppm and simultaneously fed a diet supplemented with 5% NaCl for 8 weeks. They were then fed a diet containing either 0.2% (group 1) or 0.05% (group 2) pure curcumin or kept on a basal diet alone (group 3) for 55 weeks. The rats of the curcumin-treated groups (groups 1 and 2) were then switched to the basal diet for the following 4 weeks before sacrifice. Group 4 (20 rats) served as a non-treatment control. The total incidence of combined atypical hyperplasias and adenocarcinomas in the glandular stomachs was rather lower in groups 1 (93%) and 2 (90%) than in group 3 (100%), albeit without statistical significance. However, the mean number of atypical hyperplasias or adenocarcinomas of the glandular stomachs in group 1 (4.70) was significantly less than the value of group 3 (7.17) (p<0.05). Thus, the development of cancerous and precancerous lesions in the glandular stomach was decreased by exposure to pure curcumin. The present results indicate that the compound exerts chemopreventive effects, when given during the post-initiation phase of glandular stomach carcinogenesis in rats.

  4. Histochemical evidence of β-chitin in parapodial glandular organs and tubes of Spiophanes (Annelida, Sedentaria: Spionidae), and first studies on selected Annelida.

    PubMed

    Guggolz, Theresa; Henne, Stephan; Politi, Yael; Schütz, Roman; Mašić, Admir; Müller, Carsten H G; Meißner, Karin

    2015-12-01

    A generic character of the genus Spiophanes (Annelida, Sedentaria: Spionidae) is the presence of parapodial glandular organs. Parapodial glandular organs in Spiophanes species include secretory cells with cup-shaped microvilli, similar to those present in deep-sea inhabiting vestimentiferans and frenulate Siboglinidae. These cells are supposed to secrete β-chitin for tube-building. In this study, transverse histological and/or ultrathin sections of parapodial glandular organs and tubes of Spiophanes spp. as well as of Glandulospio orestes (Spionidae) and Owenia fusiformis (Oweniidae) were examined. Fluorescent markers together with confocal laser scanning microscopy, and Raman spectroscopy were used to detect chitin in the parapodial glandular organs of Spiophanes and/or in the glands of Owenia and Glandulospio. Tubes of these taxa were tested for chitin to elucidate the use of it for tube-building. The examinations revealed a distinct labelling of the gland contents. Raman spectroscopy documented the presence of β-chitin in both gland types of Spiophanes. The tubes of Spiophanes were found to have a grid-like structure that seems to be built with this β-chitin. Tests of tubes of Dipolydora quadrilobata (Spionidae) for chitin were negative. However, the results of our study provide strong evidence that Spiophanes species, O. fusiformis and probably also G. orestes produce chitin and supposedly use it for tube-building. This implies that the production of chitin and its use as a constituent part of tube-building is more widespread among polychaetes as yet known. The histochemical data presented in this study support previous assumptions inferring homology of parapodial glandular organs of Spionidae and Siboglinidae based on ultrastructure. Furthermore, transmission electron microscopy-based evidence of secretory cells with nail-headed microvilli in O. fusiformis suggests homology of parapodial grandular organs across annelids including Sipuncula.

  5. De Novo Transcriptome Assembly in Polyploid Species.

    PubMed

    Gutierrez-Gonzalez, Juan J; Garvin, David F

    2017-01-01

    In the absence of a reference genome, the ultimate goal of a de novo transcriptome assembly is to accurately and comprehensively reconstruct the set of messenger RNA transcripts represented in the sample. Non-reference assembly of the transcriptome of polyploid species poses a particular challenge because of the presence of homeologs that are difficult to disentangle at the sequence level. This is especially true for hexaploid oats, which have three highly similar subgenomes, two of which are thought to be nearly identical. Under these circumstances, most software packages and established pipelines encounter difficulties in rendering an accurate transcriptome because they are typically developed, refined, and tested for diploid organisms. We present a protocol for transcriptome assembly in oats that can be extended both to other polyploids and species with highly duplicated genomes.

  6. Structure and properties of the glandular surface in the digestive zone of the pitcher in the carnivorous plant Nepenthes ventrata and its role in insect trapping and retention.

    PubMed

    Gorb, Elena; Kastner, Victoria; Peressadko, Andrei; Arzt, Eduard; Gaume, Laurence; Rowe, Nick; Gorb, Stanislav

    2004-08-01

    Carnivorous plants of the genus Nepenthes grow in nutrient-poor habitats and have evolved specialised trapping organs, known as pitchers. These are composed of different surface zones serving the functions of attraction, capture and digestion of insects, which represent a main source of nitrogen. To investigate the role of the glandular digestive zone in the trapping mechanism of the pitcher, structural, mechanical and physico-chemical studies were applied to N. ventrata and combined with insect behavioural experiments. It was found that the glandular surface is microscopically rough since it is regularly structured with multicellular glands situated in epidermal depressions. The presence of downward-directed 'hoods' over the upper part of glands and sloped depressions in the proximal direction of the pitcher causes a marked anisotropy of the surface. The glandular zone surface is composed of relatively stiff material (Young's modulus, 637.19+/-213.44 kPa). It is not homogeneous, in terms of adhesive properties, and contains numerous areas without adhesion as well as adhesive areas differing greatly in tenacity values (range, 1.39-28.24 kPa). The surface is readily wettable with water (contact angle, 31.9-36.0 degrees C) and has a high surface free energy (56.84-61.93 mN m(-1)) with a relatively high polar component (33.09-52.70 mN m(-1)). To examine the effect of the glandular secretion on attachment systems of insects having hairy and smooth adhesive pads, forces generated on different surfaces by Calliphora vicina flies and Pyrrhocoris apterus bugs, respectively, were measured. Flies attached equally well to both fresh and air-dried glandular surfaces whereas bugs generated a significantly lower force on the fresh glandular surface compared with the air-dried one. It is assumed that the contribution of the glandular surface to insect retention, due to its effect on insect attachment, differs depending on insect weight and the type of insect attachment system

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

    PubMed Central

    2009-01-01

    Background Prostate cancer cells in primary tumors have been typed CD10-/CD13-/CD24hi/CD26+/CD38lo/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. Methods 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. Results 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. Conclusions 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. PMID:20021671

  8. Loss of vitamin D receptor signaling from the mammary epithelium or adipose tissue alters pubertal glandular development.

    PubMed

    Johnson, Abby L; Zinser, Glendon M; Waltz, Susan E

    2014-10-15

    Vitamin D₃ receptor (VDR) signaling within the mammary gland regulates various postnatal stages of glandular development, including puberty, pregnancy, involution, and tumorigenesis. Previous studies have shown that vitamin D₃ treatment induces cell-autonomous growth inhibition and differentiation of mammary epithelial cells in culture. Furthermore, mammary adipose tissue serves as a depot for vitamin D₃ storage, and both epithelial cells and adipocytes are capable of bioactivating vitamin D₃. Despite the pervasiveness of VDR in mammary tissue, individual contributions of epithelial cells and adipocytes, as well as the VDR-regulated cross-talk between these two cell types during pubertal mammary development, have yet to be investigated. To assess the cell-type specific effect of VDR signaling during pubertal mammary development, novel mouse models with mammary epithelial- or adipocyte-specific loss of VDR were generated. Interestingly, loss of VDR in either cellular compartment accelerated ductal morphogenesis with increased epithelial cell proliferation and decreased apoptosis within terminal end buds. Conversely, VDR signaling specifically in the mammary epithelium modulated hormone-induced alveolar growth, as ablation of VDR in this cell type resulted in precocious alveolar development. In examining cellular cross-talk ex vivo, we show that ligand-dependent VDR signaling in adipocytes significantly inhibits mammary epithelial cell growth in part through the vitamin D₃-dependent production of the cytokine IL-6. Collectively, these studies delineate independent roles for vitamin D₃-dependent VDR signaling in mammary adipocytes and epithelial cells in controlling pubertal mammary gland development.

  9. A Concurrence of Adenocarcinoma with Micropapillary Features and Composite Glandular-Endocrine Cell Carcinoma in the Stomach

    PubMed Central

    Kim, Ji-Hoon; Park, Cheon-Soo; Kwak, Jae-Young; Park, Eun-Hwa; Kwak, Jin-Ho; Jang, Hyuk-Jae; Choi, Kun-Moo; Han, Myung-Sik

    2016-01-01

    We report a unique case of synchronous double primary gastric cancer consisting of adenocarcinoma components with micropapillary features and composite glandular-endocrine cell carcinoma components. The patient was a 53-year-old man presenting with a 6-month history of epigastric pain and diarrhea. A subtotal gastrectomy was performed. Histologically, one tumor was composed of micropapillary carcinoma components (50%) with tight clusters of micropapillary aggregates lying in the empty spaces, admixed with moderately differentiated adenocarcinoma components. MUC-1 was expressed at the stromal edge of the micropapillary component. The other tumor was composed of atypical carcinoid-like neuroendocrine carcinoma (50%), adenocarcinoid (30%), and adenocarcinoma components (20%). The neuroendocrine components were positive for CD56, synaptophysin, chromogranin, and creatine kinase. The adenocarcinoid components were positive for both carcinoembryonic antigen and neuroendocrine markers (amphicrine differentiation). This case is unique, due to the peculiar histologic micropapillary pattern and the histologic spectrum of adenocarcinoma adenocarcinoid-neuroendocrine carcinoma of the synchronous composite tumor. PMID:28053814

  10. The identification of Cucumis sativus Glabrous 1 (CsGL1) required for the formation of trichomes uncovers a novel function for the homeodomain-leucine zipper I gene.

    PubMed

    Li, Qiang; Cao, Chenxing; Zhang, Cunjia; Zheng, Shuangshuang; Wang, Zenghui; Wang, Lina; Ren, Zhonghai

    2015-05-01

    The spines and bloom of cucumber (Cucumis sativus L.) fruit are two important quality traits related to fruit market value. However, until now, none of the genes involved in the formation of cucumber fruit spines and bloom trichomes has been identified. Here, the characterization of trichome development in wild-type (WT) cucumber and a spontaneous mutant, glabrous 1 (csgl1) controlled by a single recessive nuclear gene, with glabrous aerial organs, is reported. Via map-based cloning, CsGL1 was isolated and it was found that it encoded a member of the homeodomain-leucine zipper I (HD-Zip I) proteins previously identified to function mainly in the abiotic stress responses of plants. Tissue-specific expression analysis indicated that CsGL1 was strongly expressed in trichomes and fruit spines. In addition, CsGL1 was a nuclear protein with weak transcriptional activation activity in yeast. A comparative analysis of the digital gene expression (DGE) profile between csgl1 and WT leaves revealed that CsGL1 had a significant influence on the gene expression profile in cucumber, especially on genes related to cellular process, which is consistent with the phenotypic difference between csgl1 and the WT. Moreover, two genes, CsMYB6 and CsGA20ox1, possibly involved in the formation of cucumber trichomes and fruit spines, were characterized. Overall, the findings reveal a new function for the HD-Zip I gene subfamily, and provide some candidate genes for genetic engineering approaches to improve cucumber fruit external quality.

  11. The transcriptome of human oocytes

    PubMed Central

    Kocabas, Arif Murat; Crosby, Javier; Ross, Pablo J.; Otu, Hasan H.; Beyhan, Zeki; Can, Handan; Tam, Wai-Leong; Rosa, Guilherme J. M.; Halgren, Robert G.; Lim, Bing; Fernandez, Emilio; Cibelli, Jose Bernardo

    2006-01-01

    The identification of genes and deduced pathways from the mature human oocyte can help us better understand oogenesis, folliculogenesis, fertilization, and embryonic development. Human metaphase II oocytes were used within minutes after removal from the ovary, and its transcriptome was compared with a reference sample consisting of a mixture of total RNA from 10 different normal human tissues not including the ovary. RNA amplification was performed by using a unique protocol. Affymetrix Human Genome U133 Plus 2.0 GeneChip arrays were used for hybridizations. Compared with reference samples, there were 5,331 transcripts significantly up-regulated and 7,074 transcripts significantly down-regulated in the oocyte. Of the oocyte up-regulated probe sets, 1,430 have unknown function. A core group of 66 transcripts was identified by intersecting significantly up-regulated genes of the human oocyte with those from the mouse oocyte and from human and mouse embryonic stem cells. GeneChip array results were validated using RT-PCR in a selected set of oocyte-specific genes. Within the up-regulated probe sets, the top overrepresented categories were related to RNA and protein metabolism, followed by DNA metabolism and chromatin modification. This report provides a comprehensive expression baseline of genes expressed in in vivo matured human oocytes. Further understanding of the biological role of these genes may expand our knowledge on meiotic cell cycle, fertilization, chromatin remodeling, lineage commitment, pluripotency, tissue regeneration, and morphogenesis. PMID:16968779

  12. Blood transcriptomics: applications in toxicology

    PubMed Central

    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

  13. Determination of Tube Output (kVp) and Exposure Mode for Breast Phantom of Various Thicknesses/Glandularity for Digital Mammography

    PubMed Central

    IZDIHAR, Kamal; KANAGA, Kumari Chelliah; KRISHNAPILLAI, Vijayalakshimi; SULAIMAN, Tamanang

    2015-01-01

    Background: Optimisation of average glandular dose (AGD) for two-dimensional (2D) mammography is important, as imaging using ionizing radiation has the probability to induce cancer resulting from stochastic effects. This study aims to observe the effects of kVp, anode/filter material, and exposure mode on the dose and image quality of 2D mammography. Methods: This experimental study was conducted using full-field digital mammography. The entrance surface air kerma was determined using thermoluminescent dosimeter (TLD) 100H and ionization chamber (IC) on three types of Computerized Imaging Reference System (CIRS) phantom with 50/50, 30/70, and 20/80 breast glandularity, respectively, in the auto-time mode and auto-filter mode. The Euref protocol was used to calculate the AGD while the image quality was evaluated using contrast-to-noise ratio (CNR), figure of merit (FOM), and image quality figure (IQF). Results: It is shown that AGD values in the auto-time mode did not decrease significantly with the increasing tube voltage of the silver filter (r = −0.187, P > 0.05) and rhodium filter (r = −0.131, P > 0.05) for all the phantoms. The general linear model showed that AGD for all phantoms had a significant effect between different exposure factors [F (6,12.3) = 4.48 and mode of exposure F (1,86) = 4.17, P < 0.05, respectively] but there is no significant difference between the different anode/filter combination [F (1,4) = 0.571]. Conclusion: In summary, the 28, 29, and 31 kVp are the optimum kVp for 50%, 30%, and 20% breast glandularity, respectively. Besides the auto-filter mode is suitable for 50%, 30%, and 20% breast glandularity because it is automatic, faster, and may avoid error done by the operator. PMID:25892949

  14. Human glandular organoid formation in murine engineering chambers after collagenase digestion and flow cytometry isolation of normal human breast tissue single cells.

    PubMed

    Huo, Cecilia W; Huang, Dexing; Chew, Grace L; Hill, Prue; Vohora, Ambika; Ingman, Wendy V; Glynn, Danielle J; Godde, Nathan; Henderson, Michael A; Thompson, Erik W; Britt, Kara L

    2016-11-01

    Women with high mammographic density (MD) are at increased risk of breast cancer (BC) after adjustment for age and body mass index. We have developed a murine biochamber model in which both high MD (HMD) and low MD (LMD) tissue can be propagated. Here, we tested whether cells isolated by collagenase digestion and fluorescence-activated cell sorting (FACS) from normal breast can be reconstituted in our biochamber model, which would allow cell-specific manipulations to be tested. Fresh breast tissue was collected from women (n = 7) undergoing prophylactic mastectomy. The tissue underwent collagenase digestion overnight and, in some cases, additional FACS enrichment to obtain mature epithelial, luminal progenitor, mammary stem, and stromal cells. Cells were then transferred bilaterally into biochambers in SCID mice (n = 5-7) and incubated for 6 weeks, before harvesting for histological analyses, and immunohistochemical staining for cytokeratins (CK), vimentin, Ki-67, murine macrophages, and Cleaved Caspase-3. Biochambers inoculated with single cells after collagenase digestion or with flow cytometry contained glandular structures of human origin (human vimentin-positive), which expressed CK-14 and pan-CK, and were proliferating (Ki-67-positive). Glandular structures from the digested tissues were smaller than those in chambers seeded with finely chopped intact mammary tissue. Mouse macrophage infiltration was higher in the chambers arising from digested tissues. Pooled single cells and FACS fractionated cells were viable in the murine biochambers and formed proliferating glandular organoids of human origin. This is among the first report to demonstrate the success of formed human glandular organoids from isolated primary mammary cells in the murine biochamber model.

  15. Polyploidization in the trophoblast and uterine glandular epithelium of the endotheliochorial placenta of silver fox (Vulpes fulvus Desm.), as revealed by the DNA content.

    PubMed

    Zybina, T G; Zybina, E V; Kiknadze, I I; Zhelezova, A I

    2001-05-01

    Dynamics of genome multiplication during establishment of interrelations between trophoblast and glandular epithelium of the endometrium has been studied in the course of formation of placenta in the silver fox. During formation of the placenta, penetration of the trophoblast into the zone of the endometrial glandular epithelium and of endometrial blood vessels into the zone of expanding trophoblast occurs. The trophoblast, which gradually replaces epithelium and a part of the stroma of the endometrium, closely adjoins endometrial vessels but does not disrupt them, thereby the endotheliochorial placenta is formed. Cytophotometric measurements of the DNA content in trophoblast nuclei have shown that most of them are polyploid: predominantly 4-64c, occasionally 128c and 256c. Polyploidy of the trophoblast may be a consequence of various types of polyploidizing mitoses. Cytophotometric measurements of the DNA content in mitotic figures have revealed the presence of mitoses of diploid cells, i.e. with the DNA amount of 4c (2n), and polyploid cells, i.e. 8c (4n), and 16c (8n), therefore trophoblast cells in the silver fox placenta are able to enter mitosis up to the octaploid level. Higher degrees of polyploidy in the trophoblast cells seem to be achieved by endoreduplication. Polyploidization of the uterine glandular epithelial cells during placentation in the silver fox occurs until the level of 8c. Thus, the tissue-specific response of the uterus to the implanting embryo consists of active proliferation and polyploidization of the glandular epithelium, which may compensate formation of prominent population of decidual cells (i.e., connective tissue cells). In the endotheliochorial placenta of the silver fox the regularity is confirmed that cells of both maternal and fetal origin are, as a rule, polyploid in sites of their contact in placenta, which may be of protective significance in the contact of allogenic organisms.

  16. Ultrastructural changes in the uterine luminal and glandular epithelium during the oestrous cycle of the marsupial Monodelphis domestica (grey short-tailed opossum).

    PubMed

    Wick, Regula; Kress, Annetrudi

    2002-01-01

    Ultrastructural changes in the endometrium associated with the oestrous cycle were studied in the South American marsupial Monodelphis domestica. The most conspicuous changes include the height and the differentiation of the uterine luminal and glandular epithelium, which consists of ciliated and non-ciliated cells. The glandular epithelium attains its maximum development during oestrus, the luminal epithelium at postoestrus. A distinct increase in the number of ciliated cells can be observed during pro-oestrus, reaching a maximum number at oestrus; this is followed by a process of deciliation. The presence of solitary cilia on the apices of non-ciliated cells is very conspicuous during all oestrous stages and can best be seen on the luminal epithelium. These findings differ from the observations in eutherian mammals, where solitary cilia are only found in the immature uterus or after ovariectomy. The secretory activity of non-ciliated cells of the luminal epithelium is hardly noticeable along the apical membrane and stains only very faintly with Alcian blue. The glandular epithelium cells are filled apically with exocytotic vesicles at oestrus and early postoestrus. However, in contrast to the cervical gland cells, they hardly stain with Alcian blue, indicating that mucins of a different type must be present. Mechanisms for the remodelling of the luminal and glandular epithelium are especially conspicuous at metoestrus and early pro-oestrus and include the presence of autolysosomes, residual bodies and apoptotic bodies. In the endometrial stroma, around the uterine glands, macrophages accumulate and attain a typical oestrous stage-dependent appearance during their phagocytotic activities.

  17. Evidence of progenitor cells of glandular and myoepithelial cell lineages in the human adult female breast epithelium: a new progenitor (adult stem) cell concept.

    PubMed

    Boecker, Werner; Buerger, Horst

    2003-10-01

    Although experimental data clearly confirm the existence of self-renewing mammary stem cells, the characteristics of such progenitor cells have never been satisfactorily defined. Using a double immunofluorescence technique for simultaneous detection of the basal cytokeratin 5, the glandular cytokeratins 8/18 and the myoepithelial differentiation marker smooth muscle actin (SMA), we were able to demonstrate the presence of CK5+ cells in human adult breast epithelium. These cells have the potential to differentiate to either glandular (CK8/18+) or myoepithelial cells (SMA+) through intermediary cells (CK5+ and CK8/18+ or SMA+). We therefore proceeded on the assumption that the CK5+ cells are phenotypically and behaviourally progenitor (committed adult stem) cells of human breast epithelium. Furthermore, we furnish evidence that most of these progenitor cells are located in the luminal epithelium of the ductal lobular tree. Based on data obtained in extensive analyses of proliferative breast disease lesions, we have come to regard usual ductal hyperplasia as a progenitor cell-derived lesion, whereas most breast cancers seem to evolve from differentiated glandular cells. Double immunofluorescence experiments provide a new tool to characterize phenotypically progenitor (adult stem) cells and their progenies. This model has been shown to be of great value for a better understanding not only of normal tissue regeneration but also of proliferative breast disease. Furthermore, this model provides a new tool for unravelling further the regulatory mechanisms that govern normal and pathological cell growth.

  18. Single-cell transcriptomics for microbial eukaryotes.

    PubMed

    Kolisko, Martin; Boscaro, Vittorio; Burki, Fabien; Lynn, Denis H; Keeling, Patrick J

    2014-11-17

    One of the greatest hindrances to a comprehensive understanding of microbial genomics, cell biology, ecology, and evolution is that most microbial life is not in culture. Solutions to this problem have mainly focused on whole-community surveys like metagenomics, but these analyses inevitably loose information and present particular challenges for eukaryotes, which are relatively rare and possess large, gene-sparse genomes. Single-cell analyses present an alternative solution that allows for specific species to be targeted, while retaining information on cellular identity, morphology, and partitioning of activities within microbial communities. Single-cell transcriptomics, pioneered in medical research, offers particular potential advantages for uncultivated eukaryotes, but the efficiency and biases have not been tested. Here we describe a simple and reproducible method for single-cell transcriptomics using manually isolated cells from five model ciliate species; we examine impacts of amplification bias and contamination, and compare the efficacy of gene discovery to traditional culture-based transcriptomics. Gene discovery using single-cell transcriptomes was found to be comparable to mass-culture methods, suggesting single-cell transcriptomics is an efficient entry point into genomic data from the vast majority of eukaryotic biodiversity.

  19. Comparative Transcriptome Analysis of Four Prymnesiophyte Algae

    PubMed Central

    Koid, Amy E.; Liu, Zhenfeng; Terrado, Ramon; Jones, Adriane C.; Caron, David A.; Heidelberg, Karla B.

    2014-01-01

    Genomic studies of bacteria, archaea and viruses have provided insights into the microbial world by unveiling potential functional capabilities and molecular pathways. However, the rate of discovery has been slower among microbial eukaryotes, whose genomes are larger and more complex. Transcriptomic approaches provide a cost-effective alternative for examining genetic potential and physiological responses of microbial eukaryotes to environmental stimuli. In this study, we generated and compared the transcriptomes of four globally-distributed, bloom-forming prymnesiophyte algae: Prymnesium parvum, Chrysochromulina brevifilum, Chrysochromulina ericina and Phaeocystis antarctica. Our results revealed that the four transcriptomes possess a set of core genes that are similar in number and shared across all four organisms. The functional classifications of these core genes using the euKaryotic Orthologous Genes (KOG) database were also similar among the four study organisms. More broadly, when the frequencies of different cellular and physiological functions were compared with other protists, the species clustered by both phylogeny and nutritional modes. Thus, these clustering patterns provide insight into genomic factors relating to both evolutionary relationships as well as trophic ecology. This paper provides a novel comparative analysis of the transcriptomes of ecologically important and closely related prymnesiophyte protists and advances an emerging field of study that uses transcriptomics to reveal ecology and function in protists. PMID:24926657

  20. Cotton AnnGh3 encoding an annexin protein is preferentially expressed in fibers and promotes initiation and elongation of leaf trichomes in transgenic Arabidopsis.

