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Sample records for glandular trichome transcriptome

  1. A Rapid Method for Isolating Glandular Trichomes

    PubMed Central

    Yerger, Ellen H.; Grazzini, Richard A.; Hesk, David; Cox-Foster, Diana L.; Craig, Richard; Mumma, Ralph O.

    1992-01-01

    A physical method is described for the rapid isolation of plant trichomes, with emphasis on stalked glandular types. The technique involved breaking frozen trichomes with powdered dry ice and collection of glandular heads by sieving from larger tissue fragments. This method was applied to several plants that bear similar stalked trichomes: geranium (Pelargonium), potato (Solanum tuberosum), tomato (Lycopersicon esculentum), squash (Cucurbita pepo), and velvetleaf (Abutilon theophrasti). The tissue preparation was of sufficient quality without further purification for biochemical and molecular studies. The preparation maintained the biochemical integrity of the trichomes for active enzymes and usable nucleic acids. A large quantity of tissue can be harvested; for example, 351 milligrams dry weight of glandular trichomes were harvested from geranium pedicels in 12 hours. The utility of the technique was demonstrated by examining the fatty acid composition of tall glandular trichomes of geraniums, Pelargonium ×hortorum L.H. Bailey. These purified cells contained high concentrations of unusual ω5-unsaturated fatty acids, proportionally 23.4% of total fatty acids in the trichomes. When the trichomes were removed, the supporting tissue contained no ω5-fatty acids, thereby unequivocally localizing ω5-fatty acids to the trichomes. Because ω5-fatty acids are unique precursors for the biosynthesis of ω5-anacardic acids, we conclude that anacardic acid synthesis must occur in the glandular trichomes. ImagesFigure 1Figure 2 PMID:16668834

  2. Secreting Glandular Trichomes: More than Just Hairs

    PubMed Central

    Wagner, George J.

    1991-01-01

    Secreting glandular plant trichome types which accumulate large quantities of metabolic products in the space between their gland cell walls and cuticle permit the plant to amass secretions in a compartment that is virtually outside the plant body. These structures not only accumulate and store what are often phytotoxic oils but they position these compounds as an apparent first line of defense at the surface of the plant. Recent advances in methods for isolation and study of trichome glands have allowed more precise analysis of gland cell metabolism and enzymology. Isolation of mutants with altered trichome phenotypes provides new systems for probing the genetic basis of trichome development. These advances and their continuation can pave the way for future attempts at modification of trichome secretion. The biochemical capability of glandular secreting trichomes and the potential for its future manipulation to exploit this external storage compartment is the focus of this review. PMID:16668241

  3. 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

  4. 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

  5. Induction of glandular and non-glandular trichomes by damage in leaves of Madia sativa under contrasting water regimes

    NASA Astrophysics Data System (ADS)

    Gonzáles, Wilfredo L.; Negritto, María A.; Suárez, Lorena H.; Gianoli, Ernesto

    2008-01-01

    Plant traits may play multiple functional roles simultaneously. Leaf trichomes have been related to resistance against herbivores as well as to enhanced water economy in the plant. In a greenhouse study, we evaluated the interactive effect of damage (control vs. mechanical damage) and water availability (control vs. low watering) on the expression of glandular and non-glandular leaf trichomes in the annual Chilean tarweed Madia sativa (Asteraceae). We found that the overall trichome density increased both after damage and when plants were grown under water shortage. Interestingly, the type of trichome induced after damage varied with each water environment. While damage induced glandular trichomes only under control watering, non-glandular trichomes were induced by damage only under experimental drought. Results indicate that in M. sativa glandular trichomes are equally induced by drought or damage but there is no additive effect of these factors. In both cases glandular trichome density apparently reached a limit, which may be interpreted in terms of constraint or efficacy. On the other hand, the synergistic effect of damage and drought on non-glandular trichomes might suggest that, compared to glandular ones, these trichomes are less responsive to each stress factor separately. Thus, for plants to induce non-glandular trichomes they must be subjected to a degree of stress above a threshold that was not reached for each individual factor in our experimental setting. We did not detect a significant correlation between trichome types. Thus, the contrasting patterns observed likely reflect independent responses of trichomes to the evaluated factors.

  6. The nonvolatile metabolome of sunflower linear glandular trichomes.

    PubMed

    Spring, Otmar; Pfannstiel, Jens; Klaiber, Iris; Conrad, Jürgen; Beifuß, Uwe; Apel, Lysanne; Aschenbrenner, Anna-Katharina; Zipper, Reinhard

    2015-11-01

    Uniseriate linear glandular trichomes occur on stems, leaves and flowering parts of Helianthus species and related taxa. Their metabolic activity and biological function are still poorly understood. A phytochemical study documented the accumulation of bisabolene type sesquiterpenes and flavonoids as the major constituents of the non-volatile metabolome of linear glandular trichomes in the common sunflower, Helianthus annuus. Besides known sesquiterpenes of the glandulone, helibisabonol and heliannuol type, four previously undescribed sesquiterpenes named glandulone D, E, F and helibisabonol C were identified by spectroscopic analysis. In addition, four known nevadensin type flavonoids varying in O-methoxy substitutions were found. None of them has previously been reported from Helianthus annuus. PMID:26412774

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

    PubMed

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

    2016-05-01

    The capitate glandular trichome is the most common type described in Asteraceae species. It is known for its ability to produce various plant metabolites of ecological and economic importance, among which sesquiterpene lactones are predominant. In this paper, we applied microscopy, phytochemical and molecular genetics techniques to characterise the capitate glandular trichome in Aldama discolor, a native Brazilian species of Asteraceae, with pharmacological potential. It was found that formation of trichomes on leaf primordia of germinating seeds starts between 24 h and 48 h after radicle growth indicates germination. The start of metabolic activity of trichomes was indicated by separation of the cuticle from the cell wall of secretory cells at the trichome tip after 72 h. This coincided with the accumulation of budlein A, the major sesquiterpene lactone of A. discolor capitate glandular trichomes, in extracts of leaf primordia after 96 h. In the same timeframe of 72-96 h post-germination, gene expression studies showed up-regulation of the putative germacrene A synthase (pGAS2) and putative germacrene A oxidase (pGAO) of A. discolor in the transcriptome of these samples, indicating the start of sesquiterpene lactone biosynthesis. Sequencing of the two genes revealed high similarity to HaGAS and HaGAO from sunflower, which shows that key steps of this pathway are highly conserved. The processes of trichome differentiation, metabolic activity and genetic regulation in A. discolor and in sunflower appear to be typical for other species of the subtribe Helianthinae. PMID:26642998

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

    PubMed

    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

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

    PubMed

    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

  11. 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

  12. Tobacco NtLTP1, a glandular-specific lipid transfer protein, is required for lipid secretion from glandular trichomes.

    PubMed

    Choi, Yong Eui; Lim, Soon; Kim, Hyun-Jung; Han, Jung Yeon; Lee, Mi-Hyun; Yang, Yanyan; Kim, Ji-Ah; Kim, Yun-Soo

    2012-05-01

    Glandular trichomes are the phytochemical factories of plants, and they secrete a wide range of commercially important natural products such as lipids, terpenes and flavonoids. Herein, we report that the Nicotiana tabacum LTP1 (NtLTP1) gene, which is specifically expressed in long glandular trichomes, plays a role in lipid secretion from trichome heads. NtLTP1 mRNA is abundantly transcribed in trichomes, but NtLTP3, NtLTP4 and NtLTP5 are not. In situ hybridization revealed that NtLTP1 mRNAs accumulate specifically in long trichomes and not in short trichomes or epidermal cells. X-gluc staining of leaves from a transgenic plant expressing the NtLTP1 promoter fused to a GUS gene revealed that NtLTP1 protein accumulated preferentially on the tops of long glandular trichomes. GFP fluorescence from transgenic tobacco plants expressing an NtLTP1-GFP fusion protein was localized at the periphery of cells and in the excreted liquid droplets from the glandular trichome heads. In vitro assays using a fluorescent 2-p-toluidinonaphthalene-6-sulfonate probe indicated that recombinant NtLTP1 had lipid-binding activity. The overexpression of NtLTP1 in transgenic tobacco plants resulted in the increased secretion of trichome exudates, including epicuticular wax. In transgenic NtLTP1-RNAi lines, liquid secretion from trichomes was strongly reduced, but epicuticular wax secretion was not altered. Moreover, transgenic tobacco plants overexpressing NtLTP1 showed increased protection against aphids. Taken together, these data suggest that NtLTP1 is abundantly expressed in long glandular trichomes, and may play a role in lipid secretion from long glandular trichomes. PMID:22171964

  13. 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...