    PubMed

    Li, Bing; Li, Deng-Di; Zhang, Jie; Xia, Hui; Wang, Xiu-Lan; Li, Ying; Li, Xue-Bao

    2013-10-01

    The annexins are a multifamily of calcium-regulated phospholipid-binding proteins. To investigate the roles of annexins in fiber development, four genes encoding putative annexin proteins were isolated from cotton (Gossypium hirsutum) and designated AnnGh3, AnnGh4, AnnGh5, and AnnGh6. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) results indicated that AnnGh3, AnnGh4, and AnnGh5 were preferentially expressed in fibers, while the transcripts of AnnGh6 were predominantly accumulated in roots. During fiber development, the transcripts of AnnGh3/4/5 genes were mainly accumulated in rapidly elongating fibers. With fiber cells further developed, their expression activity was dramatically declined to a relatively low level. In situ hybridization results indicated that AnnGh3 and AnnGh5 were expressed in initiating fiber cells (0-2 DPA). Additionally, their expression in fibers was also regulated by phytohormones and [Ca(2+)]. Subcellular localization analysis discovered that AnnGh3 protein was localized in the cytoplasm. Overexpression of AnnGh3 in Arabidopsis resulted in a significant increase in trichome density and length on leaves of the transgenic plants, suggesting that AnnGh3 may be involved in fiber cell initiation and elongation of cotton.

  1. Ectopic Expression of Capsicum-Specific Cell Wall Protein Capsicum annuum Senescence-Delaying 1 (CaSD1) Delays Senescence and Induces Trichome Formation in Nicotiana benthamiana

    PubMed Central

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

    2012-01-01

    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. PMID:22441673

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

    PubMed

    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.

  3. A direct liquid, non-equilibrium solid-phase micro-extraction application for analysing chemical variation of single peltate trichomes on leaves of Salvia officinalis.

    PubMed

    Grassi, Paolo; Novak, Johannes; Steinlesberger, Heidi; Franz, Chlodwig

    2004-01-01

    A non-equilibrium solid phase micro-extraction application was tested for the rapid extraction of essential oil from single oil glands of sage and the oil components compared with those determined by solvent extract and distillation. Oil glands were directly ruptured with a polydimethylsiloxane-coated fused silica fibre and the essential oil was sorbed. Three insertion levels of an individual plant of Salvia officinalis involving an immature apical young leaf, an expanding and a fully developed leaf, respectively, were used to determine the applicability of this method. Thirty-eight components in the oil could be identified by GC-MS. The method only showed small semi-quantitative differences compared with conventional methods. Chemical variation of single oil glands within the immature and premature leaf was higher than within the homogeneous mature leaf. The intermediary, still-expanding leaf was used to carry out a detailed study of the glands. The basal region of the intermediary leaf contained compounds in high conformity with the young leaf trichomes. The remaining oil glands of this leaf showed inconsistent accumulation patterns.

  4. Understanding the transcriptome through RNA structure

    PubMed Central

    Wan, Yue; Kertesz, Michael; Spitale, Robert C.; Segal, Eran; Chang, Howard

    2013-01-01

    RNA structure is critical for gene regulation and function. In the past, transcriptomes have been largely parsed by primary sequences and expression levels, but it is now becoming feasible to annotate and compare transcriptomes based on RNA structure. In addition to computational prediction methods, the recent advent of experimental techniques to probe RNA structure by deep sequencing has enabled genome-wide measurements of RNA structure, and provided the first picture of the structural organization of an eukaryotic transcriptome—the “RNA structurome”. With additional advances in method refinement and interpretation, structural views of the transcriptome should help to identify and validate regulatory RNA motifs that are involved in diverse cellular processes, and thereby increase understanding of RNA function. PMID:21850044

  5. The Human Transcriptome: An Unfinished Story

    PubMed Central

    Pertea, Mihaela

    2012-01-01

    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. PMID:22916334

  6. Integrated Analysis of Transcriptomic and Proteomic Data

    PubMed Central

    Haider, Saad; Pal, Ranadip

    2013-01-01

    Until recently, understanding the regulatory behavior of cells has been pursued through independent analysis of the transcriptome or the proteome. Based on the central dogma, it was generally assumed that there exist a direct correspondence between mRNA transcripts and generated protein expressions. However, recent studies have shown that the correlation between mRNA and Protein expressions can be low due to various factors such as different half lives and post transcription machinery. Thus, a joint analysis of the transcriptomic and proteomic data can provide useful insights that may not be deciphered from individual analysis of mRNA or protein expressions. This article reviews the existing major approaches for joint analysis of transcriptomic and proteomic data. We categorize the different approaches into eight main categories based on the initial algorithm and final analysis goal. We further present analogies with other domains and discuss the existing research problems in this area. PMID:24082820

  7. Transcriptome Analysis in Venom Gland of the Predatory Giant Ant Dinoponera quadriceps: Insights into the Polypeptide Toxin Arsenal of Hymenopterans

    PubMed Central

    Chong, Cheong-Meng; Leung, Siu Wai; Prieto-da-Silva, Álvaro R. B.; Havt, Alexandre; Quinet, Yves P.; Martins, Alice M. C.; Lee, Simon M. Y.; Rádis-Baptista, Gandhi

    2014-01-01

    Background Dinoponera quadriceps is a predatory giant ant that inhabits the Neotropical region and subdues its prey (insects) with stings that deliver a toxic cocktail of molecules. Human accidents occasionally occur and cause local pain and systemic symptoms. A comprehensive study of the D. quadriceps venom gland transcriptome is required to advance our knowledge about the toxin repertoire of the giant ant venom and to understand the physiopathological basis of Hymenoptera envenomation. Results We conducted a transcriptome analysis of a cDNA library from the D. quadriceps venom gland with Sanger sequencing in combination with whole-transcriptome shotgun deep sequencing. From the cDNA library, a total of 420 independent clones were analyzed. Although the proportion of dinoponeratoxin isoform precursors was high, the first giant ant venom inhibitor cysteine-knot (ICK) toxin was found. The deep next generation sequencing yielded a total of 2,514,767 raw reads that were assembled into 18,546 contigs. A BLAST search of the assembled contigs against non-redundant and Swiss-Prot databases showed that 6,463 contigs corresponded to BLASTx hits and indicated an interesting diversity of transcripts related to venom gene expression. The majority of these venom-related sequences code for a major polypeptide core, which comprises venom allergens, lethal-like proteins and esterases, and a minor peptide framework composed of inter-specific structurally conserved cysteine-rich toxins. Both the cDNA library and deep sequencing yielded large proportions of contigs that showed no similarities with known sequences. Conclusions To our knowledge, this is the first report of the venom gland transcriptome of the New World giant ant D. quadriceps. The glandular venom system was dissected, and the toxin arsenal was revealed; this process brought to light novel sequences that included an ICK-folded toxins, allergen proteins, esterases (phospholipases and carboxylesterases), and lethal

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

    PubMed

    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.

  9. OSC2 and CYP716A14v2 Catalyze the Biosynthesis of Triterpenoids for the Cuticle of Aerial Organs of Artemisia annua

    PubMed Central

    Moses, Tessa; Pollier, Jacob; Shen, Qian; Soetaert, Sandra; Reed, James; Erffelinck, Marie-Laure; Van Nieuwerburgh, Filip C.W.; Vanden Bossche, Robin; Osbourn, Anne; Thevelein, Johan M.; Deforce, Dieter; Tang, Kexuan

    2015-01-01

    Artemisia annua is widely studied for its ability to accumulate the antimalarial sesquiterpenoid artemisinin. In addition to producing a variety of sesquiterpenoids, A. annua also accumulates mono-, di-, and triterpenoids, the majority of which are produced in the glandular trichomes. A. annua also has filamentous trichomes on its aerial parts, but little is known of their biosynthesis potential. Here, through a comparative transcriptome analysis between glandular and filamentous trichomes, we identified two genes, OSC2 and CYP716A14v2, encoding enzymes involved in the biosynthesis of specialized triterpenoids in A. annua. By expressing these genes in Saccharomyces cerevisiae and Nicotiana benthamiana, we characterized the catalytic function of these proteins and could reconstitute the specialized triterpenoid spectrum of A. annua in these heterologous hosts. OSC2 is a multifunctional oxidosqualene cyclase that produces α-amyrin, β-amyrin, and δ-amyrin. CYP716A14v2 is a P450 belonging to the functionally diverse CYP716 family and catalyzes the oxidation of pentacyclic triterpenes, leading to triterpenes with a carbonyl group at position C-3, thereby providing an alternative biosynthesis pathway to 3-oxo triterpenes. Together, these enzymes produce specialized triterpenoids that are constituents of the wax layer of the cuticle covering the aerial parts of A. annua and likely function in the protection of the plant against biotic and abiotic stress. PMID:25576188

  10. Optimal Scaling of Digital Transcriptomes

    PubMed Central

    Glusman, Gustavo; Caballero, Juan; Robinson, Max; Kutlu, Burak; Hood, Leroy

    2013-01-01

    Deep sequencing of transcriptomes has become an indispensable tool for biology, enabling expression levels for thousands of genes to be compared across multiple samples. Since transcript counts scale with sequencing depth, counts from different samples must be normalized to a common scale prior to comparison. We analyzed fifteen existing and novel algorithms for normalizing transcript counts, and evaluated the effectiveness of the resulting normalizations. For this purpose we defined two novel and mutually independent metrics: (1) the number of “uniform” genes (genes whose normalized expression levels have a sufficiently low coefficient of variation), and (2) low Spearman correlation between normalized expression profiles of gene pairs. We also define four novel algorithms, one of which explicitly maximizes the number of uniform genes, and compared the performance of all fifteen algorithms. The two most commonly used methods (scaling to a fixed total value, or equalizing the expression of certain ‘housekeeping’ genes) yielded particularly poor results, surpassed even by normalization based on randomly selected gene sets. Conversely, seven of the algorithms approached what appears to be optimal normalization. Three of these algorithms rely on the identification of “ubiquitous” genes: genes expressed in all the samples studied, but never at very high or very low levels. We demonstrate that these include a “core” of genes expressed in many tissues in a mutually consistent pattern, which is suitable for use as an internal normalization guide. The new methods yield robustly normalized expression values, which is a prerequisite for the identification of differentially expressed and tissue-specific genes as potential biomarkers. PMID:24223126

  11. Transcriptomic Microenvironment of Lung Adenocarcinoma.

    PubMed

    Bossé, Yohan; Sazonova, Olga; Gaudreault, Nathalie; Bastien, Nathalie; Conti, Massimo; Pagé, Sylvain; Trahan, Sylvain; Couture, Christian; Joubert, Philippe

    2017-03-01

    Background: Tissues surrounding tumors are increasingly studied to understand the biology of cancer development and identify biomarkers.Methods: A unique geographic tissue sampling collection was obtained from patients that underwent curative lobectomy for stage I pulmonary adenocarcinoma. Tumor and nontumor lung samples located at 0, 2, 4, and 6 cm away from the tumor were collected. Whole-genome gene expression profiling was performed on all samples (n = 5 specimens × 12 patients = 60). Analyses were carried out to identify genes differentially expressed in the tumor compared with adjacent nontumor lung tissues at different distances from the tumor as well as to identify stable and transient genes in nontumor tissues with respect to tumor proximity.Results: The magnitude of gene expression changes between tumor and nontumor sites was similar with increasing distance from the tumor. A total of 482 up- and 843 downregulated genes were found in tumors, including 312 and 566 that were consistently differentially expressed across nontumor sites. Twenty-nine genes induced and 34 knocked-down in tumors were also identified. Tumor proximity analyses revealed 15,700 stable genes in nontumor lung tissues. Gene expression changes across nontumor sites were subtle and not statistically significant.Conclusions: This study describes the transcriptomic microenvironment of lung adenocarcinoma and adjacent nontumor lung tissues collected at standardized distances relative to the tumor.Impact: This study provides further insights about the molecular transitions that occur from normal tissue to lung adenocarcinoma and is an important step to develop biomarkers in nonmalignant lung tissues. Cancer Epidemiol Biomarkers Prev; 26(3); 389-96. ©2016 AACR.

  12. Atypical RNAs in the coelacanth transcriptome.

    PubMed

    Nitsche, Anne; Doose, Gero; Tafer, Hakim; Robinson, Mark; Saha, Nil Ratan; Gerdol, Marco; Canapa, Adriana; Hoffmann, Steve; Amemiya, Chris T; Stadler, Peter F

    2014-09-01

    Circular and apparently trans-spliced RNAs have recently been reported as abundant types of transcripts in mammalian transcriptome data. Both types of non-colinear RNAs are also abundant in RNA-seq of different tissue from both the African and the Indonesian coelacanth. We observe more than 8,000 lincRNAs with normal gene structure and several thousands of circularized and trans-spliced products, showing that such atypical RNAs form a substantial contribution to the transcriptome. Surprisingly, the majority of the circularizing and trans-connecting splice junctions are unique to atypical forms, that is, are not used in normal isoforms.

  13. Effect of glandular kallikrein on distal bicarbonate transport. Role of basolateral Cl-/HCO3- exchanger and vacuolar H(+)-ATPase.

    PubMed

    Manucha, W; Vallés, P

    1999-12-01

    The luminal membrane of collecting duct cells, specially the intercalated cells, is normally exposed to active kallikrein. This is due to the specific localization of renal kallikrein in the connecting tubule cells. We have previously reported inhibition of distal bicarbonate secretion by renal kallikrein. The present study was performed to evaluate the participation of basolateral Cl-/HCO3- exchanger and luminal H(+)-ATPase activity of cortical collecting duct segments (CCD) in the mechanism involved in the inhibition of bicarbonate secretion induced by the enzyme. The effect of orthograde injections of 1 microgram/ml (250 U/6.3 mg) pig pancreatic kallikrein, in the absence and presence of 1 mM DIDS (stilbene-disulfonic acid) in the renal tubule system, was evaluated. Urine fractions were collected after two-minutes stop-flow. Changes in the urine fraction (Fr) related to those in free-flow urine samples (Ff) were related to the respective polyfructosan (Inutest) ratio. Renal kallikrein activity (Fr:Ff kallikrein/Fr:Ff polyfructosan) increased significantly in the first 120 microliters urine fraction collected after glandular 1 microgram/ml kallikrein, P < 0.05, (first stop-flow) and after glandular 1 microgram/ml kallikrein plus 1 mM. DIDS P < 0.05 (second stop flow). Bicarbonate secretion rate (Fr:Ff HCO3-/Fr:Ff polyfructosan) of collecting ducts was significantly reduced in the first 120 microliters urine fraction collected, related to control, during the first and second stop-flow periods. No difference was shown in bicarbonate excretion between the first 120 microliters urine fractions collected after administration of glandular kallikrein and glandular kallikrein plus DIDS. To measure H(+)-ATPase activity, rat microdissected cortical collector tubules (CCD) were incubated in the presence of increasing glandular kallikrein doses (A: 93, B: 187 and C: 375 mU/200 microL) in the presence of ouabain (4 microM) and omeprazole (100 microM) to inhibit Na

  14. Transcriptome Encyclopedia of Early Human Development.

    PubMed

    Sahakyan, Anna; Plath, Kathrin

    2016-05-05

    Our understanding of human pre-implantation development is limited by the availability of human embryos and cannot completely rely on mouse studies. Petropoulos et al. now provide an extensive transcriptome analysis of a large number of human pre-implantation embryos at single-cell resolution, revealing previously unrecognized features unique to early human development.

  15. Illuminating the Transcriptome through the Genome.

    PubMed

    Elliott, David J

    2014-03-14

    Sequencing the human genome was a huge milestone in genetic research that revealed almost the total DNA sequence required to create a human being. However, in order to function, the DNA genome needs to be expressed as an RNA transcriptome. This article reviews how knowledge of genome sequence information has led to fundamental discoveries in how the transcriptome is processed, with a focus on new system-wide insights into how pre-mRNAs that are encoded by split genes in the genome are rearranged by splicing into functional mRNAs. These advances have been made possible by the development of new post-genome technologies to probe splicing patterns. Transcriptome-wide approaches have characterised a "splicing code" that is embedded within and has a significant role in deciphering the genome, and is deciphered by RNA binding proteins. These analyses have also found that most human genes encode multiple mRNA isoforms, and in some cases proteins, leading in turn to a re-assessment of what exactly a gene is. Analysis of the transcriptome has given insights into how the genome is packaged and transcribed, and is helping to explain important aspects of genome evolution.

  16. A Floral Transcriptome for Hippeastrum (Amaryllidaceae)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two transcriptomes have been constructed from floral tissue of two Hippeastrum (Amaryllidaceae) species, H. brasilianum (Traub & J.L.Doran) Dutilh and H. papilio (Ravenna) Van Scheepan. The former has fragrant flowers, while flowers of the latter do not produce floral fragrance. RNA was isolated a...

  17. The transcriptome landscape of early maize meiosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  18. Illuminating the Transcriptome through the Genome

    PubMed Central

    Elliott, David J.

    2014-01-01

    Sequencing the human genome was a huge milestone in genetic research that revealed almost the total DNA sequence required to create a human being. However, in order to function, the DNA genome needs to be expressed as an RNA transcriptome. This article reviews how knowledge of genome sequence information has led to fundamental discoveries in how the transcriptome is processed, with a focus on new system-wide insights into how pre-mRNAs that are encoded by split genes in the genome are rearranged by splicing into functional mRNAs. These advances have been made possible by the development of new post-genome technologies to probe splicing patterns. Transcriptome-wide approaches have characterised a “splicing code” that is embedded within and has a significant role in deciphering the genome, and is deciphered by RNA binding proteins. These analyses have also found that most human genes encode multiple mRNA isoforms, and in some cases proteins, leading in turn to a re-assessment of what exactly a gene is. Analysis of the transcriptome has given insights into how the genome is packaged and transcribed, and is helping to explain important aspects of genome evolution. PMID:24705295

  19. Mastitis associated transcriptomic disruptions in cattle

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mastitis is ranked as the top disease for dairy cattle based on traditional cost analysis. Greater than 100 organisms from a broad phylogenetic spectrum are able to cause bovine mastitis. Transcriptomic characterization facilitates our understanding of host-pathogen relations and provides mechanisti...

  20. Treatment with eCG decreases the vascular density and increases the glandular density of the bovine uterus.

    PubMed

    Mona e Pinto, J; Pavanelo, V; Alves de Fátima, L; Medeiros de Carvalho Sousa, L M; Pacheco Mendes, G; Machado Ferreira, R; Ayres, H; Sampaio Baruselli, P; Palma Rennó, F; de Carvallo Papa, P

    2014-06-01

    The uterus plays an essential role in mammalian reproduction and is a target of several hormonal protocols used to improve fertility in cattle. Many studies highlighted the importance of eCG treatment following fixed-time artificial insemination in improving follicular growth, ovulation and pregnancy rates in cattle. Moreover, eCG has been implicated in angiogenesis, leading to important changes in uterine blood flow and vascularisation. However, there is still a lack of information regarding the specific alterations induced by eCG upon glandular and vascular characteristics of bovine uterus. To investigate the influence of eCG on: uterine thickness and area; uterine artery diameter and area; uterine vascular and gland density; and the expression of the VEGFA-system, the uteri of crossbred beef cows were collected. All cows were submitted to follicular wave emergence synchronization. On day four of protocol, cows submitted to superovulation (n = 6) received 2000 IU eCG, on day eight, after expected follicular deviation, cows submitted to stimulatory treatment (n = 5) received 400 IU eCG. Control cows (n = 5) did not receive eCG. On day five po cows were subjected to ultrassonographic evaluation and slaughtered for uterine tissue sampling on day six po. Uterine vessels and glands were quantified by the counting point stereological method. The VEGFA-system was localized in different cellular types, showing no qualitative or quantitative differences in the site of expression or the intensity of the positive signal among the groups. Vascular density was decreased in the endometrium of stimulated and myometrium of superovulated cows compared with the control ones, which showed higher vascular density in the myometrium and endometrium of the ipsilateral uterine horn. The uterine gland density was higher in superovulated compared with stimulated and control cows. Thus, we can infer that stimulatory or superovulatory treatments with eCG influence the vascular

  1. Estimation of mean glandular dose for contrast enhanced digital mammography: factors for use with the UK, European and IAEA breast dosimetry protocols.

    PubMed

    Dance, D R; Young, K C

    2014-05-07

    The UK, European and IAEA protocols for breast dosimetry in mammography use tabulations of conversion factors, which relate measurements of incident air kerma to the mean glandular dose to the breast. To supplement the existing tabulations, a Monte Carlo computer program has been used to calculate conversion factors for the high-energy spectra used for contrast enhanced digital mammography. The calculations were made for the x-ray spectra from a tungsten target (tube voltage range 40-50 kV) filtered by 0.28, 0.30 and 0.32 mm of copper, and from molybdenum and rhodium targets (tube voltage range 40-49 kV), each filtered by 0.30 mm of copper. The g-factors for all of these spectra were plotted for each breast thickness as a function of half value layer (HVL) and were found to lie on smooth curves within 0.3%. These reflect the fact that the characteristic x-rays present in the spectra from molybdenum and rhodium are heavily filtered and all the spectra are essentially Bremsstrahlung. As a consequence, the s-factor previously used in the dosimetry protocols to adjust for different target/filter combinations can be taken as unity for all of the spectra considered. Tables of g-factors and c-factors are provided for breast thicknesses in the range 20-110 mm and HVLs in the range 2.4-3.6 mm of aluminium. The tables of c-factors are given for breast glandularities in the range 0.1%-100% and for typical glandularities for women in the age bands 40-49 and 50-64 attending the UK national breast screening programme.

  2. Quantitation of glandular gastric changes in rats given a proton pump inhibitor for 3 months with emphasis on sampling scheme selection.

    PubMed

    White, S L; Smith, W C; Fisher, L F; Gatlin, C L; Hanasono, G K; Jordan, W H

    1998-01-01

    Proton pump inhibitors and H2-receptor antagonists suppress gastric acid secretion and secondarily induce hypergastrinemia. Sustained hypergastrinemia has a trophic effect on stomach fundic mucosa, including enterochromaffin-like (ECL) cell hypertrophy and hyperplasia. Histomorphometric quantitation of the pharmacologic gastric effects was conducted on 10 male and 10 female rats treated orally with LY307640 sodium, a proton pump inhibitor, at daily doses of 25, 60, 130, or 300 mg/kg for 3 mo. Histologic sections of glandular stomach, stained for chromogranin A, were evaluated by image analysis to determine stomach mucosal thickness, mucosal and nonmucosal (submucosa and muscularis) area, gastric glandular area, ECL cell number/area and cross-sectional area. Total mucosal and nonmucosal tissue volumes per animal were derived from glandular stomach volumetric and area data. Daily oral doses of compound LY307640 sodium caused slight to moderate dose-related mucosal hypertrophy and ECL cell hypertrophy and hyperplasia in all treatment groups as compared with controls. All observed effects were prominent in both sexes but were generally greater in females. The morphometric sampling schemes were explored to optimize the data collection efficiency for future studies. A comparison between the sampling schemes used in this study and alternative schemes was conducted by estimating the probability of detecting a specific percentage of change between the male control and high-dose groups based on Tukey's trend test. The sampling scheme analysis indicated that mucosal thickness and mass had been oversampled. ECL cell density quantitation efficiency would have been increased by sampling the basal mucosa only for short-term studies. The ECL cell size sampling scheme was deemed appropriate for this type of study.