  14. Genetic basis for glandular trichome formation in cotton.

    PubMed

    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

  15. 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

  16. Engineering of Tomato Glandular Trichomes for the Production of Specialized Metabolites.

    PubMed

    Kortbeek, R W J; Xu, J; Ramirez, A; Spyropoulou, E; Diergaarde, P; Otten-Bruggeman, I; de Both, M; Nagel, R; Schmidt, A; Schuurink, R C; Bleeker, P M

    2016-01-01

    Glandular trichomes are specialized tissues on the epidermis of many plant species. On tomato they synthesize, store, and emit a variety of metabolites such as terpenoids, which play a role in the interaction with insects. Glandular trichomes are excellent tissues for studying the biosynthesis of specialized plant metabolites and are especially suitable targets for metabolic engineering. Here we describe the strategy for engineering tomato glandular trichomes, first with a transient expression system to provide proof of trichome specificity of selected promoters. Using microparticle bombardment, the trichome specificity of a terpene-synthase promoter could be validated in a relatively fast way. Second, we describe a method for stable expression of genes of interest in trichomes. Trichome-specific expression of another terpene-synthase promoter driving the yellow-fluorescence protein-gene is presented. Finally, we describe a case of the overexpression of farnesyl diphosphate synthase (FPS), specifically in tomato glandular trichomes, providing an important precursor in the biosynthetic pathway of sesquiterpenoids. FPS was targeted to the plastid aiming to engineer sesquiterpenoid production, but interestingly leading to a loss of monoterpenoid production in the transgenic tomato trichomes. With this example we show that trichomes are amenable to engineering though, even with knowledge of a biochemical pathway, the result of such engineering can be unexpected. PMID:27480691

  17. Bidirectional secretions from glandular trichomes of pyrethrum enable immunization of seedlings.

    PubMed

    Ramirez, Aldana M; Stoopen, Geert; Menzel, Tila R; Gols, Rieta; Bouwmeester, Harro J; Dicke, Marcel; Jongsma, Maarten A

    2012-10-01

    Glandular trichomes are currently known only to store mono- and sesquiterpene compounds in the subcuticular cavity just above the apical cells of trichomes or emit them into the headspace. We demonstrate that basipetal secretions can also occur, by addressing the organization of the biosynthesis and storage of pyrethrins in pyrethrum (Tanacetum cinerariifolium) flowers. Pyrethrum produces a diverse array of pyrethrins and sesquiterpene lactones for plant defense. The highest concentrations accumulate in the flower achenes, which are densely covered by glandular trichomes. The trichomes of mature achenes contain sesquiterpene lactones and other secondary metabolites, but no pyrethrins. However, during achene maturation, the key pyrethrin biosynthetic pathway enzyme chrysanthemyl diphosphate synthase is expressed only in glandular trichomes. We show evidence that chrysanthemic acid is translocated from trichomes to pericarp, where it is esterified into pyrethrins that accumulate in intercellular spaces. During seed maturation, pyrethrins are then absorbed by the embryo, and during seed germination, the embryo-stored pyrethrins are recruited by seedling tissues, which, for lack of trichomes, cannot produce pyrethrins themselves. The findings demonstrate that plant glandular trichomes can selectively secrete in a basipetal direction monoterpenoids, which can reach distant tissues, participate in chemical conversions, and immunize seedlings against insects and fungi. PMID:23104830

  18. Bidirectional Secretions from Glandular Trichomes of Pyrethrum Enable Immunization of Seedlings[W

    PubMed Central

    Ramirez, Aldana M.; Stoopen, Geert; Menzel, Tila R.; Gols, Rieta; Bouwmeester, Harro J.; Dicke, Marcel; Jongsma, Maarten A.

    2012-01-01

    Glandular trichomes are currently known only to store mono- and sesquiterpene compounds in the subcuticular cavity just above the apical cells of trichomes or emit them into the headspace. We demonstrate that basipetal secretions can also occur, by addressing the organization of the biosynthesis and storage of pyrethrins in pyrethrum (Tanacetum cinerariifolium) flowers. Pyrethrum produces a diverse array of pyrethrins and sesquiterpene lactones for plant defense. The highest concentrations accumulate in the flower achenes, which are densely covered by glandular trichomes. The trichomes of mature achenes contain sesquiterpene lactones and other secondary metabolites, but no pyrethrins. However, during achene maturation, the key pyrethrin biosynthetic pathway enzyme chrysanthemyl diphosphate synthase is expressed only in glandular trichomes. We show evidence that chrysanthemic acid is translocated from trichomes to pericarp, where it is esterified into pyrethrins that accumulate in intercellular spaces. During seed maturation, pyrethrins are then absorbed by the embryo, and during seed germination, the embryo-stored pyrethrins are recruited by seedling tissues, which, for lack of trichomes, cannot produce pyrethrins themselves. The findings demonstrate that plant glandular trichomes can selectively secrete in a basipetal direction monoterpenoids, which can reach distant tissues, participate in chemical conversions, and immunize seedlings against insects and fungi. PMID:23104830

  19. Glandular trichomes as an inflorescence defence mechanism against insect herbivores in Iberian columbines.

    PubMed

    Jaime, Rafael; Rey, Pedro J; Alcántara, Julio M; Bastida, Jesús M

    2013-08-01

    Glandular trichomes play a defensive role against herbivores in the leaves of many plant species. However, their functional role in inflorescences has not been studied, even though theory suggests that tissues with a higher fitness value, such as inflorescences, should be better defended. Using manipulative experiments, we analysed the defensive role of glandular trichomes against herbivorous insects in the inflorescence of Iberian columbines (genus Aquilegia), and its inter-population and inter-taxa variation in relation to herbivore abundance and potential selective pressure. The experiments were conducted in eight populations belonging to four subspecies of two columbines (Aquilegia vulgaris and Aquilegia pyrenaica). For each population, we estimated the density of glandular trichomes in the inflorescences, the abundance of insects stuck in the inflorescences, the abundance of small herbivorous insects, the incidence of damage on flowers and fruits, and the fruit set. The density of glandular trichomes on the inflorescence of A. vulgaris and A. pyrenaica was higher in regions of higher herbivore abundance. We also found that when the plants lose the protection of glandular trichomes, small insects have better access to flowers and fruits, causing more damage and reducing plant fitness. This study concludes that glandular trichomes are part of an adaptive response against phytophagous insect herbivory. The observed variation in herbivore pressure between taxa, likely caused by habitat differentiation, might have played a role in trait differentiation through divergent selection. This result adds evidence to the differentiation of the Iberian columbines through habitat specialization. PMID:23247688

  20. 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

  1. 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

  2. Peltate glandular trichomes of Colquhounia seguinii harbor new defensive clerodane diterpenoids.

    PubMed

    Li, Chun-Huan; Liu, Yan; Hua, Juan; Luo, Shi-Hong; Li, Sheng-Hong

    2014-09-01

    Glandular trichomes produce a wide variety of secondary metabolites that are considered as major defensive chemicals against herbivore attack. The morphology and secondary metabolites of the peltate glandular trichomes of a lianoid Labiatae, Colquhounia seguinii Vaniot, were investigated. Three new clerodane diterpenoids, seguiniilactones A-C (1-3), were identified through precise trichome collection with laser microdissection, metabolic analysis with ultra performance liquid chromatography-tandem mass spectrometer, target compound isolation with classical phytochemical techniques, structure elucidation with spectroscopic methods. All compounds showed significant antifeedant activity against a generalist plant-feeding insect Spodoptera exigua. Seguiniilactone A (1) was approximately 17-fold more potent than the commercial neem oil. α-Substituted α,β-unsaturated γ-lactone functionality was found to be crucial for strong antifeedant activity of this class of compounds. Quantitative results indicated that the levels of these compounds in the peltate glandular trichomes and leaves were sufficiently high to deter the feeding by generalist insects. Moderate antifungal activity was observed for seguiniilactone C (3) against six predominant fungal species isolated from the diseased leaves of C. seguinii, while seguiniilactones A and B were generally inactive. These findings suggested that seguiniilactones A-C might be specialized secondary metabolites in peltate glandular trichomes for the plant defense against insect herbivores and pathogens. PMID:25048077

  3. Changes in Structure and Histochemistry of Glandular Trichomes of Thymus quinquecostatus Celak

    PubMed Central

    Jia, Ping; Gao, Ting; Xin, Hua

    2012-01-01

    The types, morphology, distribution, structure, and development process of the glandular trichomes on the leaves of Thymus quinquecostatus Celak had been investigated in this study. Two different types of glandular trichomes were determined in detail, namely, capitate trichomes and peltate ones. Besides, there were distinct differences on morphology, distribution, structure, and development process between the two kinds of trichomes. As the peltate trichome stepping into senium stage, it caved in the epidermis integrally, which was different from the capitate one. The secretion of the capitate trichome contained essential oil, polyphenols, and flavonoids, while, in addition to these three components, the secretion of the peltate one also contained acid polysaccharides. A distinctive difference was also seen in the secretory pathway of the secretion between the two types of trichomes. The secretion of capitate one was extruded through the cuticle of the head cell, but the secretion of the peltate one kept accumulating in the subcuticular space of the head cells until it was released by cuticle rupture. PMID:22545009

  4. 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.

  5. Biochemical and Histochemical Localization of Monoterpene Biosynthesis in the Glandular Trichomes of Spearmint (Mentha spicata) 12

    PubMed Central

    Gershenzon, Jonathan; Maffei, Massimo; Croteau, Rodney

    1989-01-01

    The primary monoterpene accumulated in the glandular trichomes of spearmint (Mentha spicata) is the ketone (−)-carvone which is formed by cyclization of the C10 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. Images Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 PMID:16666709

  6. 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...

  7. Leaf Peltate Glandular Trichomes of Vernonia galamensis ssp. galamensis var. ethiopica Gilbert: Development, Ultrastructure and Chemical Composition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plants from the genus Vernonia produce a variety of flavonoids and bitter sesquiterpene lactones important for agriculture and human health. Leaf glandular trichomes of Vernonia galamensis ssp. galamensis var. ethiopica Gilbert (VGAE) were investigated for ultrastructural development and content com...

  8. 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

  9. 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. PMID:25952908

  10. 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

  11. 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

    2015-04-01

    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

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

    PubMed

    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

  13. 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

  14. Comparison of oxalate formation from ascorbic and glyoxyl acids in detached glandular heads of tobacco trichomes

    SciTech Connect

    Vogeli-Lange, R.; Wagner, G.J.

    1987-08-01

    Ca-oxalate crystal containing cells from detached glandular heads of trichomes from Nicotiana tabacum, TI 1068, are capable of converting (1-/sup 14/C) ascorbic acid (AA) and (1-/sup 14/C) glyoxylic acid (GA) to oxalate. AA was found to be a better precursor for oxalate formation than GA. In detached glandular heads, 3.6x more label was converted to oxalate from AA than from GA, in the epidermis the factor was 3x while that with petiole tissue was 7x. Oxalate formation from AA, in detached glandular heads, was only partially inhibited in the dark and in the presence of metabolic inhibitors, suggesting that a nonenzymatic component might be involved. Oxalate formation from GA increased in the presence of metabolic inhibitors. During treatment of detached glandular heads with 2 mM Ca-acetate for 2 days, oxalate formation from AA was stimulated 3 fold, while the presence of 2mM Ca-acetate had no effect on the oxalate formation from GA. These results suggest that Ca/sup 2 +/ stimulates the formation of Ca-oxalate crystals in glandular head cells, and that AA can serve as a precursor for oxalate production.

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

    PubMed Central

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

    2014-01-01

    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. PMID:24962999

  16. 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. PMID:24962999

  17. Light, Conventional and Environmental Scanning Electron Microscopy of the Trichomes of Cucurbita pepo subsp. pepo var. styriaca and Histochemistry of Glandular Secretory Products

    PubMed Central

    KOLB, DAGMAR; MÜLLER, MARIA

    2004-01-01

    • Background and Aims In the present study, the differences between glandular and non-glandular trichomes, the secretory process and the method of secretion were studied. Previous studies on leaves of Styrian oil pumpkin (Cucurbia pepo var. styriaca) plants have shown that four morphologically and ontogenetically independent glandular and non-glandular trichome types and one bristle hair type can be distinguished. The four types of trichomes can be categorized into three glandular trichome types: type I, a short-stalked trichome with four head cells including a ‘middle-cell’, two stalk cells and one basal cell; type II, a long-stalked trichome with two head cells, a ‘neck-cell’ region and a long stalk area; type IV, a ‘stipitate-capitate’ trichome with a mesophyll cell basement, a short stalk and a multicellular head; type III, a non-glandular ‘columnar-digit’ trichome, which consists of two head cells continuous with three-celled stalk, and the basal cell. • Methods The histochemical studies (the main classes of metabolite in secreted material of glandular trichomes) were conducted in fresh and fixed hand sections, using the following tests: Sudan black B, Nile blue A, osmium tetroxide, neutral red, Naturstoffreagent A, FSA (fuchsin–safranin–astra blue), NADI (naphthol + dimethylparaphenylenediamine) and ruthenium red. Each suggested differences in the intercalations during the ontogenetical development of each trichome during the development stage. • Key Results The histochemical reactions revealed the main components of the materials secreted by all types of trichomes, which include lipids, flavones and terpenes and the different cell wall compositions. Glandular secretions were observed during environmental scanning electron microscopy (ESEM) and the trichomes compared with those seen by conventional scanning electron microscopy (CSEM). • Conclusions Scanning electron microscopy and histochemical analysis demonstrated that each of

  18. 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. PMID:23058847

  19. 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. PMID:23918183

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

    PubMed Central

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

    2013-01-01

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

  1. Identifying Three Ecological Chemotypes of Xanthium strumarium Glandular Trichomes Using a Combined NMR and LC-MS Method

    PubMed Central

    Gou, Junbo; Lu, Dayan; Gong, Fujun; Tang, Huiru; Zhang, Yansheng

    2013-01-01

    Xanthanolides, as the sesquiterpene lactones, are reportedly the major components for the pharmacological properties of X. strumarium L. species. Phytochemical studies indicated that the glandular structures on the surface of plant tissues would form the primary sites for the accumulation of this class of the compounds. As the interface between plants and their natural enemies, glandular trichomes may vary with respect to which of their chemicals are sequestered against different herbivores in different ecologies. However, to date, no data are available on the chemical characterisation of X. strumarium glandular cells. In this study, the trichome secretions of the X. strumarium species originating from nineteen unique areas across eleven provinces in China, were analysed by HPLC, LC-ESI-MS and NMR. For the first time three distinct chemotypes of X. strumarium glandular trichomes were discovered along with the qualitative and quantitative evaluations of their presence of xanthanolides; these were designated glandular cell Types I, II, and III, respectively. The main xanthanolides in Type I cells were 8-epi-xanthatin and xanthumin while no xanthatin was detected. Xanthatin, 8-epi-xanthatin, and xanthumin dominated in Type II cells with comparable levels of each being present. For Type III cells, significantly higher concentrations of 8-epi-xanthatin or xanthinosin (relative to xanthatin) were detected with xanthinosin only being observed in this type. Further research will focus on understanding the ecological and molecular mechanism causing these chemotype differences in X. strumarium glandular structures. PMID:24098541