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

    PubMed Central

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

    2015-01-01

    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. PMID:26133641

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

    PubMed

    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

  5. Diversity and dynamics of the Drosophila transcriptome

    PubMed Central

    Boley, Nathan; Eisman, Robert; May, Gemma E.; Stoiber, Marcus H.; Duff, Michael O.; Booth, Ben W.; Wen, Jiayu; Park, Soo; Suzuki, Ana Maria; Wan, Kenneth H.; Yu, Charles; Zhang, Dayu; Carlson, Joseph W.; Cherbas, Lucy; Eads, Brian D.; Miller, David; Mockaitis, Keithanne; Roberts, Johnny; Davis, Carrie A.; Frise, Erwin; Hammonds, Ann S.; Olson, Sara; Shenker, Sol; Sturgill, David; Samsonova, Anastasia A.; Weiszmann, Richard; Robinson, Garret; Hernandez, Juan; Andrews, Justen; Bickel, Peter J.; Carninci, Piero; Cherbas, Peter; Gingeras, Thomas R.; Hoskins, Roger A.; Kaufman, Thomas C.; Lai, Eric C.; Oliver, Brian; Perrimon, Norbert

    2014-01-01

    Animal transcriptomes are dynamic, each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. We identified new genes, transcripts, and proteins using poly(A)+ RNA sequence from Drosophila melanogaster cultured cell lines, dissected organ systems, and environmental perturbations. We found a small set of mostly neural-specific genes has the potential to encode thousands of transcripts each through extensive alternative promoter usage and RNA splicing. The magnitudes of splicing changes are larger between tissues than between developmental stages, and most sex-specific splicing is gonad-specific. Gonads express hundreds of previously unknown coding and long noncoding RNAs (lncRNAs) some of which are antisense to protein-coding genes and produce short regulatory RNAs. Furthermore, previously identified pervasive intergenic transcription occurs primarily within newly identified introns. The fly transcriptome is substantially more complex than previously recognized arising from combinatorial usage of promoters, splice sites, and polyadenylation sites. PMID:24670639

  6. Transcriptomics analysis and human preimplantation development.

    PubMed

    Freour, Thomas; Vassena, Rita

    2016-10-17

    The study of oocyte and preimplantation embryo biology has been regarded with great curiosity throughout scientific history, but it is not until the development of robust methods for in vitro observation and manipulation of animal gametes that developmental biology has flourished as a discipline. By far the biggest technical challenge in studying transcription in oocytes and early embryo has been the necessity of developing techniques that retain a high level of accuracy when starting from small amount of material. The objective of this narrative review is to summarize the knowledge gained about the embryonic preimplantation period in the human species from transcriptomics experiments, and to discuss technical limitations and solutions to the study of transcriptomics in these samples.

  7. Oscillating Transcriptome during Rice-Magnaporthe Interaction.

    PubMed

    Sharma, T R; Das, Alok; Thakur, Shallu; Devanna, B N; Singh, Pankaj Kumar; Jain, Priyanka; Vijayan, Joshitha; Kumar, Shrawan

    2016-01-01

    Rice blast disease caused by the fungus, Magnaporthe oryzae, is one of the most devastating diseases of rice. Deciphering molecular mechanism of host-pathogen interactions is of great importance in devising disease management strategies. Transcription being the first step for gene regulation in eukaryotes, basic understanding of the transcriptome is sine qua non for devising effective management strategy. The availability of genome sequences of rice and M. oryzae has facilitated the process to a large extent. The current review summarizes recent understanding of rice-blast pathosystem, application of transcriptomics approaches to understand the interactions employing different platforms, major determinants in the interaction and possibility of using certain candidate for conditioning enhanced disease resistance (Effector Triggered Immunity and PAMP Triggered Immunity) and downstream signalling in rice. A better understanding of the interaction elements and effective strategies hold potential to reduce yield losses in rice caused by M. oryzae.

  8. Regulation of the Arabidopsis defense transcriptome.

    PubMed

    Eulgem, Thomas

    2005-02-01

    Transcriptional re-programming is a key step of plant defense in response to pathogen recognition. Microarray analyses combined with genetic and biochemical approaches are now enabling us to study basic principles and details of regulatory mechanisms controlling the defense transcriptome in Arabidopsis. Recent results show that signaling pathways used by different defense systems converge and target overlapping gene sets. Furthermore, a quantitative mechanism common to multiple defense systems modulates transcript levels of these defense-associated genes. Most importantly, some transcription factors have been proven to play a pivotal role in disease resistance. Regulatory circuits linking signaling and gene regulation are emerging, suggesting that a complex interplay of transcriptional activators and repressors fine-tunes expression of the defense transcriptome.

  9. Transcriptomic studies on liver toxicity of acetaminophen.

    PubMed

    Toska, Endrit; Zagorsky, Robert; Figler, Bryan; Cheng, Feng

    2014-09-01

    Acetaminophen is widely used as a pain reliever and to reduce fever. At high doses, it can cause severe hepatotoxicity. Acetaminophen overdose has become the leading cause of acute liver failure in the US. The mechanisms for acetaminophen-induced liver injury are unclear. Transcriptomic studies can identify the changes in expression of thousands of genes when exposed to supratherapeutic doses of acetaminophen. These studies elucidated the mechanism of acetaminophen-induced hepatotoxicity and also provide insight into future development of diagnosis and treatment options for acetaminophen-induced acute liver failure. The following is a brief overview of some recent transcriptomic studies and gene-expression-based prediction models on liver toxicity induced by acetaminophen.

  10. Blood Transcriptomics and Metabolomics for Personalized Medicine

    DTIC Science & Technology

    2015-10-31

    online 31 October 2015 Keywords: Transcriptomics Metabolomics Blood systems biology Personalized medicine Data integrationMolecular 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...article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Contents1. An overdue review of “blood systems biology

  11. Introduction to Sequencing the Brain Transcriptome

    PubMed Central

    Hitzemann, Robert; Darakjian, Priscila; Walter, Nikki; Iancu, Ovidiu Dan; Searles, Robert; McWeeney, Shannon

    2016-01-01

    High-throughput next-generation sequencing is now entering its second decade. However, it was not until 2008 that the first report of sequencing the brain transcriptome appeared (Mortazavi, Williams, Mccue, Schaeffer, & Wold, 2008). These authors compared short-read RNA-Seq data for mouse whole brain with microarray results for the same sample and noted both the advantages and disadvantages of the RNA-Seq approach. While RNA-Seq provided exon level resolution, the majority of the reads were provided by a small proportion of highly expressed genes and the data analysis was exceedingly complex. Over the past 6 years, there have been substantial improvements in both RNA-Seq technology and data analysis. This volume contains 11 chapters that detail various aspects of sequencing the brain transcriptome. Some of the chapters are very methods driven, while others focus on the use of RNA-Seq to study such diverse areas as development, schizophrenia, and drug abuse. This chapter briefly reviews the transition from microarrays to RNA-Seq as the preferred method for analyzing the brain transcriptome. Compared with microarrays, RNA-Seq has a greater dynamic range, detects both coding and noncoding RNAs, is superior for gene network construction, detects alternative spliced transcripts, and can be used to extract genotype information, e.g., nonsynonymous coding single nucleotide polymorphisms. RNA-Seq embraces the complexity of the brain transcriptome and provides a mechanism to understand the underlying regulatory code; the potential to inform the brain–behavior–disease relationships is substantial. PMID:25172469

  12. The avian transcriptome response to malaria infection.

    PubMed

    Videvall, Elin; Cornwallis, Charlie K; Palinauskas, Vaidas; Valkiūnas, Gediminas; Hellgren, Olof

    2015-05-01

    Malaria parasites are highly virulent pathogens which infect a wide range of vertebrates. Despite their importance, the way different hosts control and suppress malaria infections remains poorly understood. With recent developments in next-generation sequencing techniques, however, it is now possible to quantify the response of the entire transcriptome to infections. We experimentally infected Eurasian siskins (Carduelis spinus) with avian malaria parasites (Plasmodium ashfordi), and used high-throughput RNA-sequencing to measure the avian transcriptome in blood collected before infection (day 0), during peak parasitemia (day 21 postinfection), and when parasitemia was decreasing (day 31). We found considerable differences in the transcriptomes of infected and uninfected individuals, with a large number of genes differentially expressed during both peak and decreasing parasitemia stages. These genes were overrepresented among functions involved in the immune system, stress response, cell death regulation, metabolism, and telomerase activity. Comparative analyses of the differentially expressed genes in our study to those found in other hosts of malaria (human and mouse) revealed a set of genes that are potentially involved in highly conserved evolutionary responses to malaria infection. By using RNA-sequencing we gained a more complete view of the host response, and were able to pinpoint not only well-documented host genes but also unannotated genes with clear significance during infection, such as microRNAs. This study shows how the avian blood transcriptome shifts in response to malaria infection, and we believe that it will facilitate further research into the diversity of molecular mechanisms that hosts utilize to fight malaria infections.

  13. Cooperative role between p21cip1/waf1 and p27kip1 in premature senescence in glandular proliferative lesions in mice.

    PubMed

    García-Fernández, R A; García-Palencia, P; Suarez, C; Sánchez, M A; Gil-Gómez, G; Sánchez, B; Rollán, E; Martín-Caballero, J; Flores, J M

    2014-03-01

    Cellular senescence has been considered a novel target for cancer therapy. It has also been pointed out that p21(cip1/waf1) and p27(kip1) cyclin-dependent kinase inhibitors (CKIs) play a role in cellular senescence in some tumor types. Therefore, in order to address the possibility of a cooperative role between p21 and p27 proteins in senescence in vivo we analyzed cellular senescence in spontaneous glandular proliferative lesions (adrenal, thyroid and pituitary glands) in a double-KO mice model, using γH2AX, p53, p16, PTEN and Ki67 as senescence markers. The results obtained showed that p21p27 double-null mice had the lowest number of γH2AX positive cells in glandular hyperplasias and benign tumors. Also, in this group, Ki67 proliferation index correlated with a lower immunohistochemical expression of γH2AX and p53. The expression of p16 and PTEN do not seem to cause synergism of senescence in the benign lesions analyzed in p21p27 double-KO mice. These observations suggest an intrinsic cooperation between p21 and p27 CKIs in the activation of stress-induced cellular senescence and tumor progression in vivo, which would be a physiological mechanism to prevent tumor cell proliferation.

  14. Two new non-spiny Solanum (Solanaceae) from the Gran Chaco Americano and a key for the herbaceous glandular-pubescent solanums from the region.

    PubMed

    Särkinen, Tiina; Knapp, Sandra

    2016-01-01

    The Gran Chaco Americano is a major savanna woodland system in South America that harbours great plant and animal diversity. Two new herbaceous species of the Morelloid clade of Solanum (largely corresponding to the traditional Solanum section Solanum) are described here from the Bolivian Chaco. Both species are morphologically similar to a group of related species with glandular pubescence and enlarged, foliaceous calyces that includes Solanum atriplicifolium Gillies ex Nees, Solanum nitidibaccatum Bitter, Solanum physalifolium Rusby, Solanum sarrachoides Sendtn. and Solanum tweedianum Hook. Solanum woodii Särkinen & S.Knapp, sp. nov. is unusual in the Morelloid clade in having tapering anthers on short filaments, and is superficially similar to the unrelated Solanum anomalostemon S.Knapp & M.Nee from dry forests in Peru. Solanum michaelis Särkinen & S.Knapp, sp. nov. is distinct in its enlarged calyx with a short tube and long lobes that apparently reflex at fruit maturity. Both new taxa are illustrated, their conservation status assessed, and their distributions mapped. We also provide a key to the glandular-pubescent herbaceous Solanum species of the Chaco vegetation to aid in identification of these taxa.

  15. Apoptotic depletion of infiltrating mucosal lymphocytes associated with Fas ligand expression by Helicobacter pylori-infected gastric mucosal epithelium: human glandular stomach as a site of immune privilege.

    PubMed

    Koyama, S

    2000-04-01

    H. pylori infection almost invariably results in chronic gastritis, but only a proportion of patients develops severe destruction of epithelial glandular structure or peptic ulcer. To confirm the recent data obtained in testis and eye, showing that Fas ligand is involved in the phenomenon of "immune privilege," expression of Fas receptor and its ligand of the stomach was investigated in a panel of gastric biopsies obtained from patients H. pylori-positive (N = 42) and with H. pylori-negative (N = 18) by two-color flow cytometry. The results show that membrane-bound Fas ligand protein is constitutively expressed on freshly isolated human gastric mucosal epithelium coupled with infiltrating lymphocytes. There was significant overexpression of Fas receptor and its ligand, and a higher frequency of apoptotic cell death detected by TUNEL in epithelium and infiltrating lymphocytes in H. pylori-infected patients. These findings suggest that involvement of Fas receptor and its ligand system contributes to some extent to mucosal damage in H. pylori-associated gastritis. However, the more specific findings are apoptotic depletion of invading mucosal lymphocytes associated with Fas ligand expression by gastric epithelium. These provide the first direct quantitative evidence to support Fas receptor counterattack and/or paracrine fratricide as a mechanism of immune privilege in vivo in the H. pylori-infected glandular stomach.

  16. Yield and forage quality of glandular-haired alfalfa under alfalfa weevil (Coleoptera: Curculionidae) and potato leafhopper (Hemiptera: Cicadellidae) pest pressure in Virginia.

    PubMed

    Dellinger, Theresa A; Youngman, Roger R; Laub, Curt A; Brewster, Carlyle C; Kuhar, Thomas P

    2006-08-01

    Cultivars of glandular-haired alfalfa, Medicago sativa L., such as '54H69', are currently available and marketed as being resistant to potato leafhopper, Empoasca fabae (Harris) (Hemiptera: Cicadellidae). 54H69 and a standard, nonglandular-haired alfalfa 'Choice' were evaluated at two locations in Virginia over a 3-yr period. Dry matter yields and concentrations of crude protein and acid detergent fiber were compared at the first, second, and third harvests. Overall, the two cultivars produced similar dry matter yields of comparable forage quality in the absence of insecticides at both locations in each year. Untreated 54H69 did not produce greater dry matter yields than untreated Choice under either light or heavier potato leafhopper pest pressure. Concentrations of crude protein did not vary between the two cultivars at any harvest. Some differences in concentrations of acid detergent fiber were detected between cultivars, but these differences were not consistent among years, harvests, or between locations. Further comparisons between untreated 54H69 and treated Choice were made, but few significant differences were detected in dry matter yields or forage quality. An economic analysis for the study indicated that a grower planting 54H69 would realize less net revenue than a grower planting Choice, largely because of the seed premium for the glandular-haired cultivar and the evident need to treat 54H69 with insecticide for control of alfalfa weevil, Hypera postica (Gyllenhal) (Coleoptera: Curculionidae), and potato leafhopper.

  17. Two new non-spiny Solanum (Solanaceae) from the Gran Chaco Americano and a key for the herbaceous glandular-pubescent solanums from the region

    PubMed Central

    Särkinen, Tiina; Knapp, Sandra

    2016-01-01

    Abstract The Gran Chaco Americano is a major savanna woodland system in South America that harbours great plant and animal diversity. Two new herbaceous species of the Morelloid clade of Solanum (largely corresponding to the traditional Solanum section Solanum) are described here from the Bolivian Chaco. Both species are morphologically similar to a group of related species with glandular pubescence and enlarged, foliaceous calyces that includes Solanum atriplicifolium Gillies ex Nees, Solanum nitidibaccatum Bitter, Solanum physalifolium Rusby, Solanum sarrachoides Sendtn. and Solanum tweedianum Hook. Solanum woodii Särkinen & S.Knapp, sp. nov. is unusual in the Morelloid clade in having tapering anthers on short filaments, and is superficially similar to the unrelated Solanum anomalostemon S.Knapp & M.Nee from dry forests in Peru. Solanum michaelis Särkinen & S.Knapp, sp. nov. is distinct in its enlarged calyx with a short tube and long lobes that apparently reflex at fruit maturity. Both new taxa are illustrated, their conservation status assessed, and their distributions mapped. We also provide a key to the glandular-pubescent herbaceous Solanum species of the Chaco vegetation to aid in identification of these taxa. PMID:28127235

  18. p53 regulates the cardiac transcriptome

    PubMed Central

    Mak, Tak W.; Hauck, Ludger; Grothe, Daniela; Billia, Filio

    2017-01-01

    The tumor suppressor Trp53 (p53) inhibits cell growth after acute stress by regulating gene transcription. The mammalian genome contains hundreds of p53-binding sites. However, whether p53 participates in the regulation of cardiac tissue homeostasis under normal conditions is not known. To examine the physiologic role of p53 in adult cardiomyocytes in vivo, Cre-loxP–mediated conditional gene targeting in adult mice was used. Genome-wide transcriptome analyses of conditional heart-specific p53 knockout mice were performed. Genome-wide annotation and pathway analyses of >5,000 differentially expressed transcripts identified many p53-regulated gene clusters. Correlative analyses identified >20 gene sets containing more than 1,000 genes relevant to cardiac architecture and function. These transcriptomic changes orchestrate cardiac architecture, excitation-contraction coupling, mitochondrial biogenesis, and oxidative phosphorylation capacity. Interestingly, the gene expression signature in p53-deficient hearts confers resistance to acute biomechanical stress. The data presented here demonstrate a role for p53, a previously unrecognized master regulator of the cardiac transcriptome. The complex contributions of p53 define a biological paradigm for the p53 regulator network in the heart under physiological conditions. PMID:28193895

  19. Reshaping of the maize transcriptome by domestication

    PubMed Central

    Swanson-Wagner, Ruth; Briskine, Roman; Schaefer, Robert; Hufford, Matthew B.; Ross-Ibarra, Jeffrey; Myers, Chad L.; Tiffin, Peter; Springer, Nathan M.

    2012-01-01

    Through domestication, humans have substantially altered the morphology of Zea mays ssp. parviglumis (teosinte) into the currently recognizable maize. This system serves as a model for studying adaptation, genome evolution, and the genetics and evolution of complex traits. To examine how domestication has reshaped the transcriptome of maize seedlings, we used expression profiling of 18,242 genes for 38 diverse maize genotypes and 24 teosinte genotypes. We detected evidence for more than 600 genes having significantly different expression levels in maize compared with teosinte. Moreover, more than 1,100 genes showed significantly altered coexpression profiles, reflective of substantial rewiring of the transcriptome since domestication. The genes with altered expression show a significant enrichment for genes previously identified through population genetic analyses as likely targets of selection during maize domestication and improvement; 46 genes previously identified as putative targets of selection also exhibit altered expression levels and coexpression relationships. We also identified 45 genes with altered, primarily higher, expression in inbred relative to outcrossed teosinte. These genes are enriched for functions related to biotic stress and may reflect responses to the effects of inbreeding. This study not only documents alterations in the maize transcriptome following domestication, identifying several genes that may have contributed to the evolution of maize, but highlights the complementary information that can be gained by combining gene expression with population genetic analyses. PMID:22753482

  20. Transcriptome Dynamics during Maize Endosperm Development

    PubMed Central

    Feng, Jiaojiao; Xu, Shutu; Wang, Lei; Li, Feifei; Li, Yibo; Zhang, Renhe; Zhang, Xinghua; Xue, Jiquan; Guo, Dongwei

    2016-01-01

    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. PMID:27695101

  1. In vivo rat glandular stomach and colon micronucleus tests: Kinetics of micronucleated cells, apoptosis, and cell proliferation in the target tissues after a single oral administration of stomach- or colon-carcinogens.

    PubMed

    Ohyama, Wakako; Okada, Emiko; Fujiishi, Yohei; Narumi, Kazunori; Yasutake, Nobuyoshi

    2013-08-15

    We have developed in vivo micronucleus (MN) tests by using an epithelial cell suspension isolated from the glandular stomach and colon of rodents. In the present study, our aim was to demonstrate the characteristics of the glandular stomach and colon MN tests by analyzing time-related changes in MN frequencies, apoptosis and cell proliferation in the target tissues of male CD (SD) rats that were orally administered a single dose of a stomach- or colon-targeted carcinogen, i.e., N-nitroso-N-methylurea (MNU) or N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) for the stomach and 1,2-dimethylhydrazine dihydrochloride (DMH) for the colon. After treatment, the MN frequencies significantly increased in the respective target tissues, peaking at 48-96h and decreasing afterwards. The time-response pattern could be explained by the epithelial cell turnover confirmed with a labeling experiment using the thymidine analog, 5-ethynyl-2'-deoxyuridine (EdU). In the study with MNU and DMH, we also prepared paraffin sections of the respective target tissues for the immunohistochemical evaluation of apoptosis and cell proliferation. The incidence of apoptosis increased in the early phase (6 and/or 24h) after treatment, and then decreased. Cell proliferation was depressed when a high incidence of apoptosis was observed, and then it recovered until 72h. MN frequencies increased with the recovery of cell proliferation occurring later than the peak apoptosis response. These results indicated that micronuclei were induced in the glandular stomach and colon epithelial cells by administration of the model chemicals. On the other hand, MNU induced significant increases of MNed cells in both the glandular stomach and bone marrow in the same rats, while MNNG did only in the glandular stomach when administered orally up to 1/4 of the LD50. These results suggest that the glandular stomach- and colon-MN tests would be useful for evaluating the genotoxicity of agents in the gastrointestinal tract.

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

    PubMed

    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 (P<0.001); however, the score distribution by marker differed significantly only in GD (P=0.006) in which, compared with the other markers, p16 showed more often a 3+ pattern. Our study shows that p16, Ki-67, and ProEX C may be helpful for the diagnosis of glandular lesions of the cervix 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.

  3. Nemertean Toxin Genes Revealed through Transcriptome Sequencing

    PubMed Central

    Whelan, Nathan V.; Kocot, Kevin M.; Santos, Scott R.; Halanych, Kenneth M.

    2014-01-01

    Nemerteans are one of few animal groups that have evolved the ability to utilize toxins for both defense and subduing prey, but little is known about specific nemertean toxins. In particular, no study has identified specific toxin genes even though peptide toxins are known from some nemertean species. Information about toxin genes is needed to better understand evolution of toxins across animals and possibly provide novel targets for pharmaceutical and industrial applications. We sequenced and annotated transcriptomes of two free-living and one commensal nemertean and annotated an additional six publicly available nemertean transcriptomes to identify putative toxin genes. Approximately 63–74% of predicted open reading frames in each transcriptome were annotated with gene names, and all species had similar percentages of transcripts annotated with each higher-level GO term. Every nemertean analyzed possessed genes with high sequence similarities to known animal toxins including those from stonefish, cephalopods, and sea anemones. One toxin-like gene found in all nemerteans analyzed had high sequence similarity to Plancitoxin-1, a DNase II hepatotoxin that may function well at low pH, which suggests that the acidic body walls of some nemerteans could work to enhance the efficacy of protein toxins. The highest number of toxin-like genes found in any one species was seven and the lowest was three. The diversity of toxin-like nemertean genes found here is greater than previously documented, and these animals are likely an ideal system for exploring toxin evolution and industrial applications of toxins. PMID:25432940

  4. Transcriptome analysis of sika deer in China.

    PubMed

    Jia, Bo-Yin; Ba, Heng-Xing; Wang, Gui-Wu; Yang, Ying; Cui, Xue-Zhe; Peng, Ying-Hua; Zheng, Jun-Jun; Xing, Xiu-Mei; Yang, Fu-He

    2016-10-01

    Sika deer is of great commercial value because their antlers are used in tonics and alternative medicine and their meat is healthy and delicious. The goal of this study was to generate transcript sequences from sika deer for functional genomic analyses and to identify the transcripts that demonstrate tissue-specific, age-dependent differential expression patterns. These sequences could enhance our understanding of the molecular mechanisms underlying sika deer growth and development. In the present study, we performed de novo transcriptome assembly and profiling analysis across ten tissue types and four developmental stages (juvenile, adolescent, adult, and aged) of sika deer, using Illumina paired-end tag (PET) sequencing technology. A total of 1,752,253 contigs with an average length of 799 bp were generated, from which 1,348,618 unigenes with an average length of 590 bp were defined. Approximately 33.2 % of these (447,931 unigenes) were then annotated in public protein databases. Many sika deer tissue-specific, age-dependent unigenes were identified. The testes have the largest number of tissue-enriched unigenes, and some of them were prone to develop new functions for other tissues. Additionally, our transcriptome revealed that the juvenile-adolescent transition was the most complex and important stage of the sika deer life cycle. The present work represents the first multiple tissue transcriptome analysis of sika deer across four developmental stages. The generated data not only provide a functional genomics resource for future biological research on sika deer but also guide the selection and manipulation of genes controlling growth and development.

  5. Transcriptomics exposes the uniqueness of parasitic plants.

    PubMed

    Ichihashi, Yasunori; Mutuku, J Musembi; Yoshida, Satoko; Shirasu, Ken

    2015-07-01

    Parasitic plants have the ability to obtain nutrients directly from other plants, and several species are serious biological threats to agriculture by parasitizing crops of high economic importance. The uniqueness of parasitic plants is characterized by the presence of a multicellular organ called a haustorium, which facilitates plant-plant interactions, and shutting down or reducing their own photosynthesis. Current technical advances in next-generation sequencing and bioinformatics have allowed us to dissect the molecular mechanisms behind the uniqueness of parasitic plants at the genome-wide level. In this review, we summarize recent key findings mainly in transcriptomics that will give us insights into the future direction of parasitic plant research.

  6. [Ultrastructural changes and regeneration of the endocrine apparatus of the human gastric mucosal glandular epithelium in patients with chronic erosive gastritis].

    PubMed

    Ivanova, V F; Puzyrev, A A; Draĭ, R V

    2010-01-01

    The aim of this investigation was to study the structure and regeneration of the endocrine apparatus of the human gastric mucosal glandular epithelium. Using electron microscopy, the mucosal biopsy specimens obtained from 14 patients with chronic erosive Helicobacter pylori-associated gastritis, were studied. The most pronounced changes were seen both in the numbers and ultrastructure of G- and P-endocrinocytes. The changes were detected in the nucleus structure, endocrine granule and polysome content, and he mitochondrial structure. The regeneration of the endocrine cells took place through the differentiation of the committed precursors via the "agranular" cell stage, transformation of the exocrine cells into the endocrine ones, and as a result of the formation of the epithelial cords on the erosion surfaces that consisted of the cells in diverse differentiation stages (from the undifferentiated to specialized cells of all the endocrine and exocrine types).

  7. Mean glandular doses in mammography: a comparison of values displayed by a mammography unit with in-house values, both using the method proposed by Dance.

    PubMed

    Pasicz, Katarzyna; Fabiszewska, Ewa; Grabska, Iwona; Skrzyński, Witold

    2016-09-01

    The purpose of this work is to compare the mean glandular dose (MGD) displayed by the mammography system and the MGD calculated according to the method proposed by Dance for women. This study also attempts to analyse whether the relationship between the calculated and the displayed values is constant and what factors influence this relationship. Material for this study included data from 1200 exposures (i.e. six series; each series consisting of 200 exposures) performed with one full-field digital mammography unit. Based on collected parameters of exposures, values of the MGD for individual mammography examinations were calculated according to the methods proposed by Dance. Obtained values of the MGD were compared with the values displayed by the mammography system. The MGD displayed by the mammography system and the MGD calculated according to the method proposed by Dance for women are significantly different. This result emphasises the importance of verifying MGD values for patient radiation protection, particularly after machine servicing.

  8. Chemopreventive Activity of MGN-3/Biobran Against Chemical Induction of Glandular Stomach Carcinogenesis in Rats and Its Apoptotic Effect in Gastric Cancer Cells.

    PubMed

    Badr El-Din, Nariman K; Abdel Fattah, Salma M; Pan, Deyu; Tolentino, Lucilene; Ghoneum, Mamdooh

    2016-12-01

    In the current study, we investigated the chemopreventive activity of arabinoxylan rice bran, MGN-3/Biobran, against chemical induction of glandular stomach carcinogenesis in rats. Gastric cancer was induced by carcinogen methylnitronitrosoguanidine (MNNG), and rats received MNNG alone or MNNG plus Biobran (40 mg/kg body weight) for a total of 8 months. Averaged results from 2 separate readings showed that exposure to MNNG plus Biobran caused gastric dysplasia and cancer (adenocarcinoma) in 4.5/12 rats (9/24 readings, 37.5%), with 3.5/12 rats (7/24 readings, 29.2%) showing dysplasia and 1/12 rats (8.3%) developing adenocarcinoma. In contrast, in rats treated with MNNG alone, 8/10 (80%) developed dysplasia and adenocarcinoma, with 6/10 rats (60%) showing dysplasia and 2/10 rats (20%) developing adenocarcinoma. The effect of combining both agents was also associated with significant suppression of the expression of the tumor marker Ki-67 and remarkable induction in the apoptotic gastric cancer cells via mitochondrial-dependent pathway as indicated by the upregulation in p53 expression, Bax expression, downregulation in Bcl-2 expression, an increase in Bax/Bcl-2 ratio, and an activation of caspase-3. In addition, Biobran treatment induced cell-cycle arrest in the subG1 phase, where the hypodiploid cell population was markedly increased. Moreover, Biobran treatment protected rats against MNNG-induced significant decrease in lymphocyte levels. We conclude that Biobran provides protection against chemical induction of glandular stomach carcinogenesis in rats and may be useful for the treatment of human patients with gastric cancer.

  9. Ticks' response to feeding on host immunized with glandular extracts of Rhipicephalus sanguineus females fed for 2, 4, and 6 days. I. Inactivity or early degeneration of salivary glands?

    PubMed

    Furquim, Karim Christina Scopinho; Mathias, Maria Izabel Camargo; Hebling, Letícia Maria Gráballos Ferraz; Roma, Gislaine Cristina; Bechara, Gervásio Henrique

    2011-07-01

    The present study histologically analyzed the salivary glands of Rhipicephalus sanguineus females fed for 2, 4, and 6 days in hosts which had been previously immunized with glandular extracts obtained from females from this same species in different periods of feeding, having as main objective verify the action of these extracts in the secretor cycle of these glands. For this, glandular extract of females fed for 2 days (SGE2), glandular extract of females fed for 4 days (SGE4), and glandular extract of females fed for 6 days (SGE6) extracts were obtained from salivary glands of R. sanguineus females fed for 2, 4, and 6 days respectively. Then, New Zealand White naive rabbits were inoculated either with extracts (test group = TG), or with a mixture of phosphate buffer and Freund's complete adjuvant (control group 2 = CG2). Each inoculated rabbit (TG and CG2) and non-inoculated (control group 1 = CG1) was posteriorly infested with 15 couples of fasting R. sanguineus from which the salivary glands had been collected from females fed for 2, 4, and 6 days. The results revealed that the resistance the hosts had acquired by the immunization with the extracts affected differently the secretory activity of the glandular cells. It was verified that the resistance to SGE2 and SGE4 extracts acted in the cells of acini II and III, being c1 and c5 from II and d from III inactivated due to the action of SGE2 and c1 and c4 from II and f from III inactivated by the action of SGE4. As for the resistance to SGE6 the effect was only on cells of acini II (c1, c3 e c4), which were also inactivated. In addition, the hosts' resistance to SGE2-SGE6 extracts made the degenerative process earlier in comparison to CG1. On the other hand, the resistance to the extracts did not influence the characteristics of the degenerative process normally found in salivary glands. The assynchronism of the degenerative process was maintained-acini III were always the most affected and I the

  10. 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

    SciTech Connect

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

    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.

  11. Transcriptome marker diagnostics using big data.

    PubMed

    Han, Henry; Liu, Ying

    2016-02-01

    The big omics data are challenging translational bioinformatics in an unprecedented way for its complexities and volumes. How to employ big omics data to achieve a rivalling-clinical, reproducible disease diagnosis from a systems approach is an urgent problem to be solved in translational bioinformatics and machine learning. In this study, the authors propose a novel transcriptome marker diagnosis to tackle this problem using big RNA-seq data by viewing whole transcriptome as a profile marker systematically. The systems diagnosis not only avoids the reproducibility issue of the existing gene-/network-marker-based diagnostic methods, but also achieves rivalling-clinical diagnostic results by extracting true signals from big RNA-seq data. Their method demonstrates a better fit for personalised diagnostics by attaining exceptional diagnostic performance via using systems information than its competitive methods and prepares itself as a good candidate for clinical usage. To the best of their knowledge, it is the first study on this topic and will inspire the more investigations in big omics data diagnostics.

  12. Comparative analysis of de novo transcriptome assembly.

    PubMed

    Clarke, Kaitlin; Yang, Yi; Marsh, Ronald; Xie, Linglin; Zhang, Ke K

    2013-02-01

    The fast development of next-generation sequencing technology presents a major computational challenge for data processing and analysis. A fast algorithm, de Bruijn graph has been successfully used for genome DNA de novo assembly; nevertheless, its performance for transcriptome assembly is unclear. In this study, we used both simulated and real RNA-Seq data, from either artificial RNA templates or human transcripts, to evaluate five de novo assemblers, ABySS, Mira, Trinity, Velvet and Oases. Of these assemblers, ABySS, Trinity, Velvet and Oases are all based on de Bruijn graph, and Mira uses an overlap graph algorithm. Various numbers of RNA short reads were selected from the External RNA Control Consortium (ERCC) data and human chromosome 22. A number of statistics were then calculated for the resulting contigs from each assembler. Each experiment was repeated multiple times to obtain the mean statistics and standard error estimate. Trinity had relative good performance for both ERCC and human data, but it may not consistently generate full length transcripts. ABySS was the fastest method but its assembly quality was low. Mira gave a good rate for mapping its contigs onto human chromosome 22, but its computational speed is not satisfactory. Our results suggest that transcript assembly remains a challenge problem for bioinformatics society. Therefore, a novel assembler is in need for assembling transcriptome data generated by next generation sequencing technique.

  13. Gingival Tissue Transcriptomes Identify Distinct Periodontitis Phenotypes

    PubMed Central

    Kebschull, M.; Demmer, R.T.; Grün, B.; Guarnieri, P.; Pavlidis, P.; Papapanou, P.N.

    2014-01-01

    The currently recognized principal forms of periodontitis—chronic and aggressive—lack an unequivocal, pathobiology-based foundation. We explored whether gingival tissue transcriptomes can serve as the basis for an alternative classification of periodontitis. We used cross-sectional whole-genome gene expression data from 241 gingival tissue biopsies obtained from sites with periodontal pathology in 120 systemically healthy nonsmokers with periodontitis, with available data on clinical periodontal status, subgingival microbial profiles, and serum IgG antibodies to periodontal microbiota. Adjusted model-based clustering of transcriptomic data using finite mixtures generated two distinct clusters of patients that did not align with the current classification of chronic and aggressive periodontitis. Differential expression profiles primarily related to cell proliferation in cluster 1 and to lymphocyte activation and unfolded protein responses in cluster 2. Patients in the two clusters did not differ with respect to age but presented with distinct phenotypes (statistically significantly different whole-mouth clinical measures of extent/severity, subgingival microbial burden by several species, and selected serum antibody responses). Patients in cluster 2 showed more extensive/severe disease and were more often male. The findings suggest that distinct gene expression signatures in pathologic gingival tissues translate into phenotypic differences and can provide a basis for a novel classification. PMID:24646639

  14. Deciphering life history transcriptomes in different environments

    PubMed Central

    Etges, William J.; Trotter, Meredith V.; de Oliveira, Cássia C.; Rajpurohit, Subhash; Gibbs, Allen G.; Tuljapurkar, Shripad

    2014-01-01

    We compared whole transcriptome variation in six preadult stages and seven adult female ages in two populations of cactophilic Drosophila mojavensis reared on two host plants in order to understand how differences in gene expression influence standing life history variation. We used Singular Value Decomposition (SVD) to identify dominant trajectories of life cycle gene expression variation, performed pair-wise comparisons of stage and age differences in gene expression across the life cycle, identified when genes exhibited maximum levels of life cycle gene expression, and assessed population and host cactus effects on gene expression. Life cycle SVD analysis returned four significant components of transcriptional variation, revealing functional enrichment of genes responsible for growth, metabolic function, sensory perception, neural function, translation and aging. Host cactus effects on female gene expression revealed population and stage specific differences, including significant host plant effects on larval metabolism and development, as well as adult neurotransmitter binding and courtship behavior gene expression levels. In 3 - 6 day old virgin females, significant up-regulation of genes associated with meiosis and oogenesis was accompanied by down-regulation of genes associated with somatic maintenance, evidence for a life history tradeoff. The transcriptome of D. mojavensis reared in natural environments throughout its life cycle revealed core developmental transitions and genome wide influences on life history variation in natural populations. PMID:25442828

  15. Deciphering life history transcriptomes in different environments.

    PubMed

    Etges, William J; Trotter, Meredith V; de Oliveira, Cássia C; Rajpurohit, Subhash; Gibbs, Allen G; Tuljapurkar, Shripad

    2015-01-01

    We compared whole transcriptome variation in six pre-adult stages and seven adult female ages in two populations of cactophilic Drosophila mojavensis reared on two host plants to understand how differences in gene expression influence standing life history variation. We used singular value decomposition (SVD) to identify dominant trajectories of life cycle gene expression variation, performed pairwise comparisons of stage and age differences in gene expression across the life cycle, identified when genes exhibited maximum levels of life cycle gene expression, and assessed population and host cactus effects on gene expression. Life cycle SVD analysis returned four significant components of transcriptional variation, revealing functional enrichment of genes responsible for growth, metabolic function, sensory perception, neural function, translation and ageing. Host cactus effects on female gene expression revealed population- and stage-specific differences, including significant host plant effects on larval metabolism and development, as well as adult neurotransmitter binding and courtship behaviour gene expression levels. In 3- to 6-day-old virgin females, significant upregulation of genes associated with meiosis and oogenesis was accompanied by downregulation of genes associated with somatic maintenance, evidence for a life history trade-off. The transcriptome of D. mojavensis reared in natural environments throughout its life cycle revealed core developmental transitions and genome-wide influences on life history variation in natural populations.

  16. Transcriptome transfer produces a predictable cellular phenotype

    PubMed Central

    Sul, Jai-Yoon; Wu, Chia-wen K.; Zeng, Fanyi; Jochems, Jeanine; Lee, Miler T.; Kim, Tae Kyung; Peritz, Tiina; Buckley, Peter; Cappelleri, David J.; Maronski, Margaret; Kim, Minsun; Kumar, Vijay; Meaney, David; Kim, Junhyong; Eberwine, James

    2009-01-01

    Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function. It has been thought that differentiated postmitotic cells have their genomes hard wired, with little ability for phenotypic plasticity. Here we show that transfer of the transcriptome from differentiated rat astrocytes into a nondividing differentiated rat neuron resulted in the conversion of the neuron into a functional astrocyte-like cell in a time-dependent manner. This single-cell study permits high resolution of molecular and functional components that underlie phenotype identity. The RNA population from astrocytes contains RNAs in the appropriate relative abundances that give rise to regulatory RNAs and translated proteins that enable astrocyte identity. When transferred into the postmitotic neuron, the astrocyte RNA population converts 44% of the neuronal host cells into the destination astrocyte-like phenotype. In support of this observation, quantitative measures of cellular morphology, single-cell PCR, single-cell microarray, and single-cell functional analyses have been performed. The host-cell phenotypic changes develop over many weeks and are persistent. We call this process of RNA-induced phenotype changes, transcriptome-induced phenotype remodeling. PMID:19380745

  17. Transcriptome analysis of Ginkgo biloba kernels

    PubMed Central

    He, Bing; Gu, Yincong; Xu, Meng; Wang, Jianwen; Cao, Fuliang; Xu, Li-an

    2015-01-01

    Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics; however, genomic resources for this species are limited. In this study, we performed the first transcriptome sequencing for Ginkgo kernels at five time points using Illumina paired-end sequencing. Approximately 25.08-Gb clean reads were obtained, and 68,547 unigenes with an average length of 870 bp were generated by de novo assembly. Of these unigenes, 29,987 (43.74%) were annotated in publicly available plant protein database. A total of 3,869 genes were identified as significantly differentially expressed, and enrichment analysis was conducted at different time points. Furthermore, metabolic pathway analysis revealed that 66 unigenes were responsible for terpenoid backbone biosynthesis, with up to 12 up-regulated unigenes involved in the biosynthesis of ginkgolide and bilobalide. Differential gene expression analysis together with real-time PCR experiments indicated that the synthesis of bilobalide may have interfered with the ginkgolide synthesis process in the kernel. These data can remarkably expand the existing transcriptome resources of Ginkgo, and provide a valuable platform to reveal more on developmental and metabolic mechanisms of this species. PMID:26500663

  18. De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments

    PubMed Central

    2012-01-01

    Background Picrorhiza kurrooa Royle ex Benth. is an endangered plant species of medicinal importance. The medicinal property is attributed to monoterpenoids picroside I and II, which are modulated by temperature. The transcriptome information of this species is limited with the availability of few hundreds of expressed sequence tags (ESTs) in the public databases. In order to gain insight into temperature mediated molecular changes, high throughput de novo transcriptome sequencing and analyses were carried out at 15°C and 25°C, the temperatures known to modulate picrosides content. Results Using paired-end (PE) Illumina sequencing technology, a total of 20,593,412 and 44,229,272 PE reads were obtained after quality filtering for 15°C and 25°C, respectively. Available (e.g., De-Bruijn/Eulerian graph) and in-house developed bioinformatics tools were used for assembly and annotation of transcriptome. A total of 74,336 assembled transcript sequences were obtained, with an average coverage of 76.6 and average length of 439.5. Guanine-cytosine (GC) content was observed to be 44.6%, while the transcriptome exhibited abundance of trinucleotide simple sequence repeat (SSR; 45.63%) markers. Large scale expression profiling through "read per exon kilobase per million (RPKM)", showed changes in several biological processes and metabolic pathways including cytochrome P450s (CYPs), UDP-glycosyltransferases (UGTs) and those associated with picrosides biosynthesis. RPKM data were validated by reverse transcriptase-polymerase chain reaction using a set of 19 genes, wherein 11 genes behaved in accordance with the two expression methods. Conclusions Study generated transcriptome of P. kurrooa at two different temperatures. Large scale expression profiling through RPKM showed major transcriptome changes in response to temperature reflecting alterations in major biological processes and metabolic pathways, and provided insight of GC content and SSR markers. Analysis also identified

  19. The developmental transcriptome of Drosophila melanogaster

    SciTech Connect

    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

  20. Comparative transcriptomics across the prokaryotic tree of life

    PubMed Central

    Cohen, Ofir; Doron, Shany; Wurtzel, Omri; Dar, Daniel; Edelheit, Sarit; Karunker, Iris; Mick, Eran; Sorek, Rotem

    2016-01-01

    Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome. PMID:27154273

  1. Elucidating and mining the Tulipa and Lilium transcriptomes.

    PubMed

    Moreno-Pachon, Natalia M; Leeggangers, Hendrika A C F; Nijveen, Harm; Severing, Edouard; Hilhorst, Henk; Immink, Richard G H

    2016-10-01

    Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser ( http://www.bioinformatics.nl/bulbs/db/species/index ). The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.

  2. Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes.

    PubMed

    Nam, Kyoungwoo; Jeong, Heesu; Nam, Jin-Wu

    2016-02-24

    High-throughput RNA sequencing (RNA-seq) provides a comprehensive picture of the transcriptome, including the identity, structure, quantity, and variability of expressed transcripts in cells, through the assembly of sequenced short RNA-seq reads. Although the reference-based approach guarantees the high quality of the resulting transcriptome, this approach is only applicable when the relevant reference genome is present. Here, we developed a pseudo-reference-based assembly (PRA) that reconstructs a transcriptome based on a linear regression function of the optimized mapping parameters and genetic distances of the closest species. Using the linear model, we reconstructed transcriptomes of four different aves, the white leg horn, turkey, duck, and zebra finch, with the Gallus gallus genome as a pseudo-reference, and of three primates, the chimpanzee, gorilla, and macaque, with the human genome as a pseudo-reference. The resulting transcriptomes show that the PRAs outperformed the de novo approach for species with within about 10% mutation rate among orthologous transcriptomes, enough to cover distantly related species as far as chicken and duck. Taken together, we suggest that the PRA method can be used as a tool for reconstructing transcriptome maps of vertebrates whose genomes have not yet been sequenced.

  3. Pooled CRISPR screening with single-cell transcriptome readout.

    PubMed

    Datlinger, Paul; Rendeiro, André F; Schmidl, Christian; Krausgruber, Thomas; Traxler, Peter; Klughammer, Johanna; Schuster, Linda C; Kuchler, Amelie; Alpar, Donat; Bock, Christoph

    2017-03-01

    CRISPR-based genetic screens are accelerating biological discovery, but current methods have inherent limitations. Widely used pooled screens are restricted to simple readouts including cell proliferation and sortable marker proteins. Arrayed screens allow for comprehensive molecular readouts such as transcriptome profiling, but at much lower throughput. Here we combine pooled CRISPR screening with single-cell RNA sequencing into a broadly applicable workflow, directly linking guide RNA expression to transcriptome responses in thousands of individual cells. Our method for CRISPR droplet sequencing (CROP-seq) enables pooled CRISPR screens with single-cell transcriptome resolution, which will facilitate high-throughput functional dissection of complex regulatory mechanisms and heterogeneous cell populations.

  4. Transcriptomic characterization of fibrolamellar hepatocellular carcinoma

    PubMed Central

    Simon, Elana P.; Freije, Catherine A.; Farber, Benjamin A.; Lalazar, Gadi; Darcy, David G.; Honeyman, Joshua N.; Chiaroni-Clarke, Rachel; Dill, Brian D.; Molina, Henrik; Bhanot, Umesh K.; La Quaglia, Michael P.; Rosenberg, Brad R.; Simon, Sanford M.

    2015-01-01

    Fibrolamellar hepatocellular carcinoma (FLHCC) tumors all carry a deletion of ∼400 kb in chromosome 19, resulting in a fusion of the genes for the heat shock protein, DNAJ (Hsp40) homolog, subfamily B, member 1, DNAJB1, and the catalytic subunit of protein kinase A, PRKACA. The resulting chimeric transcript produces a fusion protein that retains kinase activity. No other recurrent genomic alterations have been identified. Here we characterize the molecular pathogenesis of FLHCC with transcriptome sequencing (RNA sequencing). Differential expression (tumor vs. adjacent normal tissue) was detected for more than 3,500 genes (log2 fold change ≥1, false discovery rate ≤0.01), many of which were distinct from those found in hepatocellular carcinoma. Expression of several known oncogenes, such as ErbB2 and Aurora Kinase A, was increased in tumor samples. These and other dysregulated genes may serve as potential targets for therapeutic intervention. PMID:26489647

  5. Transcriptome profile of the human placenta.

    PubMed

    Majewska, Marta; Lipka, Aleksandra; Paukszto, Lukasz; Jastrzebski, Jan Pawel; Myszczynski, Kamil; Gowkielewicz, Marek; Jozwik, Marcin; Majewski, Mariusz Krzysztof

    2017-03-01

    The human placenta is a particular organ that inseparably binds the mother and the fetus. The proper development and survival of the conceptus relies on the essential interplay between maternal and fetal factors involved in cooperation within the placenta. In our study, high-throughput sequencing (RNA-seq) was applied to analyze the global transcriptome of the human placenta during uncomplicated pregnancies. The RNA-seq was utilized to identify the global pattern of the gene expression in placentas (N = 4) from women in single and twin pregnancies. During analyses, we obtained 228,044 transcripts. More than 91% of them were multi-exon, and among them 134 were potentially unknown protein coding genes. Expression levels (FPKM) were estimated for 38,948 transcriptional active regions, and more than 3000 of genes were expressed with FPKM >20 in each sample. Additionally, all unannotated transcripts with estimated FPKM values were localized on the human genome. Highly covered splice junctions unannotated in the human genome (6497) were identified, and among them 30 were novel. To gain a better understanding of the biological implications, the assembled transcripts were annotated with gene ontology (GO) terms. Single nucleotide variants were predicted for the transcripts assigned to each analyzed GO category. Our results may be useful for establishing a general pattern of the gene expression in the human placenta. Characterizing placental transcriptome, which is crucial for a pregnancy's outcome, can serve as a basis for identifying the mechanisms underlying physiological pregnancy, as well as may be useful for an early detection of the genomic defects.