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

    PubMed

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

    2013-01-01

    Xanthanolides, as the sesquiterpene lactones, are reportedly the major components for the pharmacological properties of X. strumarium L. species. Phytochemical studies indicated that the glandular structures on the surface of plant tissues would form the primary sites for the accumulation of this class of the compounds. As the interface between plants and their natural enemies, glandular trichomes may vary with respect to which of their chemicals are sequestered against different herbivores in different ecologies. However, to date, no data are available on the chemical characterisation of X. strumarium glandular cells. In this study, the trichome secretions of the X. strumarium species originating from nineteen unique areas across eleven provinces in China, were analysed by HPLC, LC-ESI-MS and NMR. For the first time three distinct chemotypes of X. strumarium glandular trichomes were discovered along with the qualitative and quantitative evaluations of their presence of xanthanolides; these were designated glandular cell Types I, II, and III, respectively. The main xanthanolides in Type I cells were 8-epi-xanthatin and xanthumin while no xanthatin was detected. Xanthatin, 8-epi-xanthatin, and xanthumin dominated in Type II cells with comparable levels of each being present. For Type III cells, significantly higher concentrations of 8-epi-xanthatin or xanthinosin (relative to xanthatin) were detected with xanthinosin only being observed in this type. Further research will focus on understanding the ecological and molecular mechanism causing these chemotype differences in X. strumarium glandular structures. PMID:24098541

  3. 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. PMID:27556560

  4. 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

  5. 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. PMID:25956500

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

    PubMed

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

    2008-12-01

    This paper reports a method for the analysis of secondary metabolites stored in glandular trichomes, employing negative ion 'chip-based' nanospray tandem mass spectrometry. The analyses of glandular trichomes from Lychnophora ericoides, a plant endemic to the Brazilian 'cerrado' and used in traditional medicine as an anti-inflammatory and analgesic agent, led to the identification of five flavonoids (chrysin, pinocembrin, pinostrobin, pinobanksin and 3-O-acetylpinobanksin) by direct infusion of the extracts of glandular trichomes into the nanospray ionisation source. All the flavonoids have no oxidation at ring B, which resulted in a modification of the fragmentation pathways compared with that of the oxidised 3,4-dihydroflavonoids already described in the literature. The absence of the anti-inflammatory and antioxidant di-C-glucosylflavone vicenin-2, or any other flavonoid glycosides, in the glandular trichomes was also demonstrated. The use of the 'chip-based' nanospray QqTOF apparatus is a new fast and useful tool for the identification of secondary metabolites stored in the glandular trichomes, which can be useful for chemotaxonomic studies based on metabolites from glandular trichomes. PMID:18980260

  7. 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

  8. Glandular trichomes and essential oil composition of endemic Sideritis italica (Mill.) Greuter et Burdet from central Italy.

    PubMed

    Giuliani, Claudia; Bini, Laura Maleci; Papa, Fabrizio; Cristalli, Gloria; Sagratini, Gianni; Vittori, Sauro; Lucarini, Domenico; Maggi, Filippo

    2011-12-01

    Sideritis italica (Mill.) Greuter et Burdet belongs to the Lamiaceae family and is endemic to Italy. The glandular trichomes (morphology, distribution, histochemistry, and ultrastructure) of the plant were studied for the first time, along with the chemical composition of the essential oils. Abundant non-glandular hairs and peltate (type A) and capitate (types B, C(1), and C(x)) glandular trichomes were observed both on the vegetative and reproductive organs. The histochemical procedures and the ultrastructural investigation enabled specific location of the main site of essential oil production mainly in type-A peltate hairs. Particular emphasis is given to the release mechanism of the secreted material in all of the types of glands, and the potential taxonomic value of the indumentum in the Lamiaceae family is briefly discussed. Essential oils were hydrodistilled from flowering aerial parts of S. italica, and 136 compounds (112 in flowerheads, 79 in vegetative parts) were identified. The quantitative prevalence of diterpenoids (43.4% in flowerheads and 22.3% in vegetative parts) was the most significant characteristic of the essential oil of S. italica that could be classified as a diterpene-rich essential oil according to the classification of Kirimer. PMID:22162157

  9. 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. PMID:26880289

  10. 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. PMID:26131639

  11. Single-Cell Metabolite Profiling of Stalk and Glandular Cells of Intact Trichomes with Internal Electrode Capillary Pressure Probe Electrospray Ionization Mass Spectrometry.

    PubMed

    Nakashima, Taiken; Wada, Hiroshi; Morita, Satoshi; Erra-Balsells, Rosa; Hiraoka, Kenzo; Nonami, Hiroshi

    2016-03-15

    In this report, we developed the pressure probe electrospray ionization-mass spectrometry with internal electrode capillary (IEC-PPESI-MS) which enables high spatial-resolution cell sampling, precise postsampling manipulation, and high detection sensitivity. Using this technique, a comparative in situ single-cell metabolite profiling of stalk and glandular cells, the two adjacent cell types comprising a trichome unit in tomato plants (Solanum lycopersicum L.), were performed to clarify the extent of metabolic differentiation between two cell types as well as among different types of trichomes. Owing to high sensitivity of the system, less than a picoliter cell sap from a single stalk cell sufficiently yielded a number of peaks of amino acids, organic acids, carbohydrates, and flavonoids. The minimal cell sap removal from a stalk cell without severe disturbance of trichome structure enabled sequential analysis of adjacent glandular cell on the same trichome, which showed the presence of striking differences in metabolite compositions between two adjacent cell types. Comparison among different types of trichome also revealed significant variations in metabolite profiles, particularly in flavonoids and acyl sugars compositions. Some metabolites were found only in specific cell types or particular trichome types. Although extensive metabolomics analysis of glandular cells of tomato trichomes has been previously documented, this is the first report describing cell-to-cell variations in metabolite compositions of stalk and glandular cells as well as in different trichome types. Further application of this technique may provide new insights into distinct metabolism in plant cells displaying variations in shape, size, function and physicochemical properties. PMID:26845634

  12. 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. PMID:27534133

  13. 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. PMID:24579920

  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. PMID:23300257

  15. 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. PMID:15997848

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

    PubMed

    Liu, Yan; Luo, Shi-Hong; Schmidt, Axel; Wang, Guo-Dong; Sun, Gui-Ling; Grant, Marcus; Kuang, Ce; Yang, Min-Jie; Jing, Shu-Xi; Li, Chun-Huan; Schneider, Bernd; Gershenzon, Jonathan; Li, Sheng-Hong

    2016-03-01

    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

  17. Transcriptome analysis approaches for the isolation of trichome-specific genes from the medicinal plant Cistus creticus subsp. creticus.

    PubMed

    Falara, Vasiliki; Fotopoulos, Vasileios; Margaritis, Thanasis; Anastasaki, Thalia; Pateraki, Irene; Bosabalidis, Artemios M; Kafetzopoulos, Dimitris; Demetzos, Costas; Pichersky, Eran; Kanellis, Angelos K

    2008-12-01

    Cistus creticus subsp. creticus is a plant of intrinsic scientific interest due to the distinctive pharmaceutical properties of its resin. Labdane-type diterpenes, the main constituents of the resin, exhibit considerable antibacterial and cytotoxic activities. In this study chemical analysis of isolated trichomes from different developmental stages revealed that young leaves of 1-2 cm length displayed the highest content of labdane-type diterpenes (80 mg/g fresh weight) whereas trichomes from older leaves (2-3 or 3-4 cm) exhibited gradual decreased concentrations. A cDNA library was constructed enriched in transcripts from trichomes isolated from young leaves, which are characterized by high levels of labdane-type diterpenes. Functional annotation of 2,022 expressed sequence tags (ESTs) from the trichome cDNA library based on homology to A. thaliana genes suggested that 8% of the putative identified sequences were secondary metabolism-related and involved primarily in flavonoid and terpenoid biosynthesis. A significant proportion of the ESTs (38%) displayed no significant similarity to any other DNA deposited in databases, indicating a yet unknown function. Custom DNA microarrays constructed with 1,248 individual clones from the cDNA library facilitated transcriptome comparisons between trichomes and trichome-free tissues. In addition, gene expression studies in various Cistus tissues and organs for one of the genes highlighted as the most differentially expressed by the microarray experiments revealed a putative sesquiterpene synthase with a trichome-specific expression pattern. Full length cDNA isolation and heterologous expression in E. coli followed by biochemical analysis, led to the characterization of the produced protein as germacrene B synthase. PMID:18819010

  18. Characterization and mechanism of (4S)-limonene synthase, a monoterpene cyclase from the glandular trichomes of peppermint (Mentha x piperita).

    PubMed

    Rajaonarivony, J I; Gershenzon, J; Croteau, R

    1992-07-01

    (4S)-Limonene synthase, a monoterpene cyclase isolated from the secretory cells of the glandular trichomes of Mentha x piperita (peppermint), catalyzes the cyclization of geranyl pyrophosphate to (4S)-limonene, a key intermediate in the biosynthesis of p-menthane monoterpenes in Mentha species. The enzyme synthesizes principally (-)-(4S)-limonene (greater than 94% of the total products), plus several other monoterpene olefins. The general properties of (4S)-limonene synthase resemble those of other monoterpene cyclases. The enzyme shows a pH optimum near 6.7, an isoelectric point of 4.35, and requires a divalent metal ion for catalysis, either Mg2+ or Mn2+, with Mn2+ preferred. The Km value measured for geranyl pyrophosphate was 1.8 microM. The activity of (4S)-limonene synthase was inhibited by sodium phosphate, sodium pyrophosphate, and reagents directed against the amino acids cysteine, methionine, and histidine. In the presence of Mn2+, geranyl pyrophosphate protected against cysteine-directed inhibition, suggesting that at least one cysteine residue is located at or near the active site. Experiments with alternate substrates and substrate analogs confirmed many elements of the proposed reaction mechanism, including the binding of geranyl pyrophosphate in the form of a complex with the divalent metal ion, the preliminary isomerization of geranyl pyrophosphate to linalyl pyrophosphate (a bound intermediate capable of cyclization), and the participation of a series of carbocation:pyrophosphate anion pairs in the reaction sequence. PMID:1605644

  19. Analysis of Natural and Induced Variation in Tomato Glandular Trichome Flavonoids Identifies a Gene Not Present in the Reference Genome[W][OPEN

    PubMed Central

    Kim, Jeongwoon; Matsuba, Yuki; Ning, Jing; Schilmiller, Anthony L.; Hammar, Dagan; Jones, A. Daniel; Pichersky, Eran; Last, Robert L.

    2014-01-01

    Flavonoids are ubiquitous plant aromatic specialized metabolites found in a variety of cell types and organs. Methylated flavonoids are detected in secreting glandular trichomes of various Solanum species, including the cultivated tomato (Solanum lycopersicum). Inspection of the sequenced S. lycopersicum Heinz 1706 reference genome revealed a close homolog of Solanum habrochaites MOMT1 3′/5′ myricetin O-methyltransferase gene, but this gene (Solyc06g083450) is missing the first exon, raising the question of whether cultivated tomato has a distinct 3′ or 3′/5′ O-methyltransferase. A combination of mining genome and cDNA sequences from wild tomato species and S. lycopersicum cultivar M82 led to the identification of Sl-MOMT4 as a 3′ O-methyltransferase. In parallel, three independent ethyl methanesulfonate mutants in the S. lycopersicum cultivar M82 background were identified as having reduced amounts of di- and trimethylated myricetins and increased monomethylated myricetin. Consistent with the hypothesis that Sl-MOMT4 is a 3′ O-methyltransferase gene, all three myricetin methylation defective mutants were found to have defects in MOMT4 sequence, transcript accumulation, or 3′-O-methyltransferase enzyme activity. Surprisingly, no MOMT4 sequence is found in the Heinz 1706 reference genome sequence, and this cultivar accumulates 3-methyl myricetin and is deficient in 3′-methyl myricetins, demonstrating variation in this gene among cultivated tomato varieties. PMID:25128240

  20. Influence of life history differences of two tachinid parasitoids ofHelicoverpa zea (Boddie) (Lepidoptera: Noctuidae) on their interactions with glandular trichome/methyl ketone-based insect resistance in tomato.

    PubMed

    Farrar, R R; Kennedy, G G; Kashyap, R K

    1992-03-01

    The effects of glandular trichome/methyl ketone (2-tridecanone and 2-undecanone) -based insect resistance in the wild tomato,Lycopersicon hirsutum f.glabratum C.H. Mull, accession PI 134417, onArchytas marmoratus (Townsend) andEucelatoria bryani (Sabrosky) (Diptera: Tachinidae), both parasitoids ofHelicoverpa (=Heliothis)zea (Boddie) (Lepidoptera: Noctuidae), were investigated in the laboratory.A. marmoratus deposits larvae (planidia) on the foliage of its host's food plant; planidia attach to passing hosts, penetrate the cuticle, and develop in the host pupae.E. bryani larviposits directly into its host; its larvae develop in the host larva.A. marmoratus planidia are killed by glandular trichomes of PI 134417 and also by trichomes of hybrid lines with no methyl ketones. The methyl ketones are toxic to planidia, but at least part of the effect is due to other factors, possibly physical entanglement. Both species can be affected indirectly by methyl ketones in the diet of the host. 2-Undecanone reduces the percentage ofA. marmoratus larvae that reach pupation. This effect is evidently due to premature death and desiccation of the host pupa caused by 2-undecanone. 2-Tridecanone in host diets had no effect onA. marmoratus. InE. bryani, 2-tridecanone in the diet of the host reduced the number of parasitoids yielded by each parasitized host, although not the overall percentage of hosts parasitized. 2-Undecanone in the diet of the host had no effect onE. bryani. PMID:24254953

  1. 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

  2. Morphology and biochemistry of non-glandular trichomes in Cistus salvifolius L. leaves growing in extreme habitats of the Mediterranean basin.