  6. Comparative transcriptomics of Arabidopsis sperm cells.

    PubMed

    Borges, Filipe; Gomes, Gabriela; Gardner, Rui; Moreno, Nuno; McCormick, Sheila; Feijó, José A; Becker, Jörg D

    2008-10-01

    In flowering plants, the two sperm cells are embedded within the cytoplasm of the growing pollen tube and as such are passively transported to the embryo sac, wherein double fertilization occurs upon their release. Understanding the mechanisms and conditions by which male gametes mature and take part in fertilization are crucial goals in the study of plant reproduction. Studies of gene expression in male gametes of maize (Zea mays) and Plumbago and in lily (Lilium longiflorum) generative cells already showed that the previously held view of transcriptionally inert male gametes was not true, but genome-wide studies were lacking. Analyses in the model plant Arabidopsis (Arabidopsis thaliana) were hindered, because no method to isolate sperm cells was available. Here, we used fluorescence-activated cell sorting to isolate sperm cells from Arabidopsis, allowing GeneChip analysis of their transcriptome at a genome-wide level. Comparative analysis of the sperm cell transcriptome with those of representative sporophytic tissues and of pollen showed that sperm has a distinct and diverse transcriptional profile. Functional classifications of genes with enriched expression in sperm cells showed that DNA repair, ubiquitin-mediated proteolysis, and cell cycle progression are overrepresented Gene Ontology categories. Moreover, analysis of the small RNA and DNA methylation pathways suggests that distinct mechanisms might be involved in regulating the epigenetic state of the paternal genome. We identified numerous candidate genes whose involvement in sperm cell development and fertilization can now be directly tested in Arabidopsis. These results provide a roadmap to decipher the role of sperm-expressed proteins.

  7. Integrative analysis of the mouse embryonic transcriptome

    PubMed Central

    Singh, Amar V; Knudsen, Kenneth B; Knudsen, Thomas B

    2007-01-01

    Monitoring global gene expression provides insight into how genes and regulatory signals work together to guide embryo development. The fields of developmental biology and teratology are now confronted with the need for automated access to a reference library of gene-expression signatures that benchmark programmed (genetic) and adaptive (environmental) regulation of the embryonic transcriptome. Such a library must be constructed from highly-distributed microarray data. Birth Defects Systems Manager (BDSM), an open access knowledge management system, provides custom software to mine public microarray data focused on developmental health and disease. The present study describes tools for seamless data integration in the BDSM library (MetaSample, MetaChip, CIAeasy) using the QueryBDSM module. A field test of the prototype was run using published microarray data series derived from a variety of laboratories, experiments, microarray platforms, organ systems, and developmental stages. The datasets focused on several developing systems in the mouse embryo, including preimplantation stages, heart and nerve development, testis and ovary development, and craniofacial development. Using BDSM data integration tools, a gene-expression signature for 346 genes was resolved that accurately classified samples by organ system and developmental sequence. The module builds a potential for the BDSM approach to decipher a large number developmental processes through comparative bioinformatics analysis of embryological systems at-risk for specific defects, using multiple scenarios to define the range of probabilities leading from molecular phenotype to clinical phenotype. We conclude that an integrative analysis of global gene-expression of the developing embryo can form the foundation for constructing a reference library of signaling pathways and networks for normal and abnormal regulation of the embryonic transcriptome. These tools are available free of charge from the web-site http

  8. Integrative analysis of the mouse embryonic transcriptome.

    PubMed

    Singh, Amar V; Knudsen, Kenneth B; Knudsen, Thomas B

    2007-04-10

    Monitoring global gene expression provides insight into how genes and regulatory signals work together to guide embryo development. The fields of developmental biology and teratology are now confronted with the need for automated access to a reference library of gene-expression signatures that benchmark programmed (genetic) and adaptive (environmental) regulation of the embryonic transcriptome. Such a library must be constructed from highly-distributed microarray data. Birth Defects Systems Manager (BDSM), an open access knowledge management system, provides custom software to mine public microarray data focused on developmental health and disease. The present study describes tools for seamless data integration in the BDSM library (MetaSample, MetaChip, CIAeasy) using the QueryBDSM module. A field test of the prototype was run using published microarray data series derived from a variety of laboratories, experiments, microarray platforms, organ systems, and developmental stages. The datasets focused on several developing systems in the mouse embryo, including preimplantation stages, heart and nerve development, testis and ovary development, and craniofacial development. Using BDSM data integration tools, a gene-expression signature for 346 genes was resolved that accurately classified samples by organ system and developmental sequence. The module builds a potential for the BDSM approach to decipher a large number developmental processes through comparative bioinformatics analysis of embryological systems at-risk for specific defects, using multiple scenarios to define the range of probabilities leading from molecular phenotype to clinical phenotype. We conclude that an integrative analysis of global gene-expression of the developing embryo can form the foundation for constructing a reference library of signaling pathways and networks for normal and abnormal regulation of the embryonic transcriptome. These tools are available free of charge from the web-site http

  9. Draft Transcriptome Assembly of the Tobacco Budworm, Heliothis virescens (L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Massively parallel next generation sequencing technologies have revolutionized the acquisition and analysis of transcriptomes from beneficial and pest insects. Heliothine moths are major polyphagous pests of commodity crops such as maize, cotton, soybeans and vegetables throughout the world. Contr...

  10. Adult Mouse Cortical Cell Taxonomy by Single Cell Transcriptomics

    PubMed Central

    Tasic, Bosiljka; Menon, Vilas; Nguyen, Thuc Nghi; Kim, Tae Kyung; Jarsky, Tim; Yao, Zizhen; Levi, Boaz; Gray, Lucas T.; Sorensen, Staci A.; Dolbeare, Tim; Bertagnolli, Darren; Goldy, Jeff; Shapovalova, Nadiya; Parry, Sheana; Lee, Changkyu; Smith, Kimberly; Bernard, Amy; Madisen, Linda; Sunkin, Susan M.; Hawrylycz, Michael; Koch, Christof; Zeng, Hongkui

    2016-01-01

    Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. Here, we construct a cellular taxonomy of one cortical region, primary visual cortex, in adult mice based on single cell RNA-sequencing. We identify 49 transcriptomic cell types including 23 GABAergic, 19 glutamatergic and seven non-neuronal types. We also analyze cell-type specific mRNA processing and characterize genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we show that some of our transcriptomic cell types display specific and differential electrophysiological and axon projection properties, thereby confirming that the single cell transcriptomic signatures can be associated with specific cellular properties. PMID:26727548

  11. Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis

    PubMed Central

    Dijkstra, Annereinou R.; Alkema, Wynand; Starrenburg, Marjo J. C.; van Hijum, Sacha A. F. T.; Bron, Peter A.

    2016-01-01

    Recently, we demonstrated that fermentation conditions have a strong impact on subsequent survival of Lactococcus lactis strain MG1363 during heat and oxidative stress, two important parameters during spray drying. Moreover, employment of a transcriptome-phenotype matching approach revealed groups of genes associated with robustness towards heat and/or oxidative stress. To investigate if other strains have similar or distinct transcriptome signatures for robustness, we applied an identical transcriptome-robustness phenotype matching approach on the L. lactis strains IL1403, KF147 and SK11, which have previously been demonstrated to display highly diverse robustness phenotypes. These strains were subjected to an identical fermentation regime as was performed earlier for strain MG1363 and consisted of twelve conditions, varying in the level of salt and/or oxygen, as well as fermentation temperature and pH. In the exponential phase of growth, cells were harvested for transcriptome analysis and assessment of heat and oxidative stress survival phenotypes. The variation in fermentation conditions resulted in differences in heat and oxidative stress survival of up to five 10-log units. Effects of the fermentation conditions on stress survival of the L. lactis strains were typically strain-dependent, although the fermentation conditions had mainly similar effects on the growth characteristics of the different strains. By association of the transcriptomes and robustness phenotypes highly strain-specific transcriptome signatures for robustness towards heat and oxidative stress were identified, indicating that multiple mechanisms exist to increase robustness and, as a consequence, robustness of each strain requires individual optimization. However, a relatively small overlap in the transcriptome responses of the strains was also identified and this generic transcriptome signature included genes previously associated with stress (ctsR and lplL) and novel genes, including nan

  12. Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis.

    PubMed

    Dijkstra, Annereinou R; Alkema, Wynand; Starrenburg, Marjo J C; Hugenholtz, Jeroen; van Hijum, Sacha A F T; Bron, Peter A

    2016-01-01

    Recently, we demonstrated that fermentation conditions have a strong impact on subsequent survival of Lactococcus lactis strain MG1363 during heat and oxidative stress, two important parameters during spray drying. Moreover, employment of a transcriptome-phenotype matching approach revealed groups of genes associated with robustness towards heat and/or oxidative stress. To investigate if other strains have similar or distinct transcriptome signatures for robustness, we applied an identical transcriptome-robustness phenotype matching approach on the L. lactis strains IL1403, KF147 and SK11, which have previously been demonstrated to display highly diverse robustness phenotypes. These strains were subjected to an identical fermentation regime as was performed earlier for strain MG1363 and consisted of twelve conditions, varying in the level of salt and/or oxygen, as well as fermentation temperature and pH. In the exponential phase of growth, cells were harvested for transcriptome analysis and assessment of heat and oxidative stress survival phenotypes. The variation in fermentation conditions resulted in differences in heat and oxidative stress survival of up to five 10-log units. Effects of the fermentation conditions on stress survival of the L. lactis strains were typically strain-dependent, although the fermentation conditions had mainly similar effects on the growth characteristics of the different strains. By association of the transcriptomes and robustness phenotypes highly strain-specific transcriptome signatures for robustness towards heat and oxidative stress were identified, indicating that multiple mechanisms exist to increase robustness and, as a consequence, robustness of each strain requires individual optimization. However, a relatively small overlap in the transcriptome responses of the strains was also identified and this generic transcriptome signature included genes previously associated with stress (ctsR and lplL) and novel genes, including nan

  13. Terpene synthases from Cannabis sativa

    PubMed Central

    Booth, Judith K.; Page, Jonathan E.

    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. PMID:28355238

  14. Assembly, Assessment, and Availability of De novo Generated Eukaryotic Transcriptomes

    PubMed Central

    Moreton, Joanna; Izquierdo, Abril; Emes, Richard D.

    2016-01-01

    De novo assembly of a complete transcriptome without the need for a guiding reference genome is attractive, particularly where the cost and complexity of generating a eukaryote genome is prohibitive. The transcriptome should not however be seen as just a quick and cheap alternative to building a complete genome. Transcriptomics allows the understanding and comparison of spatial and temporal samples within an organism, and allows surveying of multiple individuals or closely related species. De novo assembly in theory allows the building of a complete transcriptome without any prior knowledge of the genome. It also allows the discovery of alternate splice forms of coding RNAs and also non-coding RNAs, which are often missed by proteomic approaches, or are incompletely annotated in genome studies. The limitations of the method are that the generation of a truly complete assembly is unlikely, and so we require some methods for the assessment of the quality and appropriateness of a generated transcriptome. Whilst no single consensus pipeline or tool is agreed as optimal, various algorithms, and easy to use software do exist making transcriptome generation a more common approach. With this expansion of data, questions still exist relating to how do we make these datasets fully discoverable, comparable and most useful to understand complex biological systems? PMID:26793234

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

    PubMed

    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.

  16. De novo transcriptome assembly of heavy metal tolerant Silene dioica.

    PubMed

    Cegan, Radim; Hudzieczek, Vojtech; Hobza, Roman

    2017-03-01

    Silene dioica is a dioecious plant of the family Caryophyllaceae. In the present study, we used Illumina sequencing technology (MiSeq) to sequence, de novo assembly and annotate the transcriptomes of male and female copper tolerant S. dioica individuals. We sequenced the normalized mRNA of roots, shoots, flower buds and flowers for each sex. Raw reads of the transcriptome assembly project for S. dioica male and female individual have been deposited in NCBI's Sequence Read Archive (SRA) database with the accession number SRP094611. The Trinity and Detonate program was used to de novo assembly 92,347 transcripts for male and 94,757 transcripts for female transcriptome. The assembled transcriptome sequences for S. dioica male and female individuals can be accessed at NCBI with the following accession numbers: GFCG00000000 (male); GFCH00000000 (female). The obtained transcriptomic data will be useful for further studies focusing on copper tolerance, comparative transcriptome analysis with other Silene species and sex chromosomes evolution.

  17. Helicobacter pylori CagA Suppresses Apoptosis through Activation of AKT in a Nontransformed Epithelial Cell Model of Glandular Acini Formation

    PubMed Central

    Vallejo-Flores, Gabriela; Torres, Javier; Sandoval-Montes, Claudia; Arévalo-Romero, Haruki; Meza, Isaura; Camorlinga-Ponce, Margarita; Torres-Morales, Julián; Chávez-Rueda, Adriana Karina; Legorreta-Haquet, María Victoria; Fuentes-Pananá, Ezequiel M.

    2015-01-01

    H. pylori infection is the most important environmental risk to develop gastric cancer, mainly through its virulence factor CagA. In vitro models of CagA function have demonstrated a phosphoprotein activity targeting multiple cellular signaling pathways, while cagA transgenic mice develop carcinomas of the gastrointestinal tract, supporting oncogenic functions. However, it is still not completely clear how CagA alters cellular processes associated with carcinogenic events. In this study, we evaluated the capacity of H. pylori CagA positive and negative strains to alter nontransformed MCF-10A glandular acini formation. We found that CagA positive strains inhibited lumen formation arguing for an evasion of apoptosis activity of central acini cells. In agreement, CagA positive strains induced a cell survival activity that correlated with phosphorylation of AKT and of proapoptotic proteins BIM and BAD. Anoikis is a specific type of apoptosis characterized by AKT and BIM activation and it is the mechanism responsible for lumen formation of MCF-10A acini in vitro and mammary glands in vivo. Anoikis resistance is also a common mechanism of invading tumor cells. Our data support that CagA positive strains signaling function targets the AKT and BIM signaling pathway and this could contribute to its oncogenic activity through anoikis evasion. PMID:26557697

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

    PubMed Central

    Domínguez Hernández, Karem R.; Aguilar Lasserre, Alberto A.; Posada Gómez, Rubén; Palet Guzmán, José A.; González Sánchez, Blanca E.

    2013-01-01

    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. PMID:23690881

  19. Mean glandular dose estimation using MCNPX for a digital breast tomosynthesis system with tungsten/aluminum and tungsten/aluminum+silver x-ray anode-filter combinations

    SciTech Connect

    Ma, Andy K. W.; Darambara, Dimitra G.; Stewart, Alexander; Gunn, Spencer; Bullard, Edward

    2008-12-15

    Breast cancer screening with x-ray mammography, using one or two projection images of the breast, is an indispensible tool in the early detection of breast cancer in women. Digital breast tomosynthesis (DBT) is a 3D imaging technique that promises higher sensitivity and specificity in breast cancer screening at a similar radiation dose to conventional two-view screening mammography. In DBT a 3D volume is reconstructed with anisotropic voxels from a limited number of x-ray projection images acquired over a limited angle. Although the benefit of early cancer detection through screening mammography outweighs the potential risks associated with radiation, the radiation dosage to women in terms of mean glandular dose (MGD) is carefully monitored. This work studies the MGD arising from a prototype DBT system under various parameters. Two anode/filter combinations (W/Al and W/Al+Ag) were investigated; the tube potential ranges from 20 to 50 kVp; and the breast size varied between 4 and 10 cm chest wall-to-nipple distance and between 3 and 7 cm compressed breast thickness. The dosimetric effect of breast positioning with respect to the imaging detector was also reviewed. It was found that the position of the breast can affect the MGD by as much as 5% to 13% depending on the breast size.

  20. Anogenital Mammary-Like Glands: A Study of Their Normal Histology With Emphasis on Glandular Depth, Presence of Columnar Epithelial Cells, and Distribution of Elastic Fibers.

    PubMed

    Konstantinova, Anastasia M; Kyrpychova, Liubov; Belousova, Irena E; Spagnolo, Dominic V; Kacerovska, Denisa; Michal, Michal; Kerl, Katrin; Kazakov, Dmitry V

    2016-10-18

    The normal histology of anogenital mammary-like glands (AGMLG) has been studied previously, but some aspects, including glandular depth, presence of columnar epithelium resembling columnar cell change/hyperplasia as defined in mammary pathology, and distribution of elastic fibers, have not been previously investigated. To address these issues, we studied 148 AGMLG identified in 133 paraffin blocks sampled from 64 vulvar wide excision or vulvectomy specimens (64 patients, various indications for surgery). The depth of AGMLG ranged from 0.64 to 3.9 mm. Epithelial columnar cell change was noted in 33.1% of all AGMLG, whereas columnar cell hyperplasia was detected in 10.1%. Occasionally, combinations of cuboidal epithelium and columnar cell change were seen within 1 histological section. Of 22 specimens stained for elastic fibers, in only 6 (27.3%) cases were elastic fibers found around glands. Periductal elastic fibers were demonstrated around 3 of the only 5 ducts, which were available for analysis in slides stained for elastic fibers. The depth of AGMLG should be taken into account when planning topical and surgical therapies for lesions derived or evolving from AGMLG. Alterations identical to columnar cell change may represent a normal variation of AGMLG.

  1. Development of cystic glandular hyperplasia of the endometrium in Mullerian inhibitory substance type II receptor-pituitary tumor transforming gene transgenic mice.

    PubMed

    El-Naggar, Shahenda M; Malik, Mohammad T; Martin, Alvin; Moore, Joseph P; Proctor, Mary; Hamid, Tariq; Kakar, Sham S

    2007-07-01

    The pituitary tumor transforming gene (PTTG)/securin is an oncogene that is involved in cell cycle regulation and sister chromatid separation. PTTG is highly expressed in various tumors including ovarian tumors, suggesting that PTTG may play a role in ovarian tumorigenesis. Overexpression of PTTG resulted in induction of cellular transformation in vitro and tumor formation in nude mice. To ascertain PTTG function in ovarian tumorigenesis, we generated a transgenic mouse model of PTTG by cloning PTTG cDNA downstream of Mullerian inhibitory substance type II receptor gene promoter (MISIIR) in order to target the ovarian surface epithelium. By screening of transgenic animals, we identified five founders (four males and one female). Using the four male founders, we developed four transgenic lines. PTTG expression was increased in ovarian surface epithelium, ovarian granulosa cells, as well as in the pituitary gland. Transgenic females did not develop any visible ovarian tumors at 8-10 months of age; however, there was an overall increase in the corpus luteum mass in transgenic ovary, suggesting increased luteinization. These changes were associated with an increase in serum LH and testosterone levels. In addition, there was a generalized hypertrophy of the myometrium of MISIIR-PTTG transgenic uteri with cystic glandular and hyperplasia of the endometrium. Based on these results, we conclude that the overexpression of PTTG may be required to initiate precancerous conditions but is not sufficient to induce ovarian tumorigenesis and may require another partner to initiate cellular transformation.

  2. A Pyloric Gland-Phenotype Ovarian Mucinous Tumor Resembling Lobular Endocervical Glandular Hyperplasia in a Patient with Peutz-Jeghers Syndrome.

    PubMed

    Kim, Eun Na; Kim, Gu-Hwan; Kim, Jiyoon; Park, In Ah; Shin, Jin Ho; Chai, Yun; Kim, Kyu-Rae

    2017-03-01

    We describe an ovarian mucinous neoplasm that histologically resembles lobular endocervical glandular hyperplasia (LEGH) containing pyloric gland type mucin in a patient with Peutz-Jeghers syndrome (PJS). Although ovarian mucinous tumors rarely occur in PJS patients, their pyloric gland phenotype has not been clearly determined. The histopathologic features of the ovarian mucinous tumor were reminiscent of LEGH. The cytoplasmic mucin was stained with periodic acid-Schiff reaction after diastase treatment but was negative for Alcian blue pH 2.5, suggesting the presence of neutral mucin. Immunohistochemically, the epithelium expressed various gastric markers, including MUC6, HIK1083, and carbonic anhydrase-IX. Multiple ligation-dependent probe amplification detected a germline heterozygous deletion mutation at exons 1-7 of the STK11 gene (c.1-?_920+?del) in peripheral blood leukocytes and mosaic loss of heterozygosity in ovarian tumor tissue. Considering that LEGH and/or gastric-type cervical adenocarcinoma can be found in patients with PJS carrying germline and/or somatic STK11 mutations, our case indicates that STK11 mutations have an important role in the proliferation of pyloric-phenotype mucinous epithelium at various anatomical locations.

  3. A Pyloric Gland-Phenotype Ovarian Mucinous Tumor Resembling Lobular Endocervical Glandular Hyperplasia in a Patient with Peutz-Jeghers Syndrome

    PubMed Central

    Kim, Eun Na; Kim, Gu-Hwan; Kim, Jiyoon; Park, In Ah; Shin, Jin Ho; Chai, Yun; Kim, Kyu-Rae

    2017-01-01

    We describe an ovarian mucinous neoplasm that histologically resembles lobular endocervical glandular hyperplasia (LEGH) containing pyloric gland type mucin in a patient with Peutz-Jeghers syndrome (PJS). Although ovarian mucinous tumors rarely occur in PJS patients, their pyloric gland phenotype has not been clearly determined. The histopathologic features of the ovarian mucinous tumor were reminiscent of LEGH. The cytoplasmic mucin was stained with periodic acid-Schiff reaction after diastase treatment but was negative for Alcian blue pH 2.5, suggesting the presence of neutral mucin. Immunohistochemically, the epithelium expressed various gastric markers, including MUC6, HIK1083, and carbonic anhydrase-IX. Multiple ligation-dependent probe amplification detected a germline heterozygous deletion mutation at exons 1–7 of the STK11 gene (c.1-?_920+?del) in peripheral blood leukocytes and mosaic loss of heterozygosity in ovarian tumor tissue. Considering that LEGH and/or gastric-type cervical adenocarcinoma can be found in patients with PJS carrying germline and/or somatic STK11 mutations, our case indicates that STK11 mutations have an important role in the proliferation of pyloric-phenotype mucinous epithelium at various anatomical locations. PMID:27550049

  4. Allele-specific recognition by LILRB3 and LILRA6 of a cytokeratin 8 - associated ligand on necrotic glandular epithelial cells

    PubMed Central

    López-Álvarez, María R.; Jahnke, Martin; Russell, Alasdair I.; Radjabova, Valeria; Trowsdale, Alice R.Z.; Trowsdale, John

    2016-01-01

    The LILRs are a family of receptors that regulate the activities of myelomonocytic cells. We found that specific allelic variants of two related members of the LILR family, LILRB3 and LILRA6, interact with a ligand exposed on necrotic glandular epithelial cells. The extracellular domains of LILRB3 and LILRA6 are very similar and their genes are highly polymorphic. A commonly occurring allele, LILRB3*12, displayed particularly strong binding of these necrotic cells and further screening of the products of LILRB3 alleles identified motifs that correlated with binding. Immunoprecipitation of the ligand from epithelial cell lysates using recombinant LILRB3*12, identified cytokeratins 8, 18 and 19. Purified proteins obtained from epithelial cell lysates, using anti-cytokeratin 8 antibodies, were able to activate LILRB3*12 reporter cells. Knock-down of cytokeratin 8 in epithelial cells abrogated expression of the LILRB3 ligand, while staining with recombinant LILRB3*12 showed co-localisation with cytokeratin 8 and 18 in permeabilised breast cancer cells. Necrosis is a common feature of tumours. The finding of a necrosis-associated ligand for these two receptors raises the possibility of a novel interaction that alters immune responses within the tumour microenvironment. Since LILRB3 and LILRA6 genes are highly polymorphic the interaction may influence an individual's immune response to tumours. PMID:26769854

  5. Development of an expert system as a diagnostic support of cervical cancer in atypical glandular cells, based on fuzzy logics and image interpretation.

    PubMed

    Domínguez Hernández, Karem R; Aguilar Lasserre, Alberto A; Posada Gómez, Rubén; Palet Guzmán, José A; González Sánchez, Blanca E

    2013-01-01

    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.

  6. Changes in transcriptome of macrophages in atherosclerosis

    PubMed Central

    Chistiakov, Dimitry A; Bobryshev, Yuri V; Orekhov, Alexander N

    2015-01-01

    Macrophages display significant phenotypic heterogeneity. Two growth factors, macrophage colony-stimulating factor and chemokine (C-X-C motif) ligand 4, drive terminal differentiation of monocytes to M0 and M4 macrophages respectively. Compared to M0 macrophages, M4 cells have a unique transcriptome, with expression of surface markers such as S100A8, mannose receptor CD206 and matrix metalloproteinase 7. M4 macrophages did not express CD163, a scavenger receptor for haemoglobin/haptoglobin complex. Depending on the stimuli, M0 macrophages could polarize towards the proinflammatory M1 subset by treatment with lipopolysaccharide or interferon-γ. These macrophages produce a range of proinflammatory cytokines, nitric oxide, reactive oxygen species and exhibit high chemotactic and phagocytic activity. The alternative M2 type could be induced from M0 macrophage by stimulation with interleukin (IL)-4. M2 macrophages express high levels of CD206 and produce anti-inflammatory cytokines IL-10 and transforming growth factor-β. M1, M2 and M4 macrophages could be found in atherosclerotic plaques. In the plaque, macrophages are subjected to the intensive influence not only by cytokines and chemokines but also with bioactive lipids such as cholesterol and oxidized phospholipids. Oxidized phospholipids induce a distinct Mox phenotype in murine macrophages that express a unique panel of antioxidant enzymes under control of the redox-regulated transcription factor Klf2, resistant to lipid accumulation. In unstable human lesions, atheroprotective M(Hb) and HA-mac macrophage subsets could be found. These two subsets are induced by the haemoglobin/haptoglobin complex, highly express haeme oxygenase 1 and CD163, and are implicated in clearance of haemoglobin and erythrocyte remnants. In atherogenesis, the macrophage phenotype is plastic and could therefore be switched to proinflammatory (i.e. proatherogenic) and anti-inflammatory (i.e. atheroprotective). The aim of this review was to

  7. A quantitative transcriptome reference map of the normal human hippocampus.

    PubMed

    Caracausi, Maria; Rigon, Vania; Piovesan, Allison; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara

    2016-01-01

    We performed an innovative systematic meta-analysis of 41 gene expression profiles of normal human hippocampus to provide a quantitative transcriptome reference map of it, i.e. a reference typical value of expression for each of the 30,739 known mapped and the 16,258 uncharacterized (unmapped) transcripts. For this aim, we used the software called TRAM (Transcriptome Mapper), which is able to generate transcriptome maps based on gene expression data from multiple sources. We also analyzed differential expression by comparing the hippocampus with the whole brain transcriptome map to identify a typical expression pattern of this subregion compared with the whole organ. Finally, due to the fact that the hippocampus is one of the main brain region to be severely affected in trisomy 21 (the best known genetic cause of intellectual disability), a particular attention was paid to the expression of chromosome 21 (chr21) genes. Data were downloaded from microarray databases, processed, and analyzed using TRAM software. Among the main findings, the most over-expressed loci in the hippocampus are the expressed sequence tag cluster Hs.732685 and the member of the calmodulin gene family CALM2. The tubulin folding cofactor B (TBCB) gene is the best gene at behaving like a housekeeping gene. The hippocampus vs. the whole brain differential transcriptome map shows the over-expression of LINC00114, a long non-coding RNA mapped on chr21. The hippocampus transcriptome map was validated in vitro by assaying gene expression through several magnitude orders by "Real-Time" reverse transcription polymerase chain reaction (RT-PCR). The highly significant agreement between in silico and experimental data suggested that our transcriptome map may be a useful quantitative reference benchmark for gene expression studies related to human hippocampus. Furthermore, our analysis yielded biological insights about those genes that have an intrinsic over-/under-expression in the hippocampus.

  8. International Standards for Genomes, Transcriptomes, and Metagenomes.

    PubMed

    Mason, Christopher E; Afshinnekoo, Ebrahim; Tighe, Scott; Wu, Shixiu; Levy, Shawn

    2017-03-17

    Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous. Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data. Here we review current standards and their applications in genomics, including whole genomes, transcriptomes, mixed genomic samples (metagenomes), and the modified bases within each (epigenomes and epitranscriptomes). These standards, tools, and metrics are critical for quantifying the accuracy of NGS methods, which will be essential for robust approaches in clinical genomics and precision medicine.

  9. Ameloblastoma Phenotypes Reflected in Distinct Transcriptome Profiles

    PubMed Central

    Hu, Shijia; Parker, Joel; Divaris, Kimon; Padilla, Ricardo; Murrah, Valerie; Wright, John Timothy

    2016-01-01

    Ameloblastoma is a locally invasive benign neoplasm derived from odontogenic epithelium and presents with diverse phenotypes yet to be characterized molecularly. High recurrence rates of 50–80% with conservative treatment in some sub-types warrants radical surgical resections resulting in high morbidity. The objective of the study was to characterize the transcriptome of ameloblastoma and identify relevant genes and molecular pathways using normal odontogenic tissue (human “dentome”) for comparison. Laser capture microdissection was used to obtain neoplastic epithelial tissue from 17 tumors which were examined using the Agilent 44 k whole genome microarray. Ameloblastoma separated into 2 distinct molecular clusters that were associated with pre-secretory ameloblast and odontoblast. Within the pre-secretory cluster, 9/10 of samples were of the follicular type while 6/7 of the samples in the odontoblast cluster were of the plexiform type (p < 0.05). Common pathways altered in both clusters included cell-cycle regulation, inflammatory and MAPkinase pathways, specifically known cancer-driving genes such as TP53 and members of the MAPkinase pathways. The pre-secretory ameloblast cluster exhibited higher activation of inflammatory pathways while the odontoblast cluster showed greater disturbances in transcription regulators. Our results are suggestive of underlying inter-tumor molecular heterogeneity of ameloblastoma sub-types and have implications for the use of tailored treatment. PMID:27491308

  10. Transcriptomic analysis of degraded forensic body fluids.

    PubMed

    Lin, Meng-Han; Jones, Daniel F; Fleming, Rachel

    2015-07-01

    Massively parallel sequencing (MPS) has facilitated a significant increase in transcriptomic studies in all biological disciplines. However, the analysis of degraded RNA remains a genuine challenge in practice. In forensic science the biological samples encountered are often extensively degraded and of low abundance. RNA from these compromised samples is used for body fluid identification through the detection of body fluid-specific transcripts. Here we demonstrate the sequencing of four forensically relevant body fluids: oral mucosa/saliva (buccal), circulatory blood, menstrual blood and vaginal fluid. RNA was extracted from fresh, two and six week aged samples. Despite the extensive degradation of most body fluids, significant high quality sequencing output (>80% sequence above Q30) was generated. An average of over 80% of reads from all but one sample aligned successfully to the reference human genome. Furthermore, FPKMs (fragments per kilobase of exon per million fragments mapped) generated indicate the accurate detection of known body fluid markers in respective body fluids. Assessment of global gene expression levels over degradation time enabled the characterisation of differential RNA degradation in different body fluids. This study demonstrates the practical application of MPS technology for the accurate analysis of degraded RNA from minimal samples.

  11. Applying thiouracil tagging to mouse transcriptome analysis.

    PubMed

    Gay, Leslie; Karfilis, Kate V; Miller, Michael R; Doe, Chris Q; Stankunas, Kryn

    2014-02-01

    Transcriptional profiling is a powerful approach for studying mouse development, physiology and disease models. Here we describe a protocol for mouse thiouracil tagging (TU tagging), a transcriptome analysis technology that includes in vivo covalent labeling, purification and analysis of cell type-specific RNA. TU tagging enables the isolation of RNA from a given cell population of a complex tissue, avoiding transcriptional changes induced by cell isolation trauma, as well as the identification of actively transcribed RNAs and not preexisting transcripts. Therefore, in contrast to other cell-specific transcriptional profiling methods based on the purification of tagged ribosomes or nuclei, TU tagging provides a direct examination of transcriptional regulation. We describe how to (i) deliver 4-thiouracil to transgenic mice to thio-label cell lineage-specific transcripts, (ii) purify TU-tagged RNA and prepare libraries for Illumina sequencing and (iii) follow a straightforward bioinformatics workflow to identify cell type-enriched or differentially expressed genes. Tissue containing TU-tagged RNA can be obtained in 1 d, RNA-seq libraries can be generated within 2 d and, after sequencing, an initial bioinformatics analysis can be completed in 1 additional day.

  12. International Standards for Genomes, Transcriptomes, and Metagenomes

    PubMed Central

    Mason, Christopher E.; Afshinnekoo, Ebrahim; Tighe, Scott; Wu, Shixiu; Levy, Shawn

    2017-01-01

    Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous. Fortunately, a variety of methods, standards, and technologies have recently emerged that improve measurements in genomics and sequencing, from the initial input material to the computational pipelines that process and annotate the data. Here we review current standards and their applications in genomics, including whole genomes, transcriptomes, mixed genomic samples (metagenomes), and the modified bases within each (epigenomes and epitranscriptomes). These standards, tools, and metrics are critical for quantifying the accuracy of NGS methods, which will be essential for robust approaches in clinical genomics and precision medicine. PMID:28337071

  13. Transcriptomic analysis of Salmonella desiccation resistance.

    PubMed

    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.

  14. A transcriptome approach to ecdysozoan phylogeny.

    PubMed

    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.

  15. Thorium impact on tobacco root transcriptome.

    PubMed

    Mazari, Kateřina; Landa, Přemysl; Přerostová, Sylva; Müller, Karel; Vaňková, Radomíra; Soudek, Petr; Vaněk, Tomáš

    2017-03-05

    Thorium is natural actinide metal with potential use in nuclear energetics. Contamination by thorium, originated from mining activities or spills, represents environmental risk due to its radioactivity and chemical toxicity. A promising approach for cleaning of contaminated areas is phytoremediation, which need to be based, however, on detail understanding of the thorium effects on plants. In this study we investigated transcriptomic response of tobacco roots exposed to 200μM thorium for one week. Thorium application resulted in up-regulation of 152 and down-regulation of 100 genes (p-value <0.01, fold change ≥2). The stimulated genes were involved in components of jasmonic acid and salicylic acid signaling pathways and various abiotic (e.g. oxidative stress) and biotic stress (e.g. pathogens, wounding) responsive genes. Further, up-regulation of phosphate starvation genes and down-regulation of genes involved in phytic acid biosynthesis indicated that thorium disturbed phosphate uptake or signaling. Also expression of iron responsive genes was influenced. Negative regulation of several aquaporins indicated disturbance of water homeostasis. Genes potentially involved in thorium transport could be zinc-induced facilitator ZIF2, plant cadmium resistance PCR2, and ABC transporter ABCG40. This study provides the first insight at the processes in plants exposed to thorium.

  16. Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays

    PubMed Central

    Mathavan, Sinnakaruppan; Lee, Serene G. P; Mak, Alicia; Miller, Lance D; Murthy, Karuturi Radha Krishna; Govindarajan, Kunde R; Tong, Yan; Wu, Yi Lian; Lam, Siew Hong; Yang, Henry; Ruan, Yijun; Korzh, Vladimir; Gong, Zhiyuan; Liu, Edison T; Lufkin, Thomas

    2005-01-01

    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). PMID:16132083

  17. The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.

    PubMed

    Habuka, Masato; Fagerberg, Linn; Hallström, Björn M; Pontén, Fredrik; Yamamoto, Tadashi; Uhlen, Mathias

    2015-01-01

    To understand functions and diseases of urinary bladder, it is important to define its molecular constituents and their roles in urinary bladder biology. Here, we performed genome-wide deep RNA sequencing analysis of human urinary bladder samples and identified genes up-regulated in the urinary bladder by comparing the transcriptome data to those of all other major human tissue types. 90 protein-coding genes were elevated in the urinary bladder, either with enhanced expression uniquely in the urinary bladder or elevated expression together with at least one other tissue (group enriched). We further examined the localization of these proteins by immunohistochemistry and tissue microarrays and 20 of these 90 proteins were localized to the whole urothelium with a majority not yet described in the context of the urinary bladder. Four additional proteins were found specifically in the umbrella cells (Uroplakin 1a, 2, 3a, and 3b), and three in the intermediate/basal cells (KRT17, PCP4L1 and ATP1A4). 61 of the 90 elevated genes have not been previously described in the context of urinary bladder and the corresponding proteins are interesting targets for more in-depth studies. In summary, an integrated omics approach using transcriptomics and antibody-based profiling has been used to define a comprehensive list of proteins elevated in the urinary bladder.

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

    PubMed Central

    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 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. PMID:26276382

  19. Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom).

    PubMed

    Nadiya, F; Anjali, N; Thomas, Jinu; Gangaprasad, A; Sabu, K K

    2017-03-01

    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.

  20. The eyestalk transcriptome of red swamp crayfish Procambarus clarkii.

    PubMed

    Manfrin, Chiara; Tom, Moshe; De Moro, Gianluca; Gerdol, Marco; Giulianini, Piero Giulio; Pallavicini, Alberto

    2015-02-15

    The red swamp crayfish (Procambarus clarkii, Girard 1852) is among the most economically important freshwater crustacean species, and it is also considered one of the most aggressive invasive species worldwide. Despite its commercial importance and being one of the most studied crayfish species, its genomic and transcriptomic layout has only been partially studied. Illumina RNA-sequencing was applied to characterize the eyestalk transcriptome and identify its most characterizing genes. A collection of 83,170,732 reads from eyestalks was obtained using Illumina paired-end sequencing technology. A de novo assembly was performed with the Trinity assembly software generating 119,255 contigs (average length of 1,007 bp) and identifying the first sequenced transcriptome in this species. The eyestalk is a major site for the production of neurohormones and controls a variety of physiological functions such as osmotic regulation, molting, epidermal color patterns and reproduction. Hence, its transcriptomic characterization is interesting and potentially instrumental to the elucidation of genes which have not been comprehensively described yet. Moreover, the availability of such a large amount of information supported the characterization of molecular families which have never been described before. The P. clarkii eyestalk transcriptome reported here provides a resource for improving the knowledge of the still incompletely defined neuroendocrinology of this species and represents an important source of data for all the interested carcinologists.

  1. Novel Approaches for Fungal Transcriptomics from Host Samples

    PubMed Central

    Amorim-Vaz, Sara; Sanglard, Dominique

    2016-01-01

    Candida albicans adaptation to the host requires a profound reprogramming of the fungal transcriptome as compared to in vitro laboratory conditions. A detailed knowledge of the C. albicans transcriptome during the infection process is necessary in order to understand which of the fungal genes are important for host adaptation. Such genes could be thought of as potential targets for antifungal therapy. The acquisition of the C. albicans transcriptome is, however, technically challenging due to the low proportion of fungal RNA in host tissues. Two emerging technologies were used recently to circumvent this problem. One consists of the detection of low abundance fungal RNA using capture and reporter gene probes which is followed by emission and quantification of resulting fluorescent signals (nanoString). The other is based first on the capture of fungal RNA by short biotinylated oligonucleotide baits covering the C. albicans ORFome permitting fungal RNA purification. Next, the enriched fungal RNA is amplified and subjected to RNA sequencing (RNA-seq). Here we detail these two transcriptome approaches and discuss their advantages and limitations and future perspectives in microbial transcriptomics from host material. PMID:26834721

  2. Analysis of the Citrullus colocynthis transcriptome during water deficit stress.

    PubMed

    Wang, Zhuoyu; Hu, Hongtao; Goertzen, Leslie R; McElroy, J Scott; Dane, Fenny

    2014-01-01

    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. Novel Approaches for Fungal Transcriptomics from Host Samples.

    PubMed

    Amorim-Vaz, Sara; Sanglard, Dominique

    2015-01-01

    Candida albicans adaptation to the host requires a profound reprogramming of the fungal transcriptome as compared to in vitro laboratory conditions. A detailed knowledge of the C. albicans transcriptome during the infection process is necessary in order to understand which of the fungal genes are important for host adaptation. Such genes could be thought of as potential targets for antifungal therapy. The acquisition of the C. albicans transcriptome is, however, technically challenging due to the low proportion of fungal RNA in host tissues. Two emerging technologies were used recently to circumvent this problem. One consists of the detection of low abundance fungal RNA using capture and reporter gene probes which is followed by emission and quantification of resulting fluorescent signals (nanoString). The other is based first on the capture of fungal RNA by short biotinylated oligonucleotide baits covering the C. albicans ORFome permitting fungal RNA purification. Next, the enriched fungal RNA is amplified and subjected to RNA sequencing (RNA-seq). Here we detail these two transcriptome approaches and discuss their advantages and limitations and future perspectives in microbial transcriptomics from host material.

  4. The testes transcriptome derived from the New World Screwworm, Cochliomyia hominivorax TSA

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  5. Transcriptome assembly and digital gene expression atlas of the rainbow trout

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Transcriptome analysis is a preferred method for gene discovery, marker development and gene expression profiling in non-model organisms. Previously, we sequenced a transcriptome reference using Sanger-based and 454-pyrosequencing, however, a transcriptome assembly is still incomplete an...

  6. Magnetic Resonance Imaging- Versus Computed Tomography-Based Target Volume Delineation of the Glandular Breast Tissue (Clinical Target Volume Breast) in Breast-Conserving Therapy: An Exploratory Study

    SciTech Connect

    Giezen, Marina; Kouwenhoven, Erik; Scholten, Astrid N.; Coerkamp, Emile G.; Heijenbrok, Mark; Jansen, Wim P.A.; Mast, Mirjam E.; Petoukhova, Anna L.; Struikmans, Henk

    2011-11-01

    Purpose: To examine MRI and CT for glandular breast tissue (GBT) volume delineation and to assess interobserver variability. Methods and Materials: Fifteen breast cancer patients underwent a planning CT and MRI, consecutively, in the treatment position. Four observers (two radiation oncologists and two radiologists) delineated the GBT according to the CT and separately to the MR images. Volumes, centers of mass, maximum extensions with standard deviations (SD), and interobserver variability were quantified. Observers viewed delineation differences between MRI and CT and delineation differences among observers. Results: In cranio-lateral and cranio-medial directions, GBT volumes were delineated larger using MRI when compared with those delineated with CT. Center of mass on MRI shifted a mean (SD) 17% (4%) into the cranial direction and a mean 3% (4%) into the dorsal direction when compared with that on the planning CT. Only small variations between observers were noted. The GBT volumes were approximately 4% larger on MRI (mean [SD] ratio MRI to CT GBT volumes, 1.04 [0.06]). Findings were concordant with viewed MRI and CT images and contours. Conformity indices were only slightly different; mean conformity index was 77% (3%) for MRI and 79% (4%) for CT. Delineation differences arising from personal preferences remained recognizable irrespective of the imaging modality used. Conclusions: Contoured GBT extends substantially further into the cranio-lateral and cranio-medial directions on MRI when compared with CT. Interobserver variability is comparable for both imaging modalities. Observers should be aware of existing personal delineation preferences. Institutions are recommended to review and discuss target volume delineations and to design supplementary guidelines if necessary.

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

    SciTech Connect

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

    2013-03-22

    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.

  8. Interferon regulatory factor-two restricts expression of interferon-stimulated genes to the endometrial stroma and glandular epithelium of the ovine uterus.

    PubMed

    Choi, Y; Johnson, G A; Burghardt, R C; Berghman, L R; Joyce, M M; Taylor, K M; Stewart, M D; Bazer, F W; Spencer, T E

    2001-10-01

    Interferon tau (IFNtau) is the signal for maternal recognition of pregnancy in ruminants. The positive effects of IFNtau on IFN-stimulated gene (ISG) expression are mediated by ISG factor 3 (ISGF3), which is composed of signal transducer and activator of transcription (Stat) 1, Stat 2, and IFN regulatory factor-9 (IRF-9), and by gamma-activated factor (GAF), which is a Stat 1 homodimer. Induction of ISGs, such as ISG17 and 2',5'-oligoadenylate synthetase, by IFNtau during pregnancy is limited to the endometrial stroma (S) and glandular epithelium (GE) of the ovine uterus. The IRF-2, a potent transcriptional repressor of ISG expression, is expressed in the luminal epithelium (LE). This study determined effects of the estrous cycle, pregnancy, and IFNtau on expression of Stat 1, Stat 2, IRF-9, IRF-1, and IRF-2 genes in the ovine endometrium. In cyclic ewes, Stat 1, Stat 2, IRF-1, and IRF-9 mRNA and protein were detected at low levels in the S and GE. During pregnancy, expression of these genes increased only in the S and GE. Expression of IRF-2 was detected only in the LE and superficial GE (sGE) of both cyclic and pregnant ewes. In cyclic ewes, intrauterine administration of IFNtau stimulated Stat 1, Stat 2, IRF-9, and IRF-1 expression in the endometrium. Ovine IRF-2 repressed transcriptional activity driven by IFN-stimulated response elements that bind ISGF3, but not by gamma-activation sequences that bind GAF. These results suggest that IRF-2 in the LE and sGE restricts IFNtau induction of ISGs to the S and GE. In the S and GE, IFNtau hyperactivation of ISG expression likely involves formation and actions of the transcription factors ISGF3 and, perhaps, IRF-1.

  9. Effects of long-term progesterone exposure on porcine uterine gene expression: progesterone alone does not induce secreted phosphoprotein 1 (osteopontin) in glandular epithelium.

    PubMed

    Bailey, Daniel W; Dunlap, Kathrin A; Erikson, David W; Patel, Atish K; Bazer, Fuller W; Burghardt, Robert C; Johnson, Greg A

    2010-10-01

    Pigs experience significant conceptus loss near mid-gestation, correlating with increasing glandular epithelial (GE) development and secretory activity. Secreted phosphoprotein 1 (SPP1, osteopontin) increases in GE between days 30 and 40 of pregnancy and is expressed in the GE of day 90 pseudopregnant pigs, suggesting that progesterone (P(4)) from corpora lutea is responsible for induction of SPP1 in GE. In this study, pigs were ovariectomized and treated daily with P(4) to assess effects of 40 days of P(4) exposure on SPP1, P(4) receptor (PGR), uteroferrin (ACP5), and fibroblast growth factor 7 (FGF7) expression in porcine endometria. PGR mRNA decreased in pigs injected with P(4) compared with pigs injected with corn oil (CO), and PGRs were downregulated in the luminal epithelium (LE) and GE. ACP5 mRNA increased in pigs injected with P(4) compared with pigs injected with CO, and ACP5 was induced in the GE of P(4)-treated pigs. FGF7 mRNA increased in pigs injected with P(4) compared with pigs injected with CO, and FGF7 was induced in the LE and GE of P(4)-treated pigs. SPP1 mRNA was not different between pigs injected with P(4) compared with pigs injected with CO, and SPP1 was not present in the GE of P(4)-treated pigs. Therefore, long-term P(4), in the absence of ovarian and/or conceptus factors, does not induce SPP1 expression in GE. We hypothesize that a servomechanism involving sequential effects of multiple hormones and cytokines, similar to those for sheep and humans, is required for GE differentiation and function, including the synthesis and secretion of SPP1.

  10. Evaluation of scatter-to-primary ratio, grid performance and normalized average glandular dose in mammography by Monte Carlo simulation including interference and energy broadening effects

    NASA Astrophysics Data System (ADS)

    Cunha, D. M.; Tomal, A.; Poletti, M. E.

    2010-08-01

    In this work, a computational code for the study of imaging systems and dosimetry in conventional and digital mammography through Monte Carlo simulations is described. The developed code includes interference and Doppler energy broadening for simulation of elastic and inelastic photon scattering, respectively. The code estimates the contribution of scattered radiation to image quality through the spatial distribution of the scatter-to-primary ratio (S/P). It allows the inclusion of different designs of anti-scatter grids (linear or cellular), for evaluation of contrast improvement factor (CIF), Bucky factor (BF) and signal difference-to-noise ratio improvement factor (SIF). It also allows the computation of the normalized average glandular dose, \\bar{D}_{g,N} . These quantities were studied for different breast thicknesses and compositions, anode/filter combinations and tube potentials. Results showed that the S/P increases linearly with breast thickness, varying slightly with breast composition or the spectrum used. Evaluation of grid performance showed that the cellular grid provides the highest CIF with smaller BF. The SIF was also greater for the cellular grid, although both grids showed SIF < 1 for thin breasts. Results for \\bar{D}_{g,N} showed that it increases with the half-value layer (HVL) of the spectrum, decreases considerably with breast thickness and has a small dependence on the anode/filter combination. Inclusion of interference effects of breast tissues affected the values of S/P obtained with the grid up to 25%, while the energy broadening effect produced smaller variations on the evaluated quantities.