    PubMed

    Tattini, M; Matteini, P; Saracini, E; Traversi, M L; Giordano, C; Agati, G

    2007-05-01

    Here the functional roles of stellate and dendritic trichomes in Cistus salvifolius L leaves were studied by analysing i) both leaf surface and trichome morphology using scanning electron and light microscopy; and ii) the composition and localisation of polyphenols by coupling liquid chromatography with fluorescence spectroscopy and fluorescence microimaging. Red-coloured compounds were detected in the stalk cells and the channel in the trichome arm, and appeared to be released at the tip end of the trichome branch. We identified such metabolites as ellagitannins, namely punicalagin and two galloyl derivatives of punicalagin. These ellagitannins accounted for 4.3 % of leaf dry weight and their concentration in the leaf leachate averaged 289.4 mg L (-1). The trichome arms exhibited an appreciable orange-red autofluorescence (centred at 620 nm) when excited with UV light (at 365 nm) or emitted in the yellow waveband (peak centred at 566 nm) when stained with the Naturstoff reagent, and excited at 488 nm. The fluorescence signatures of the trichome arms were consistent with the presence of mono-hydroxy B-ring substituted flavonoids, which were identified as the mono- and di-coumaroyl derivative of a kaempferol 3-O-glycoside. Our data may provide some insights on the functional roles of stellate and dendritic trichomes in the response mechanisms of C. salvifolius to Mediterranean-type climate, based upon (i) the potential effect of released ellagitannins on the soil nitrogen dynamic and (ii) the ability of acylated kaempferol 3-O-glycosides to effectively absorb both the UV-B and UV-A wavelengths. PMID:17143807

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

    PubMed

    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. 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

  5. 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

  6. 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. PMID:20592816

  7. Terpenoid biosynthesis in trichomes--current status and future opportunities.

    PubMed

    Lange, B Markus; Turner, Glenn W

    2013-01-01

    Glandular trichomes are anatomical structures specialized for the synthesis of secreted natural products. In this review we focus on the description of glands that accumulate terpenoid essential oils and oleoresins. We also provide an in-depth account of the current knowledge about the biosynthesis of terpenoids and secretion mechanisms in the highly specialized secretory cells of glandular trichomes, and highlight the implications for metabolic engineering efforts. PMID:22979959

  8. 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

  9. 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. PMID:22353623

  10. EST analysis and annotation of transcripts derived from a trichome-specific cDNA library from Salvia fruticosa.

    PubMed

    Chatzopoulou, Fani M; Makris, Antonios M; Argiriou, Anagnostis; Degenhardt, Jörg; Kanellis, Angelos K

    2010-05-01

    Greek sage (Salvia fruticosa Mill., Syn. Salvia triloba L.) is appreciated for its essential oil which is used as an aromatic spice and active against a wide range of microorganisms and viruses. The essential oil is dominated by terpenoids and flavonoids which are produced and stored in glandular trichomes on the plant surface. The present study aims to give insights into the metabolic activities of S. fruticosa trichomes on a transcriptome level. A total of 2,304 clones were sequenced from a cDNA library from leaves' trichomes of S. fruticosa. Exclusion of sequences shorter than 100 bp resulted in 1,615 high-quality ESTs with a mean length of 592 bp. Cluster analysis indicated the presence of 197 contigs (908 clones) and 707 singletons, generating a total of 904 unique sequences. Of the 904 unique ESTs, 628 (69.5%) had significant hits in the non-redundant protein database and were annotated. A total of 517 (82.3%) sequences were functionally classified using the gene ontologies (GO) and established pathway associations to 220 (24.3%) sequences in Kyoto encyclopedia of genes and genomes (KEGG). In addition, 52 (5.8%) of the unique ESTs revealed a GO biological term with relation to terpenoid (78 ESTs), phenylpropanoid (43 ESTs), flavonoid (18 ESTs) or alkaloid (10 ESTs) biosynthesis or to P450s (26 ESTs). Expression analysis of a selected set of genes known to be involved in the pathways of secondary metabolite synthesis showed higher expression levels in trichomes, validating the tissue specificity of the analyzed glandular trichome library. PMID:20333525

  11. Analysis of purified glabra3-shapeshifter trichomes reveals a role for NOECK in regulating early trichome morphogenic events.

    PubMed

    Gilding, Edward K; Marks, M David

    2010-10-01

    Transcriptome analysis using the Affymetrix ATH1 platform has been completed on purified trichomes from the gl3-sst mutant. These trichomes display immature features, such as glassy cell walls and blunted branches. The gl3-sst trichome transcriptome was greatly enriched for genes involved in lipid biosynthesis, including those mediating the synthesis of fatty acids and wax. In addition, gl3-sst trichomes displayed reduced expression of the R3 MYBs TRY and CPC, which normally function to limit trichome development. The expression of the MIXTA-like MYB gene NOK was elevated. Members of the MIXTA-like family promote conical cell outgrowth, and in some cases, trichome initiation in diverse plant species. In contrast, NOK limits trichome outgrowth in wild-type Arabidopsis plants. Similar to other MIXTA-like genes, NOK was required for the expansion of gl3-sst trichomes, as the gl3-sst nok double mutant trichomes were greatly reduced in size. Expression of NOK in nok mutants reduced branch formation, whereas in gl3-sst nok, NOK expression promoted trichome cell outgrowth, illustrating duel roles for NOK in both promoting and limiting trichome development. MIXTA-like genes from phylogenetically diverse plant species could substitute for NOK in both nok and gl3-sst nok backgrounds. These findings suggest that certain aspects of NOK and MIXTA-like gene function have been conserved. PMID:21070410

  12. Trichome morphogenesis in Arabidopsis.

    PubMed Central

    Schwab, B; Folkers, U; Ilgenfritz, H; Hülskamp, M

    2000-01-01

    Trichomes (plant hairs) in Arabidopsis thaliana are large non-secreting epidermal cells with a characteristic three-dimensional architecture. Because trichomes are easily accessible to a combination of genetic, cell biological and molecular methods they have become an ideal model system to study various aspects of plant cell morphogenesis. In this review we will summarize recent progress in the understanding of trichome morphogenesis. PMID:11128981

  13. Studies of the site and mode of biosynthesis of tobacco trichome exudate components.

    PubMed

    Kandra, L; Wagner, G J

    1988-09-01

    Detached glandular trichome head preparations and epidermal strips with and without trichome heads were used to identify glandular trichome heads as the site of sucrose ester biosynthesis in tobacco. Carbon dioxide in solution as well as sucrose, glucose, and acetate were shown to serve as precursors to both sucrose esters and duvatrienediol diterpenes in detached trichome heads or epidermal strips, and gaseous CO2 was also efficiently utilized by epidermal strips. Thus, glandular heads can biosynthesize these principal exudate components from a molecule as simple as CO2. While formation of duvatriendiols from all precursors tested and conversion of sucrose and glucose to sucrose esters was light dependent, utilization of acetate to label the 6-O-acetyl group of the glucose moiety of sucrose esters occurred equally well in light and dark. The data suggest that CO2 and/or monosaccharides produced in trichome head cells and perhaps that supplied by other epidermal cells can act as carbon sources for sucrose ester and duvatrienediol biosynthesis which occurs in the glandular trichome head. PMID:3138948

  14. 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. PMID:23280038

  15. 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

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

    PubMed

    Weinhold, Alexander; Baldwin, Ian Thomas

    2011-05-10

    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

  17. 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

  18. 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. PMID:26879931

  19. 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%). PMID:26982621

  20. 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

  1. Endogenous overexpression of Populus MYB186 increases trichome density, improves insect pest resistance, and impacts plant growth.