  11. Transcriptomic Response to Nitric Oxide Treatment in Larix olgensis Henry

    PubMed Central

    Hu, Xiaoqing; Yang, Jingli; Li, Chenghao

    2015-01-01

    Larix olgensis Henry is an important coniferous species found in plantation forests in northeastern China, but it is vulnerable to pathogens. Nitric oxide (NO) is an important molecule involved in plant resistance to pathogens. To study the regulatory role of NO at the transcriptional level, we characterized the transcriptomic response of L. olgensis seedlings to sodium nitroprusside (SNP, NO donor) using Illumina sequencing and de novo transcriptome assembly. A significant number of putative metabolic pathways and functions associated with the unique sequences were identified. Genes related to plant pathogen infection (FLS2, WRKY33, MAPKKK, and PR1) were upregulated with SNP treatment. This report describes the potential contribution of NO to disease resistance in L. olgensis as induced by biotic stress. Our results provide a substantial contribution to the genomic and transcriptomic resources for L. olgensis, as well as expanding our understanding of the involvement of NO in defense responses at the transcriptional level. PMID:26633380

  12. Transcriptomic insights into human brain evolution: acceleration, neutrality, heterochrony.

    PubMed

    Somel, Mehmet; Rohlfs, Rori; Liu, Xiling

    2014-12-01

    Primate brain transcriptome comparisons within the last 12 years have yielded interesting but contradictory observations on how the transcriptome evolves, and its adaptive role in human cognitive evolution. Since the human-chimpanzee common ancestor, the human prefrontal cortex transcriptome seems to have evolved more than that of the chimpanzee. But at the same time, most expression differences among species, especially those observed in adults, appear as consequences of neutral evolution at cis-regulatory sites. Adaptive expression changes in the human brain may be rare events involving timing shifts, or heterochrony, in specific neurodevelopmental processes. Disentangling adaptive and neutral expression changes, and associating these with human-specific features of the brain require improved methods, comparisons across more species, and further work on comparative development.

  13. Genomic and Transcriptomic Analyses of Foodborne Bacterial Pathogens

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Dudley, Edward G.; Wade, Joseph T.

    DNA microarrays (often interchangeably called DNA chips or DNA arrays) are among the most popular analytical tools for high-throughput comparative genomic and transcriptomic analyses of foodborne bacterial pathogens. A typical DNA microarray contains hundreds to millions of small DNA probes that are chemically attached (or "printed") onto the surface of a microscopic glass slide. Depending on the specific "printing" and probe synthesis technologies for different microarray platforms, such DNA probes can be PCR amplicons or in situ synthesized short oligonucleotides. DNA microarray technologies have revolutionized the way that we investigate the biology of foodborne bacterial pathogens. The major advantage of these technologies is that DNA microarrays allow comparison of subtle genomic or transcriptomic variations between two bacterial samples, such as genomic variations between two different bacterial strains or transcriptomic alterations of same bacterial strain under two different treatments. Some applications of comparative genomic hybridization microarrays and global gene expression microarrays have been covered in previous chapters of this book.

  14. Transcriptomic Analysis of Phenotypic Changes in Birch (Betula platyphylla) Autotetraploids

    PubMed Central

    Mu, Huai-Zhi; Liu, Zi-Jia; Lin, Lin; Li, Hui-Yu; Jiang, Jing; Liu, Gui-Feng

    2012-01-01

    Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and transcriptomes of these autotetraploid individuals were compared with those of diploid trees. Autotetraploids were generally superior in breast-height diameter, volume, leaf, fruit and stoma and were generally inferior in height compared to diploids. Transcriptome data revealed numerous changes in gene expression attributable to autotetraploidization, which resulted in the upregulation of 7052 unigenes and the downregulation of 3658 unigenes. Pathway analysis revealed that the biosynthesis and signal transduction of indoleacetate (IAA) and ethylene were altered after genome duplication, which may have contributed to phenotypic changes. These results shed light on variations in birch autotetraploidization and help identify important genes for the genetic engineering of birch trees. PMID:23202935

  15. Transcriptomics as a tool to discover new antibacterial targets.

    PubMed

    Domínguez, Ángel; Muñoz, Elisa; López, M Carmen; Cordero, Miguel; Martínez, José Pedro; Viñas, Miguel

    2017-03-13

    The emergence of antibiotic-resistant pathogens, multiple drug-resistance, and extremely drug-resistant strains demonstrates the need for improved strategies to discover new drug-based compounds. The development of transcriptomics, proteomics, and metabolomics has provided new tools for global studies of living organisms. However, the compendium of expression profiles produced by these methods has introduced new scientific challenges into antimicrobial research. In this review, we discuss the practical value of transcriptomic techniques as well as their difficulties and pitfalls. We advocate the construction of new databases of transcriptomic data, using standardized formats in addition to standardized models of bacterial and yeast similar to those used in systems biology. The inclusion of proteomic and metabolomic data is also essential, as the resulting networks can provide a landscape to rationally predict and exploit new drug targets and to understand drug synergies.

  16. Transcriptomic analysis of incised leaf-shape determination in birch.

    PubMed

    Mu, Huaizhi; Lin, Lin; Liu, Guifeng; Jiang, Jing

    2013-12-01

    Plant researchers have focused much attention on leaf shape because of its importance in the identification. To evaluate the impact of intraspecies leaf-shape variation on the transcriptome, a series of Betula pendula 'Dalecarlica' and B. pendula saplings were generated through tissue culture. The leaf shapes and transcriptomes of B. pendula 'Dalecarlica' clones were compared with those of B. pendula clones. The leaf shape of B. pendula 'Dalecarlica' was incised and that of B. pendula was ovate. Transcriptome data revealed numerous changes in gene expression between B. pendula 'Dalecarlica' and B. pendula, including upregulation of 8767 unigenes and downregulation of 8379 unigenes in B. pendula 'Dalecarlica'. A pathway analysis revealed that the transport and signal transduction of auxin were altered in 'Dalecarlica', which may have contributed to its altered leaf shape. These results shed light on variation in birch leaf shape and help identify important genes for the genetic engineering of birch trees.

  17. Transcriptomics of the Bed Bug (Cimex lectularius)

    PubMed Central

    Rajarapu, Swapna P.; Jones, Susan C.; Mittapalli, Omprakash

    2011-01-01

    Background Bed bugs (Cimex lectularius) are blood-feeding insects poised to become one of the major pests in households throughout the United States. Resistance of C. lectularius to insecticides/pesticides is one factor thought to be involved in its sudden resurgence. Despite its high-impact status, scant knowledge exists at the genomic level for C. lectularius. Hence, we subjected the C. lectularius transcriptome to 454 pyrosequencing in order to identify potential genes involved in pesticide resistance. Methodology and Principal Findings Using 454 pyrosequencing, we obtained a total of 216,419 reads with 79,596,412 bp, which were assembled into 35,646 expressed sequence tags (3902 contigs and 31744 singletons). Nearly 85.9% of the C. lectularius sequences showed similarity to insect sequences, but 44.8% of the deduced proteins of C. lectularius did not show similarity with sequences in the GenBank non-redundant database. KEGG analysis revealed putative members of several detoxification pathways involved in pesticide resistance. Lamprin domains, Protein Kinase domains, Protein Tyrosine Kinase domains and cytochrome P450 domains were among the top Pfam domains predicted for the C. lectularius sequences. An initial assessment of putative defense genes, including a cytochrome P450 and a glutathione-S-transferase (GST), revealed high transcript levels for the cytochrome P450 (CYP9) in pesticide-exposed versus pesticide-susceptible C. lectularius populations. A significant number of single nucleotide polymorphisms (296) and microsatellite loci (370) were predicted in the C. lectularius sequences. Furthermore, 59 putative sequences of Wolbachia were retrieved from the database. Conclusions To our knowledge this is the first study to elucidate the genetic makeup of C. lectularius. This pyrosequencing effort provides clues to the identification of potential detoxification genes involved in pesticide resistance of C. lectularius and lays the foundation for future

  18. A human glomerular SAGE transcriptome database

    PubMed Central

    2009-01-01

    Background To facilitate in the identification of gene products important in regulating renal glomerular structure and function, we have produced an annotated transcriptome database for normal human glomeruli using the SAGE approach. Description The database contains 22,907 unique SAGE tag sequences, with a total tag count of 48,905. For each SAGE tag, the ratio of its frequency in glomeruli relative to that in 115 non-glomerular tissues or cells, a measure of transcript enrichment in glomeruli, was calculated. A total of 133 SAGE tags representing well-characterized transcripts were enriched 10-fold or more in glomeruli compared to other tissues. Comparison of data from this study with a previous human glomerular Sau3A-anchored SAGE library reveals that 47 of the highly enriched transcripts are common to both libraries. Among these are the SAGE tags representing many podocyte-predominant transcripts like WT-1, podocin and synaptopodin. Enrichment of podocyte transcript tags SAGE library indicates that other SAGE tags observed at much higher frequencies in this glomerular compared to non-glomerular SAGE libraries are likely to be glomerulus-predominant. A higher level of mRNA expression for 19 transcripts represented by glomerulus-enriched SAGE tags was verified by RT-PCR comparing glomeruli to lung, liver and spleen. Conclusion The database can be retrieved from, or interrogated online at http://cgap.nci.nih.gov/SAGE. The annotated database is also provided as an additional file with gene identification for 9,022, and matches to the human genome or transcript homologs in other species for 1,433 tags. It should be a useful tool for in silico mining of glomerular gene expression. PMID:19500374

  19. Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly.

    PubMed

    Yazawa, Takayuki; Kawahigashi, Hiroyuki; Matsumoto, Takashi; Mizuno, Hiroshi

    2013-01-01

    The recent development of RNA sequencing (RNA-seq) technology has enabled us to analyze the transcriptomes of plants and their pathogens simultaneously. However, RNA-seq often relies on aligning reads to a reference genome and is thus unsuitable for analyzing most plant pathogens, as their genomes have not been fully sequenced. Here, we analyzed the transcriptomes of Sorghum bicolor (L.) Moench and its pathogen Bipolaris sorghicola simultaneously by using RNA-seq in combination with de novo transcriptome assembly. We sequenced the mixed transcriptome of the disease-resistant sorghum cultivar SIL-05 and B. sorghicola in infected leaves in the early stages of infection (12 and 24 h post-inoculation) by using Illumina mRNA-Seq technology. Sorghum gene expression was quantified by aligning reads to the sorghum reference genome. For B. sorghicola, reads that could not be aligned to the sorghum reference genome were subjected to de novo transcriptome assembly. We identified genes of B. sorghicola for growth of this fungus in sorghum, as well as genes in sorghum for the defense response. The genes of B. sorghicola included those encoding Woronin body major protein, LysM domain-containing intracellular hyphae protein, transcriptional factors CpcA and HacA, and plant cell-wall degrading enzymes. The sorghum genes included those encoding two receptors of the simple eLRR domain protein family, transcription factors that are putative orthologs of OsWRKY45 and OsWRKY28 in rice, and a class III peroxidase that is a homolog involved in disease resistance in the Poaceae. These defense-related genes were particularly strongly induced among paralogs annotated in the sorghum genome. Thus, in the absence of genome sequences for the pathogen, simultaneous transcriptome analysis of plant and pathogen by using de novo assembly was useful for identifying putative key genes in the plant-pathogen interaction.

  20. Simultaneous Transcriptome Analysis of Sorghum and Bipolaris sorghicola by Using RNA-seq in Combination with De Novo Transcriptome Assembly

    PubMed Central

    Yazawa, Takayuki; Kawahigashi, Hiroyuki; Matsumoto, Takashi; Mizuno, Hiroshi

    2013-01-01

    The recent development of RNA sequencing (RNA-seq) technology has enabled us to analyze the transcriptomes of plants and their pathogens simultaneously. However, RNA-seq often relies on aligning reads to a reference genome and is thus unsuitable for analyzing most plant pathogens, as their genomes have not been fully sequenced. Here, we analyzed the transcriptomes of Sorghum bicolor (L.) Moench and its pathogen Bipolaris sorghicola simultaneously by using RNA-seq in combination with de novo transcriptome assembly. We sequenced the mixed transcriptome of the disease-resistant sorghum cultivar SIL-05 and B. sorghicola in infected leaves in the early stages of infection (12 and 24 h post-inoculation) by using Illumina mRNA-Seq technology. Sorghum gene expression was quantified by aligning reads to the sorghum reference genome. For B. sorghicola, reads that could not be aligned to the sorghum reference genome were subjected to de novo transcriptome assembly. We identified genes of B. sorghicola for growth of this fungus in sorghum, as well as genes in sorghum for the defense response. The genes of B. sorghicola included those encoding Woronin body major protein, LysM domain-containing intracellular hyphae protein, transcriptional factors CpcA and HacA, and plant cell-wall degrading enzymes. The sorghum genes included those encoding two receptors of the simple eLRR domain protein family, transcription factors that are putative orthologs of OsWRKY45 and OsWRKY28 in rice, and a class III peroxidase that is a homolog involved in disease resistance in the Poaceae. These defense-related genes were particularly strongly induced among paralogs annotated in the sorghum genome. Thus, in the absence of genome sequences for the pathogen, simultaneous transcriptome analysis of plant and pathogen by using de novo assembly was useful for identifying putative key genes in the plant–pathogen interaction. PMID:23638091

  1. Transcriptome analysis of adiposity in domestic ducks by transcriptomic comparison with their wild counterparts.

    PubMed

    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.

  2. Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants

    PubMed Central

    2010-01-01

    Background 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. Results 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. Conclusions 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. PMID:20565927

  3. Analysis, annotation, and profiling of the oat seed transcriptome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Novel high-throughput next generation sequencing (NGS) technologies are providing opportunities to explore genomes and transcriptomes in a cost-effective manner. To construct a gene expression atlas of developing oat (Avena sativa) seeds, two software packages specifically designed for RNA-seq (Trin...

  4. Shooting through time: new insights from transcriptomic data.

    PubMed

    Harrison, C Jill

    2015-08-01

    Plant evo-devo research aims to identify the nature of genetic change underpinning the evolution of diverse plant forms. A transcriptomic study comparing gene expression profiles in the meristematic shoot tips of three distantly related vascular plants suggests that different genes were recruited to regulate similar meristematic processes during evolution.

  5. Transcriptome of the Antarctic brooding gastropod mollusc Margarella antarctica.

    PubMed

    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.

  6. The effect of 2-phenylethanol treatment on Aspergillus flavus transcriptome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pichia anomalais, which produces the antimicrobial volatile 2-phenylethanol (2-PE), is effective in reducing A. flavus growth and aflatoxin production. We treated A. flavus NRRL3357 with 2-PE and analyzed changes in the transcriptomic profiles at different stages of fungal growth. RNA-Seq reads from...

  7. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Premise of the study: Chloroplast microsatellite loci were characterized from transcriptomes of Artocarpus (A.) altilis (breadfruit) and A. camansi (breadnut). They were tested in A. odoratissimus (terap) and A. altilis and evaluated in silico for two congeners. Methods and Results: 15 simple seque...

  8. Bacillus anthracis genome organization in light of whole transcriptome sequencing

    SciTech Connect

    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. A comprehensive analysis of the human placenta transcriptome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As the conduit for nutrients and growth signals, the placenta is critical to establishing an environment sufficient for fetal growth and development. To better understand the mechanisms regulating placental development and gene expression, we characterized the transcriptome of term placenta from 20 ...

  10. The transcriptomics of an experimentally evolved plant-virus interaction

    PubMed Central

    Hillung, Julia; García-García, Francisco; Dopazo, Joaquín; Cuevas, José M.; Elena, Santiago F.

    2016-01-01

    Models of plant-virus interaction assume that the ability of a virus to infect a host genotype depends on the matching between virulence and resistance genes. Recently, we evolved tobacco etch potyvirus (TEV) lineages on different ecotypes of Arabidopsis thaliana, and found that some ecotypes selected for specialist viruses whereas others selected for generalists. Here we sought to evaluate the transcriptomic basis of such relationships. We have characterized the transcriptomic responses of five ecotypes infected with the ancestral and evolved viruses. Genes and functional categories differentially expressed by plants infected with local TEV isolates were identified, showing heterogeneous responses among ecotypes, although significant parallelism existed among lineages evolved in the same ecotype. Although genes involved in immune responses were altered upon infection, other functional groups were also pervasively over-represented, suggesting that plant resistance genes were not the only drivers of viral adaptation. Finally, the transcriptomic consequences of infection with the generalist and specialist lineages were compared. Whilst the generalist induced very similar perturbations in the transcriptomes of the different ecotypes, the perturbations induced by the specialist were divergent. Plant defense mechanisms were activated when the infecting virus was specialist but they were down-regulated when infecting with generalist. PMID:27113435

  11. The transcriptomics of an experimentally evolved plant-virus interaction.

    PubMed

    Hillung, Julia; García-García, Francisco; Dopazo, Joaquín; Cuevas, José M; Elena, Santiago F

    2016-04-26

    Models of plant-virus interaction assume that the ability of a virus to infect a host genotype depends on the matching between virulence and resistance genes. Recently, we evolved tobacco etch potyvirus (TEV) lineages on different ecotypes of Arabidopsis thaliana, and found that some ecotypes selected for specialist viruses whereas others selected for generalists. Here we sought to evaluate the transcriptomic basis of such relationships. We have characterized the transcriptomic responses of five ecotypes infected with the ancestral and evolved viruses. Genes and functional categories differentially expressed by plants infected with local TEV isolates were identified, showing heterogeneous responses among ecotypes, although significant parallelism existed among lineages evolved in the same ecotype. Although genes involved in immune responses were altered upon infection, other functional groups were also pervasively over-represented, suggesting that plant resistance genes were not the only drivers of viral adaptation. Finally, the transcriptomic consequences of infection with the generalist and specialist lineages were compared. Whilst the generalist induced very similar perturbations in the transcriptomes of the different ecotypes, the perturbations induced by the specialist were divergent. Plant defense mechanisms were activated when the infecting virus was specialist but they were down-regulated when infecting with generalist.

  12. Translating Cancer Genomes and Transcriptomes for Precision Oncology

    PubMed Central

    Roychowdhury, Sameek; Chinnaiyan, Arul M.

    2015-01-01

    Understanding the molecular landscape of cancer has facilitated the development of diagnostic, prognostic, and predictive biomarkers for clinical oncology. Developments in next generation DNA sequencing technologies have increased the speed and reduced the cost of sequencing the nucleic acids of cancer cells. This has unlocked opportunities to characterize the genomic and transcriptomic landscapes of cancer for basic science research through projects such as The Cancer Genome Atlas. The cancer genome includes DNA-based alterations such as point mutations or gene duplications. The cancer transcriptome involves RNA-based alterations including changes in messenger RNAs. Together the genome and transcriptome can provide a comprehensive view of an individual patient’s cancer and is beginning to impact real-time clinical decision-making. We discuss several opportunities for translating this basic science knowledge into clinical practice including a molecular classification of cancer, heritable risk of cancer, eligibility for targeted therapies, and the development of innovative genomic-based clinical trials. In this review, we outline key applications and new directions for translating the cancer genome and transcriptome into patient care in the clinic. PMID:26528881

  13. The Anopheles gambiae transcriptome - a turning point for malaria control.

    PubMed

    Domingos, A; Pinheiro-Silva, R; Couto, J; do Rosário, V; de la Fuente, J

    2017-04-01

    Mosquitoes are important vectors of several pathogens and thereby contribute to the spread of diseases, with social, economic and public health impacts. Amongst the approximately 450 species of Anopheles, about 60 are recognized as vectors of human malaria, the most important parasitic disease. In Africa, Anopheles gambiae is the main malaria vector mosquito. Current malaria control strategies are largely focused on drugs and vector control measures such as insecticides and bed-nets. Improvement of current, and the development of new, mosquito-targeted malaria control methods rely on a better understanding of mosquito vector biology. An organism's transcriptome is a reflection of its physiological state and transcriptomic analyses of different conditions that are relevant to mosquito vector competence can therefore yield important information. Transcriptomic analyses have contributed significant information on processes such as blood-feeding parasite-vector interaction, insecticide resistance, and tissue- and stage-specific gene regulation, thereby facilitating the path towards the development of new malaria control methods. Here, we discuss the main applications of transcriptomic analyses in An. gambiae that have led to a better understanding of mosquito vector competence.

  14. Transcriptomics and proteomics of drought tolerance in peanuts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Two peanut mini-core accessions exhibiting divergent responses to water-deficit stress were identified from a suite of physiological screening assays. In the present study we employed a combined transcriptomics and proteomics approach to study both the primary transcriptional networks and functional...

  15. A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns.

    PubMed

    Domazet-Lošo, Tomislav; Tautz, Diethard

    2010-12-09

    Parallels between phylogeny and ontogeny have been discussed for almost two centuries, and a number of theories have been proposed to explain such patterns. Especially elusive is the phylotypic stage, a phase during development where species within a phylum are particularly similar to each other. Although this has formerly been interpreted as a recapitulation of phylogeny, it is now thought to reflect an ontogenetic progression phase, where strong constraints on developmental regulation and gene interactions exist. Several studies have shown that genes expressed during this stage evolve at a slower rate, but it has so far not been possible to derive an unequivocal molecular signature associated with this stage. Here we use a combination of phylostratigraphy and stage-specific gene expression data to generate a cumulative index that reflects the evolutionary age of the transcriptome at given ontogenetic stages. Using zebrafish ontogeny and adult development as a model, we find that the phylotypic stage does indeed express the oldest transcriptome set and that younger sets are expressed during early and late development, thus faithfully mirroring the hourglass model of morphological divergence. Reproductively active animals show the youngest transcriptome, with major differences between males and females. Notably, ageing animals express increasingly older genes. Comparisons with similar data sets from flies and nematodes show that this pattern occurs across phyla. Our results indicate that an old transcriptome marks the phylotypic phase and that phylogenetic differences at other ontogenetic stages correlate with the expression of newly evolved genes.

  16. Response of sunflower (Helianthus annuus L.) leaf surface defenses to exogenous methyl jasmonate.

    PubMed

    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.

  17. Dynamics of the chili pepper transcriptome during fruit development

    PubMed Central

    2014-01-01

    Background The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. Results RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; ‘Tampiqueño 74’) collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40–60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. Conclusions In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all

  18. Effects of steroid hormones on differentiated glandular epithelial and stromal cells in a three dimensional cell culture model of the canine endometrium

    PubMed Central

    2013-01-01

    Background Oestrogens and progesterone have a significant impact on the endometrium during the canine oestrous cycle. Their receptors mediate plasma steroid hormone levels and are expressed in several endometrial cell types. Altered steroid receptor expression patterns are involved in serious uterine diseases; however the mechanisms of hormone action during pathogenesis in these tissues remain unclear. The development of 3D culture systems of canine endometrial cells provides an opportunity for the effects of steroid hormones to be quantitatively assessed in a more in vivo-like setting. The present study aimed to determine the effects of the steroid hormones 17β-estradiol (E) and progesterone (P) on the expression of the oestrogen and progesterone receptors (ER and PR), and on proliferative activity, in a 3D co-culture system of canine uterine origin, comprising differentiated endometrial glands, and stromal cells (SCs). Results Morphology, differentiation, and apical-basolateral polarity of cultured glandular epithelial cells (GECs) were comparable to those in native uterine tissue as assessed by immunohistochemistry using differentiation markers (β-catenin, laminin), lectin histochemistry, and transmission electron microscopy. Supplementation of our 3D-culture system with E (at 15, 30 and 100 pg/mL) resulted in constant levels of ER expression in GECs, but reduced expression levels in SCs. PR expression was reduced in both GECs and SCs following treatment with E. 3 ng/mL P resulted in increased ER expression in GECs, but a decrease in SCs. PR expression in GECs increased in all P-treated groups, whereas PRs in SCs decreased with the lowest and highest doses, but increased with the middle dose of treatment. Proliferative activity, assessed by Ki67 staining, remained below 1% in all assays and cell types. Conclusions The present study demonstrates the applicability of our 3D organotypic canine endometrium-derived culture system for cellular-level studies. 3D

  19. Carbonic anhydrase IX (CA-IX) and human papillomavirus (HPV) as diagnostic biomarkers of cervical dysplasia/neoplasia in women with a cytologic diagnosis of atypical glandular cells (AGC): a Gynecologic Oncology Group (GOG) Study

    PubMed Central

    Liao, Shu-Yuan; Rodgers, William H.; Kauderer, James; Bonfiglio, Thomas A.; Walker, Joan L.; Darcy, Kathleen M.; Carter, Randy; Hatae, Masayuji; Levine, Lyuba; Spirtos, Nick M; Stanbridge, Eric J.