    PubMed

    Plett, Jonathan M; Wilkins, Olivia; Campbell, Malcolm M; Ralph, Steven G; Regan, Sharon

    2010-11-01

    Trichomes are specialized epidermal cells that generally play a role in reducing transpiration and act as a deterrent to herbivory. In a screen of activation-tagged Populus tremula × Populus alba 717-1B4 trees, we identified a mutant line, fuzzy, with increased foliar trichome density. This mutant also had a 35% increase in growth rate and a 200% increase in the rate of photosynthesis as compared with wild-type poplar. The fuzzy mutant had significant resistance to feeding by larvae of the white-spotted tussock moth (Orgyia leucostigma), a generalist insect pest of poplar trees. The fuzzy trichome phenotype is attributable to activation tagging and increased expression of the gene encoding PtaMYB186, which is related to Arabidopsis thaliana MYB106, a known regulator of trichome initiation. The fuzzy phenotype can be recapitulated by overexpressing PtaMYB186 in poplar. PtaMYB186 overexpression results in reconfiguration of the poplar transcriptome, with changes in the transcript abundance of suites of genes that are related to trichome differentiation. It is notable that a plant with misexpression of a gene responsible for trichome development also had altered traits related to growth rate and pest resistance, suggesting that non-intuitive facets of plant development might be useful targets for plant improvement. PMID:20807210

  2. Proteomics of terpenoid biosynthesis and secretion in trichomes of higher plant species.

    PubMed

    Champagne, Antoine; Boutry, Marc

    2016-08-01

    Among the specialized (secondary) plant metabolites, terpenoids represent the most diverse family and are often involved in the defense against pathogens and herbivores. Terpenoids can be produced both constitutively and in response to the environment. At the front line of this defense strategy are the glandular trichomes, which are organs dedicated primarily to the production of specialized metabolites. Mass spectrometry-based proteomics is a powerful tool, which is very useful to investigate enzymes involved in metabolic pathways, such as the synthesis and secretion of terpenoids in glandular trichomes. Here we review the strategies used to investigate the specific roles of these particular organs from non-model plant species, mainly belonging to the Lamiaceae, Solanaceae, and Cannabaceae families. We discuss how proteomics helps to accurately pinpoint candidate proteins to be functionally characterized, and how technological progresses create opportunities for studying low-abundance proteins, such as the ones related to the synthesis and transport of specialized metabolites. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26873244

  3. Quantification of variability in trichome patterns

    PubMed Central

    Greese, Bettina; Hülskamp, Martin; Fleck, Christian

    2014-01-01

    While pattern formation is studied in various areas of biology, little is known about the noise leading to variations between individual realizations of the pattern. One prominent example for de novo pattern formation in plants is the patterning of trichomes on Arabidopsis leaves, which involves genetic regulation and cell-to-cell communication. These processes are potentially variable due to, e.g., the abundance of cell components or environmental conditions. To elevate the understanding of regulatory processes underlying the pattern formation it is crucial to quantitatively analyze the variability in naturally occurring patterns. Here, we review recent approaches toward characterization of noise on trichome initiation. We present methods for the quantification of spatial patterns, which are the basis for data-driven mathematical modeling and enable the analysis of noise from different sources. Besides the insight gained on trichome formation, the examination of observed trichome patterns also shows that highly regulated biological processes can be substantially affected by variability. PMID:25431575

  4. 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.

  5. Gene expression profile analysis of tobacco leaf trichomes

    PubMed Central

    2011-01-01

    Background Leaf trichomes of Nicotiana tabacum are distinguished by their large size, high density, and superior secretion ability. They contribute to plant defense response against biotic and abiotic stress, and also influence leaf aroma and smoke flavor. However, there is limited genomic information about trichomes of this non-model plant species. Results We have characterized Nicotiana tabacum leaf trichome gene expression using two approaches. In the first, a trichome cDNA library was randomly sequenced, and 2831 unique genes were obtained. The most highly abundant transcript was ribulose bisphosphate carboxylase (RuBisCO). Among the related sequences, most encoded enzymes involved in primary metabolism. Secondary metabolism related genes, such as isoprenoid and flavonoid biosynthesis-related, were also identified. In the second approach, a cDNA microarray prepared from these 2831 clones was used to compare gene expression levels in trichome and leaf. There were 438 differentially expressed genes between trichome and leaves-minus-trichomes. Of these, 207 highly expressed genes in tobacco trichomes were enriched in second metabolic processes, defense responses, and the metabolism regulation categories. The expression of selected unigenes was confirmed by semi-quantitative RT-PCR analysis, some of which were specifically expressed in trichomes. Conclusion The expression feature of leaf trichomes in Nicotiana tabacum indicates their metabolic activity and potential importance in stress resistance. Sequences predominantly expressed in trichomes will facilitate gene-mining and metabolism control of plant trichome. PMID:21548994

  6. 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). PMID:24124164

  7. 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

  8. Compositions of essential oils and trichomes of Teucrium chamaedrys L. subsp. trapezunticum Rech. fil. and subsp. syspirense (C. Koch) Rech. fil.

    PubMed

    Kaya, Ayla; Demirci, Betül; Başer, K Hüsnü C

    2009-01-01

    Teucrium chamaedrys L. is a member of the Lamiaceae family and is represented in the Flora of Turkey by six subspecies. The aerial organs of T. chamaedrys L. subsp. trapezunticum Rech. fil. and subsp. syspirense (C. Koch) Rech. fil. bears numerous eglandular and glandular trichomes. Eglandular trichomes are simple, long-multicellular with cuticular micropapillae, and glandular hairs are of peltate and capitate types. The peltate hairs consist of a basal cell, a short unicellular stalk, and multicellular secretory head, and the capitate ones possess 1-2 stalk cells and one glandular head cell. The aerial parts were subjected to microdistillation for the isolation of volatiles. The analysis was simultaneously performed by using gas chromatography (GC) and gas chromatography/mass spectrometry (GC/MS). The major components were characterized as beta-caryophyllene (18%), nonacosane (12%), germacrene D (11%), caryophyllene oxide (7%), and alpha-pinene (7%) for subsp. trapezunticum, and caryophyllene oxide (23%), alpha-pinene (11%), and caryophyllenol II (5%) for subsp. syspirense. PMID:19180459

  9. TEMPRANILLO Reveals the Mesophyll as Crucial for Epidermal Trichome Formation.

    PubMed

    Matías-Hernández, Luis; Aguilar-Jaramillo, Andrea E; Osnato, Michela; Weinstain, Roy; Shani, Eilon; Suárez-López, Paula; Pelaz, Soraya

    2016-03-01

    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

  10. Modified branched-chain amino acid pathways give rise to acyl acids of sucrose esters exuded from tobacco leaf trichomes.

    PubMed

    Kandra, G; Severson, R; Wagner, G J

    1990-03-10

    A major diversion of carbon from branched-chain amino acid biosynthesis/catabolism to form acyl moieties of sucrose esters (6-O-acetyl-2,3,4-tri-O-acyl-alpha-D-glucopyranosyl-beta-D- fructofuranosides) was observed to be associated with specialized trichome head cells which secrete large amounts of sucrose esters. Surface chemistry and acetyl and acyl substituent groups of tobacco (T.I. 1068) sucrose esters were identified and quantified by gas chromatography/mass spectrometry. Sucrose esters were prominent surface constituents and 3-methylvaleric acid, 2- and 3-methylbutyric acid, and methylpropionic acid accounted for 60%, 25% and 9%, respectively, of total C3--C7 acyl substituents. Radiolabeled Thr, Ile, Val, Leu, pyruvate and Asp, metabolites of branched-chain amino acid pathways, were compared with radioactively labeled acetate and sucrose as donors of carbon to sucrose, acetyl and acyl components of sucrose esters using epidermal peels with undisturbed trichomes. Preparations of biosynthetically competent trichome heads (site of sucrose ester formation) were also examined. Results indicate that 3-methylvaleryl and 2-methylbutyryl groups are derived from the Thr pathway of branched-chain amino acid metabolism, 3-methylbutyryl and methylpropionyl groups are formed via the pyruvate pathway, and that acetyl groups are principally formed directly via acetyl-CoA. Arguments are presented which rule out participation of fatty acid synthase in the formation of prominent acyl acids. Results suggest that the shunting of carbon away from the biosynthesis of Val, Leu and Ile may be due to a low level of amino acid utilization in protein synthesis in specialized glandular head cells of trichomes. This would result in the availability of corresponding oxo acids for CoA activation and esterification to form sucrose esters. Preliminary evidence was found for the involvement of cycling reactions in oxo-acid-chain lengthening and for utilization of pyruvate-derived 2