    2009-01-01

    High-risk human papillomavirus (H-HPV) infection is strongly linked to cervical neoplasia but its role in detecting glandular lesions is unclear. In the cervix, carbonic anhydrase IX (CA-IX) is expressed in cervical neoplasia, but rarely in the benign cervix. The diagnostic utility of these biomarkers was evaluated in women with a cytologic diagnosis of atypical glandular cells (AGC). H-HPV was detected using Hybrid Capture 2 (HC2) in liquid based cytology and CA-IX immunoreactivity was studied on conventional Pap smears. Of 403 patients, 111 (28%) were positive for significant cervical lesions (SCLs) including CIN2, CIN3, adenocarcinoma in situ or invasive carcinoma. CA-IX testing alone (n=403) had a sensitivity of 75%, 95%, or 65% for SCLs, significant glandular lesions (GLs) or squamous lesions (SLs), respectively, with a specificity of 88%, and a false negative rate (FNR defined as one minus negative predictive value) of 10%. Testing for H-HPV (n=122) had a sensitivity of 97%, 100%, or 96% for SCLs, GLs or SLs, respectively, with a specificity of 87%, and a FNRof 1%. The combination of CA-IX and H-HPV testing (n=122), collectively, had the same sensitivity, specificity and FNR for SCLs, GLs or SLs as H-HPV testing alone. The conclusions of this study are that both H-HPV and CA-IX testing are useful diagnostic markers for GLs. However, H-HPV testing is a better diagnostic marker for SLs. The combination of CA-IX with H-HPV testing does not improve the diagnostic accuracy for cervical neoplasia in women with AGC diagnosis over that of H-HPV testing alone. PMID:19670419

  20. The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development

    PubMed Central

    Rosengarten, Rafael D.; Santhanam, Balaji; Kokosar, Janez; Shaulsky, Gad

    2016-01-01

    Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs) in D. discoideum. To characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq) library preparation method that selectively depletes ribosomal RNAs (rRNAs). We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs), 621 lncRNAs, and 162 putative antisense RNAs (asRNAs). The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA) transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by which D. discoideum compensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development. PMID:27932387

  1. Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome.

    PubMed

    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.

  2. A quantitative transcriptome reference map of the normal human brain.

    PubMed

    Caracausi, Maria; Vitale, Lorenza; Pelleri, Maria Chiara; Piovesan, Allison; Bruno, Samantha; Strippoli, Pierluigi

    2014-10-01

    We performed an innovative systematic meta-analysis of 60 gene expression profiles of whole normal human brain, to provide a quantitative transcriptome reference map of it, i.e. a reference typical value of expression for each of the 39,250 known, mapped and 26,026 uncharacterized (unmapped) transcripts. To this aim, we used the software named Transcriptome Mapper (TRAM), which is able to generate transcriptome maps based on gene expression data from multiple sources. We also analyzed differential expression by comparing the brain transcriptome with those derived from human foetal brain gene expression, from a pool of human tissues (except the brain) and from the two normal human brain regions cerebellum and cerebral cortex, which are two of the main regions severely affected when cognitive impairment occurs, as happens in the case of trisomy 21. Data were downloaded from microarray databases, processed and analyzed using TRAM software and validated in vitro by assaying gene expression through several magnitude orders by 'real-time' reverse transcription polymerase chain reaction (RT-PCR). The excellent agreement between in silico and experimental data suggested that our transcriptome maps may be a useful quantitative reference benchmark for gene expression studies related to the human brain. Furthermore, our analysis yielded biological insights about those genes which have an intrinsic over-/under-expression in the brain, in addition offering a basis for the regional analysis of gene expression. This could be useful for the study of chromosomal alterations associated to cognitive impairment, such as trisomy 21, the most common genetic cause of intellectual disability.

  3. The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development.

    PubMed

    Rosengarten, Rafael D; Santhanam, Balaji; Kokosar, Janez; Shaulsky, Gad

    2017-02-09

    Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs) in D. discoideum To characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq) library preparation method that selectively depletes ribosomal RNAs (rRNAs). We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs), 621 lncRNAs, and 162 putative antisense RNAs (asRNAs). The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA) transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by which D. discoideum compensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development.

  4. Combined genome and transcriptome analysis of single disseminated cancer cells from bone marrow of prostate cancer patients reveals unexpected transcriptomes.

    PubMed

    Gužvić, Miodrag; Braun, Bernhard; Ganzer, Roman; Burger, Maximilian; Nerlich, Michael; Winkler, Sebastian; Werner-Klein, Melanie; Czyż, Zbigniew T; Polzer, Bernhard; Klein, Christoph A

    2014-12-15

    Bone is the most frequent site of metastasis in prostate cancer and patients with bone metastases are deemed incurable. Targeting prostate cancer cells that disseminated to the bone marrow before surgery and before metastatic outgrowth may therefore prevent lethal metastasis. This prompted us to directly analyze the transcriptome of disseminated cancer cells (DCC) isolated from patients with nonmetastatic (UICC stage M0) prostate cancer. We screened 105 bone marrow samples of patients with M0-stage prostate cancer and 18 bone marrow samples of patients without malignancy for the presence of EpCAM(+) single cells. In total, we isolated 270 cells from both groups by micromanipulation and globally amplified their mRNA. We used targeted transcriptional profiling to unambiguously identify DCCs for subsequent in-depth analysis. Transcriptomes of all cells were examined for the expression of EPCAM, KRT8, KRT18, KRT19, KRT14, KRT6a, KRT5, KLK3 (PSA), MAGEA2, MAGEA4, PTPRC (CD45), CD33, CD34, CD19, GYPC, SCL4A1 (band 3), and HBA2. Using these transcripts, we found it impossible to reliably identify true DCCs. We then applied combined genome and transcriptome analysis of single cells and found that EpCAM(+) cells from controls expressed transcripts thought to be epithelial-specific, whereas true DCCs may express hematopoietic transcripts. These results point to an unexpected transcriptome plasticity of epithelial cancer cells in bone marrow and question common transcriptional criteria to identify DCCs.

  5. Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis

    PubMed Central

    Forestan, Cristian; Aiese Cigliano, Riccardo; Farinati, Silvia; Lunardon, Alice; Sanseverino, Walter; Varotto, Serena

    2016-01-01

    Plant’s response and adaptation to abiotic stresses involve sophisticated genetic and epigenetic regulatory systems. To obtain a global view of molecular response to osmotic stresses, including the non-coding portion of genome, we conducted a total leaf transcriptome analysis on maize plants subjected to prolonged drought and salt stresses. Stress application to both B73 wild type and the epiregulator mutant rpd1-1/rmr6 allowed dissection of the epigenetic component of stress response. Coupling total RNA-Seq and transcriptome re-assembly we annotated thousands of new maize transcripts, together with 13,387 lncRNAs that may play critical roles in regulating gene expression. Differential expression analysis revealed hundreds of genes modulated by long-term stress application, including also many lncRNAs and transposons specifically induced by stresses. The amplitude and dynamic of the stress-modulated gene sets are very different between B73 and rpd1-1/rmr6 mutant plants, as result of stress-like effect on genome regulation caused by the mutation itself, which activates many stress-related genes even in control condition. The analyzed extensive set of total RNA-Seq data, together with the improvement of the transcriptome and the identification of the non-coding portion of the transcriptome give a revealing insight into the genetic and epigenetic mechanism responsible for maize molecular response to abiotic stresses. PMID:27461139

  6. Transcriptome and Biochemical Analyses of Fungal Degradation of Wood

    SciTech Connect

    Tien, Ming

    2009-03-14

    Lignocellulosic accounts for a large percentage of material that can be utilized for biofuels. The most costly part of lignocellulosic material processing is the initial hydrolysis of the wood which is needed to circumvent the lignin barrier and the crystallinity of cellulose. Enzymes will play an increased role in this conversion in that they potentially provide an alternative to costly and caustic high temperature and acid treatment. The increasing use of enzymes in biotechnology is facilitated by both continued improvements in enzyme technology but also in the discovery of new and novel enzymes. The present proposal is aimed at identifying the enzymes which are known to depolymerize woody biomass. Fundamental understanding of how nature gains access to cellulose and hemicellulose will impact all applications. Because fungi are the only known microbes capable of circumventing the lignin barrier, knowledge of the enzyme they use is of great potential for biofuel processing. Nature has evolved different fungal mechanisms for enzymatic hydrolysis of wood. Most notable are the white-rot fungi (wrf) and the brown-rot fungi (brf). This proposed research aims at determining the complete transcriptome of three wrf and two brf to determine the enzymes involved in lignocellulose degradation. The transcriptome work will be supported by enzyme characterization (and zymograms) and finally analysis of the lignin component to determine the mode of lignin modification. In this proposed research, we hypothesize that: 1) Determination of the complete transcriptome of closely related white and brown rot fungi will lead to knowledge of the relevant enzymes involved in wood degradation. 2) Knowledge of the extracellular transcriptome and the mechanism of wood decay can only be obtained if the products of the decay are known. As such, characterization of the lignin oxidation products will correlate the enzymes involved (obtained from the transcriptome) to the lignin oxidation products

  7. Ameliorated de novo transcriptome assembly using Illumina paired end sequence data with Trinity Assembler

    PubMed Central

    Bankar, Kiran Gopinath; Todur, Vivek Nagaraj; Shukla, Rohit Nandan; Vasudevan, Madavan

    2015-01-01

    Advent of Next Generation Sequencing has led to possibilities of de novo transcriptome assembly of organisms without availability of complete genome sequence. Among various sequencing platforms available, Illumina is the most widely used platform based on data quality, quantity and cost. Various de novo transcriptome assemblers are also available today for construction of de novo transcriptome. In this study, we aimed at obtaining an ameliorated de novo transcriptome assembly with sequence reads obtained from Illumina platform and assembled using Trinity Assembler. We found that, primary transcriptome assembly obtained as a result of Trinity can be ameliorated on the basis of transcript length, coverage, and depth and protein homology. Our approach to ameliorate is reproducible and could enhance the sensitivity and specificity of the assembled transcriptome which could be critical for validation of the assembled transcripts and for planning various downstream biological assays. PMID:26484285

  8. Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis.

    PubMed

    Woo, Hye Ryun; Koo, Hee Jung; Kim, Jeongsik; Jeong, Hyobin; Yang, Jin Ok; Lee, Il Hwan; Jun, Ji Hyung; Choi, Seung Hee; Park, Su Jin; Kang, Byeongsoo; Kim, You Wang; Phee, Bong-Kwan; Kim, Jin Hee; Seo, Chaehwa; Park, Charny; Kim, Sang Cheol; Park, Seongjin; Lee, Byungwook; Lee, Sanghyuk; Hwang, Daehee; Nam, Hong Gil; Lim, Pyung Ok

    2016-05-01

    Plant leaves, harvesting light energy and fixing CO2, are a major source of foods on the earth. Leaves undergo developmental and physiological shifts during their lifespan, ending with senescence and death. We characterized the key regulatory features of the leaf transcriptome during aging by analyzing total- and small-RNA transcriptomes throughout the lifespan of Arabidopsis (Arabidopsis thaliana) leaves at multidimensions, including age, RNA-type, and organelle. Intriguingly, senescing leaves showed more coordinated temporal changes in transcriptomes than growing leaves, with sophisticated regulatory networks comprising transcription factors and diverse small regulatory RNAs. The chloroplast transcriptome, but not the mitochondrial transcriptome, showed major changes during leaf aging, with a strongly shared expression pattern of nuclear transcripts encoding chloroplast-targeted proteins. Thus, unlike animal aging, leaf senescence proceeds with tight temporal and distinct interorganellar coordination of various transcriptomes that would be critical for the highly regulated degeneration and nutrient recycling contributing to plant fitness and productivity.

  9. Robust Dinoflagellata phylogeny inferred from public transcriptome databases.

    PubMed

    Price, Dana C; Bhattacharya, Debashish

    2017-03-08

    Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number. To address this issue, we used recently generated public sequencing data, including from the Moore Microbial Eukaryote Transcriptome Sequencing Project, to identify dinoflagellate-specific ortholog groups. These orthologs were combined to create a broadly sampled and highly resolved phylogeny of dinoflagellates. Our results emphasize the scope and utility of public sequencing databases in creating broad and robust phylogenies for large and complex taxonomic lineages, while also providing unique insights into the evolution of thecate dinoflagellates.

  10. Candidate olfaction genes identified within the Helicoverpa armigera Antennal Transcriptome.

    PubMed

    Liu, Yang; Gu, Shaohua; Zhang, Yongjun; Guo, Yuyuan; Wang, Guirong

    2012-01-01

    Antennal olfaction is extremely important for insect survival, mediating key behaviors such as host preference, mate choice, and oviposition site selection. Multiple antennal proteins are involved in olfactory signal transduction pathways. Of these, odorant receptors (ORs) and ionotropic receptors (IRs) confer specificity on olfactory sensory neuron responses. In this study, we identified the olfactory gene repertoire of the economically important agricultural pest moth, Helicoverpa armigera, by assembling the adult male and female antennal transcriptomes. Within the male and female antennal transcriptomes we identified a total of 47 OR candidate genes containing 6 pheromone receptor candidates. Additionally, 12 IR genes as well as 26 odorant-binding proteins and 12 chemosensory proteins were annotated. Our results allow a systematic functional analysis across much of conventional ORs repertoire and newly reported IRs mediating the key olfaction-mediated behaviors of H. armigera.

  11. InsectBase: a resource for insect genomes and transcriptomes

    PubMed Central

    Yin, Chuanlin; Shen, Gengyu; Guo, Dianhao; Wang, Shuping; Ma, Xingzhou; Xiao, Huamei; Liu, Jinding; Zhang, Zan; Liu, Ying; Zhang, Yiqun; Yu, Kaixiang; Huang, Shuiqing; Li, Fei

    2016-01-01

    The genomes and transcriptomes of hundreds of insects have been sequenced. However, insect community lacks an integrated, up-to-date collection of insect gene data. Here, we introduce the first release of InsectBase, available online at http://www.insect-genome.com. The database encompasses 138 insect genomes, 116 insect transcriptomes, 61 insect gene sets, 36 gene families of 60 insects, 7544 miRNAs of 69 insects, 96 925 piRNAs of Drosophila melanogaster and Chilo suppressalis, 2439 lncRNA of Nilaparvata lugens, 22 536 pathways of 78 insects, 678 881 untranslated regions (UTR) of 84 insects and 160 905 coding sequences (CDS) of 70 insects. This release contains over 12 million sequences and provides search functionality, a BLAST server, GBrowse, insect pathway construction, a Facebook-like network for the insect community (iFacebook), and phylogenetic analysis of selected genes. PMID:26578584

  12. InsectBase: a resource for insect genomes and transcriptomes.

    PubMed

    Yin, Chuanlin; Shen, Gengyu; Guo, Dianhao; Wang, Shuping; Ma, Xingzhou; Xiao, Huamei; Liu, Jinding; Zhang, Zan; Liu, Ying; Zhang, Yiqun; Yu, Kaixiang; Huang, Shuiqing; Li, Fei

    2016-01-04

    The genomes and transcriptomes of hundreds of insects have been sequenced. However, insect community lacks an integrated, up-to-date collection of insect gene data. Here, we introduce the first release of InsectBase, available online at http://www.insect-genome.com. The database encompasses 138 insect genomes, 116 insect transcriptomes, 61 insect gene sets, 36 gene families of 60 insects, 7544 miRNAs of 69 insects, 96,925 piRNAs of Drosophila melanogaster and Chilo suppressalis, 2439 lncRNA of Nilaparvata lugens, 22,536 pathways of 78 insects, 678,881 untranslated regions (UTR) of 84 insects and 160,905 coding sequences (CDS) of 70 insects. This release contains over 12 million sequences and provides search functionality, a BLAST server, GBrowse, insect pathway construction, a Facebook-like network for the insect community (iFacebook), and phylogenetic analysis of selected genes.

  13. Transcriptomes of the desiccation-tolerant resurrection plant Craterostigma plantagineum.

    PubMed

    Rodriguez, Maria C Suarez; Edsgärd, Daniel; Hussain, Syed S; Alquezar, David; Rasmussen, Morten; Gilbert, Thomas; Nielsen, Bjørn H; Bartels, Dorothea; Mundy, John

    2010-07-01

    Studies of the resurrection plant Craterostigma plantagineum have revealed some of the mechanisms which these desiccation-tolerant plants use to survive environments with extreme dehydration and restricted seasonal water. Most resurrection plants are polyploid with large genomes, which has hindered efforts to obtain whole genome sequences and perform mutational analysis. However, the application of deep sequencing technologies to transcriptomics now permits large-scale analyses of gene expression patterns despite the lack of a reference genome. Here we use pyro-sequencing to characterize 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 of the array of cellular responses controlled by gene expression that allow resurrection plants to survive desiccation.

  14. Overview and perspectives the transcriptome of Paracoccidioides brasiliensis.

    PubMed

    Andrade, Rosângela V; Da Silva, Silvana P; Torres, Fernando A G; Poças-Fonseca, Marcio José; Silva-Pereira, Ildenete; Maranhão, Andrea Q; Campos, Elida G; Moraes, Lídia Maria P; Jesuíno, Rosália S A; Pereira, Maristela; Soares, Célia M A; Walter, Maria Emília M T; Carvalho, Maria Joseá A; Almeida, Nalvo F; Brigido, Marcelo M; Felipe, Maria Sueli S

    2005-12-01

    Paracoccidioides brasiliensis is a dimorphic and thermo-regulated fungus which is the causative agent of paracoccidioidomycosis, an endemic disease widespread in Latin America that affects 10 million individuals. Pathogenicity is assumed to be a consequence of the dimorphic transition from mycelium to yeast cells during human infection. This review shows the results of the P. brasiliensis transcriptome project which generated 6,022 assembled groups from mycelium and yeast phases. Computer analysis using the tools of bioinformatics revealed several aspects from the transcriptome of this pathogen such as: general and differential metabolism in mycelium and yeast cells; cell cycle, DNA replication, repair and recombination; RNA biogenesis apparatus; translation and protein fate machineries; cell wall; hydrolytic enzymes; proteases; GPI-anchored proteins; molecular chaperones; insights into drug resistance and transporters; oxidative stress response and virulence. The present analysis has provided a more comprehensive view of some specific features considered relevant for the understanding of basic and applied knowledge of P. brasiliensis.

  15. Transcriptome complexity in cardiac development and diseases--an expanding universe between genome and phenome.

    PubMed

    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.

  16. RNA G-Quadruplexes as Key Motifs of the Transcriptome.

    PubMed

    Rouleau, Samuel; Jodoin, Rachel; Garant, Jean-Michel; Perreault, Jean-Pierre

    2017-04-06

    G-Quadruplexes are non-canonical secondary structures that can be adopted under physiological conditions by guanine-rich DNA and RNA molecules. They have been reported to occur, and to perform multiple biological functions, in the genomes and transcriptomes of many species, including humans. This chapter focuses specifically on RNA G-quadruplexes and reviews the most recent discoveries in the field, as well as addresses the upcoming challenges researchers studying these structures face.

  17. Analysis of the transcriptome in molecular epidemiology studies

    PubMed Central

    McHale, Cliona M.; Zhang, Luoping; Thomas, Reuben; smith, Martyn T.

    2016-01-01

    The human transcriptome is complex, comprising multiple transcript types, mostly in the form of non-coding RNA (ncRNA). The majority of ncRNA is of the long form (lncRNA, ≥200bp), which plays an important role in gene regulation through multiple mechanisms including epigenetics, chromatin modification, control of transcription factor binding, and regulation of alternative splicing. Both mRNA and ncRNA exhibit additional variability in the form of alternative splicing and RNA editing. All aspects of the human transcriptome can potentially be dysregulated by environmental exposures. Next-generation RNA sequencing (RNA-Seq) is the best available methodology to measure this although it has limitations, including experimental bias. The third phase of the MicroArray Quality Control Consortium project (MAQC-III), also called Sequencing Quality Control (SeQC), aims to address these limitations through standardization of experimental and bioinformatic methodologies. A limited number of toxicogenomic studies have been conducted to date using RNA-Seq. This review describes the complexity of the human transcriptome, the application of transcriptomics by RNA-Seq or microarray in molecular epidemiology studies, and limitations of these approaches including the type of cell or tissue analyzed, experimental variation, and confounding. By using good study designs with precise, individual exposure measurements, sufficient power and incorporation of phenotypic anchors, studies in human populations can identify biomarkers of exposure and/or early effect and elucidate mechanisms of action underlying associated diseases, even at low doses. Analysis of datasets at the pathway level can compensate for some of the limitations of RNA-Seq and, as more datasets become available, will increasingly elucidate the exposure-disease continuum. PMID:23907930

  18. Deep Sequencing of the Murine Olfactory Receptor Neuron Transcriptome

    PubMed Central

    Kanageswaran, Ninthujah; Demond, Marilen; Nagel, Maximilian; Schreiner, Benjamin S. P.; Baumgart, Sabrina; Scholz, Paul; Altmüller, Janine; Becker, Christian; Doerner, Julia F.; Conrad, Heike; Oberland, Sonja; Wetzel, Christian H.; Neuhaus, Eva M.; Hatt, Hanns; Gisselmann, Günter

    2015-01-01

    The ability of animals to sense and differentiate among thousands of odorants relies on a large set of olfactory receptors (OR) and a multitude of accessory proteins within the olfactory epithelium (OE). ORs and related signaling mechanisms have been the subject of intensive studies over the past years, but our knowledge regarding olfactory processing remains limited. The recent development of next generation sequencing (NGS) techniques encouraged us to assess the transcriptome of the murine OE. We analyzed RNA from OEs of female and male adult mice and from fluorescence-activated cell sorting (FACS)-sorted olfactory receptor neurons (ORNs) obtained from transgenic OMP-GFP mice. The Illumina RNA-Seq protocol was utilized to generate up to 86 million reads per transcriptome. In OE samples, nearly all OR and trace amine-associated receptor (TAAR) genes involved in the perception of volatile amines were detectably expressed. Other genes known to participate in olfactory signaling pathways were among the 200 genes with the highest expression levels in the OE. To identify OE-specific genes, we compared olfactory neuron expression profiles with RNA-Seq transcriptome data from different murine tissues. By analyzing different transcript classes, we detected the expression of non-olfactory GPCRs in ORNs and established an expression ranking for GPCRs detected in the OE. We also identified other previously undescribed membrane proteins as potential new players in olfaction. The quantitative and comprehensive transcriptome data provide a virtually complete catalogue of genes expressed in the OE and present a useful tool to uncover candidate genes involved in, for example, olfactory signaling, OR trafficking and recycling, and proliferation. PMID:25590618

  19. Characterisation of Caenorhabditis elegans sperm transcriptome and proteome

    PubMed Central

    2014-01-01

    Background Although sperm is transcriptionally and translationally quiescent, complex populations of RNAs, including mRNAs and non-coding RNAs, exist in sperm. Previous microarray analysis of germ cell mutants identified hundreds of sperm genes in Caenorhabditis elegans. To take a more comprehensive view on C. elegans sperm genes, here, we isolate highly pure sperm cells and employ high-throughput technologies to obtain sperm transcriptome and proteome. Results First, sperm transcriptome consists of considerable amounts of non-coding RNAs, many of which have not been annotated and may play functional roles during spermatogenesis. Second, apart from kinases/phosphatases as previously reported, ion binding proteins are also enriched in sperm, underlying the crucial roles of intracellular ions in post-translational regulation in sperm. Third, while the majority of sperm genes/proteins have low abundance, a small number of sperm genes/proteins are hugely enriched in sperm, implying that sperm only rely on a small set of proteins for post-translational regulation. Lastly, by extensive RNAi screening of sperm enriched genes, we identified a few genes that control fertility. Our further analysis reveals a tight correlation between sperm transcriptome and sperm small RNAome, suggesting that the endogenous siRNAs strongly repress sperm genes. This leads to an idea that the inefficient RNAi screening of sperm genes, a phenomenon currently with unknown causes, might result from the competition between the endogenous RNAi pathway and the exogenous RNAi pathway. Conclusions Together, the obtained sperm transcriptome and proteome serve as valuable resources to systematically study spermatogenesis in C. elegans. PMID:24581041

  20. Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii

    PubMed Central

    Puigvert, Marina; Guarischi-Sousa, Rodrigo; Zuluaga, Paola; Coll, Núria S.; Macho, Alberto P.; Setubal, João C.; Valls, Marc

    2017-01-01

    Bacterial wilt of potatoes—also called brown rot—is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by