  11. Coupling membranes as energy-transmitting cables. II. Cyanobacterial trichomes.

    PubMed

    Severina, I I; Skulachev, V P; Zorov, D B

    1988-08-01

    Power transmission along trichomes of filamentous cyanobacteria Phormidium uncinatum has been studied with the use of ethylrhodamine fluorescence as a probe for the transmembrane electric potential difference (delta psi). It is found that agents preventing the light-induced delta psi formation (photosynthetic redox chain inhibitor dibromothymoquinone) or dissipating delta psi (uncoupler tetrachlorotrifluoromethylbenzimidazole) strongly decrease the fluorescence of the ethyl-rhodamine-stained trichomes. K+-H+ antiporter nigericin converting delta pH to delta psi increases the fluorescence. These relationships are in agreement with the assumption that ethylrhodamine electrophoretically accumulates inside the cyanobacterial cells. Illumination of a single cell in the P. uncinatum trichome gives rise to quenching of the fluorescence in this cell and usually in one or two neighbor cells, whereas the rest of trichome remains fluorescing. A small light spot (5% of the trichome length) causes an increase in the ethylrhodamine fluorescence not only in the illuminated but also in the nonilluminated parts of the trichome up to the laser-treated cell or its neighbor(s). It is concluded ethylrhodamine can be used to monitor the power transmission which was previously demonstrated by microelectrode studies of the cyanobacterial trichomes. In certain trichomes, several "dark" cells appear during the storage of the trichomes without energy sources. Illumination for several minutes results in dark cells becoming fluorescing. Thus some cells or cell clusters can be reversibly excluded from the lateral delta psi-transmitting system of the trichome, the rest being still electrically connected. This means that filamentous cyanobacteria possess mechanisms to transmit power along the trichome and to switch off this transmission. PMID:3138245

  12. 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

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

    PubMed

    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

  14. 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 ...

  15. 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...

  16. Acylsugar Acylhydrolases: Carboxylesterase-Catalyzed Hydrolysis of Acylsugars in Tomato Trichomes.

    PubMed

    Schilmiller, Anthony L; Gilgallon, Karin; Ghosh, Banibrata; Jones, A Daniel; Last, Robert L

    2016-03-01

    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

  17. 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

  18. RNA-seq discovery, functional characterization, and comparison of sesquiterpene synthases from Solanum lycopersicum and Solanum habrochaites trichomes.

    PubMed

    Bleeker, Petra M; Spyropoulou, Eleni A; Diergaarde, Paul J; Volpin, Hanne; De Both, Michiel T J; Zerbe, Philipp; Bohlmann, Joerg; Falara, Vasiliki; Matsuba, Yuki; Pichersky, Eran; Haring, Michel A; Schuurink, Robert C

    2011-11-01

    Solanum lycopersicum and Solanum habrochaites (f. typicum) accession PI127826 emit a variety of sesquiterpenes. To identify terpene synthases involved in the production of these volatile sesquiterpenes, we used massive parallel pyrosequencing (RNA-seq) to obtain the transcriptome of the stem trichomes from these plants. This approach resulted initially in the discovery of six sesquiterpene synthase cDNAs from S. lycopersicum and five from S. habrochaites. Searches of other databases and the S. lycopersicum genome resulted in the discovery of two additional sesquiterpene synthases expressed in trichomes. The sesquiterpene synthases from S. lycopersicum and S. habrochaites have high levels of protein identity. Several of them appeared to encode for non-functional proteins. Functional recombinant proteins produced germacrenes, β-caryophyllene/α-humulene, viridiflorene and valencene from (E,E)-farnesyl diphosphate. However, the activities of these enzymes do not completely explain the differences in sesquiterpene production between the two tomato plants. RT-qPCR confirmed high levels of expression of most of the S. lycopersicum sesquiterpene synthases in stem trichomes. In addition, one sesquiterpene synthase was induced by jasmonic acid, while another appeared to be slightly repressed by the treatment. Our data provide a foundation to study the evolution of terpene synthases in cultivated and wild tomato. PMID:21818683

  19. 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

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

    PubMed

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

    2016-01-01

    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). PMID:27322517

  1. Glandular Odontogenic Cyst of the Anterior Mandible

    PubMed Central

    Raju, Srinivasa Pathapati; Reddy, Sridhar Padala; Ananthnag, Jakkula

    2015-01-01

    Context: Glandular odontogenic cyst (GOC) is a rare cyst occurring in the middle-age people with mandibular anterior as the common site of occurrence. Case Report: We report a case of massive GOC in a 65-year-old female with an emphasis on its clinical course, histological features, and treatment modalities. Conclusion: The aggressiveness and recurrences of GOC warrants clinicians for the careful examination, treatment, and long-term follow-up. PMID:25789251

  2. Inflammatory and glandular skin disease in pregnancy.

    PubMed

    Yang, Catherine S; Teeple, Mary; Muglia, Jennie; Robinson-Bostom, Leslie

    2016-01-01

    A switch from cell-mediated to humoral immunity (helper T 1 [Th1] to helper T 2 [Th2] shift) during gestation plays a key role in placental immune tolerance. As a result, skin diseases that are Th2 mediated often worsen, whereas skin diseases that are Th1 mediated often improve during gestation. Also, due to fluctuations in glandular activity, skin diseases involving sebaceous and eccrine glands may flare, whereas those involving apocrine glands may improve during pregnancy. Despite these trends, inflammatory and glandular skin diseases do not always follow the predicted pattern, and courses are often diverse. We review the gestational course of inflammatory skin diseases, such as atopic dermatitis (atopic eruption of pregnancy), psoriasis, impetigo herpetiformis, urticaria, erythema annulare centrifugum, pityriasis rosea, sarcoidosis, Sweet syndrome, and erythema nodosum, as well as glandular skin diseases, including acne vulgaris, acne rosacea, perioral dermatitis, hidradenitis suppurativa, Fox-Fordyce disease, hyperhidrosis, and miliaria. For each of these diseases, we discuss the pathogenesis, clinical presentation, and management with special consideration for maternal and fetal safety. PMID:27265071

  3. Clade-specific positive selection on a developmental gene: BRANCHLESS TRICHOME and the evolution of stellate trichomes in Physaria (Brassicaceae).

    PubMed

    Mazie, Abigail R; Baum, David A

    2016-07-01

    Positive selection is known to drive the evolution of genes involved in evolutionary arms races, but what role does it play in the evolution of genes involved in developmental processes? We used the single-celled epidermal trichomes of Brassicaceae as a model to uncover the molecular evolutionary processes that contributed to the transition from dendritic trichomes, as seen in most species of Brassicaceae, to the distinctive stellate trichomes of the genus Physaria. We explored the role of positive selection on the evolution of BRANCHLESS TRICHOME (BLT), a candidate gene for changes in trichome branching pattern. Maximum likelihood models of codon evolution point to a shift in selective pressure affecting the evolution of BLT across the entire Physaria clade, and we found strong evidence that positive selection has acted on a subset of Physaria BLT codons. Almost all of the 10 codon sites with the highest probability of having evolved under positive selection are clustered in a predicted coiled-coil domain, pointing to changes in protein-protein interactions. Thus, our findings suggest that selection acted on BLT to modify its interactions with other proteins. The fact that positive selection occurred throughout the radiation of Physaria could reflect selection to stabilize development in response to an abrupt switch from the dendritic form to the stellate form, divergent selection for diversification of the stellate form, or both. These results point to the need for evolutionary developmental studies of BLT and its interacting proteins in Physaria. PMID:27015897

  4. 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 ...

  5. SIAMESE, a gene controlling the endoreduplication cell cycle in Arabidopsis thaliana trichomes.

    PubMed

    Walker, J D; Oppenheimer, D G; Concienne, J; Larkin, J C

    2000-09-01

    Cell differentiation is generally tightly coordinated with the cell cycle, typically resulting in a nondividing cell with a unique differentiated morphology. The unicellular trichomes of Arabidopsis are a well-established model for the study of plant cell differentiation. Here, we describe a new genetic locus, SIAMESE (SIM), required for coordinating cell division and cell differentiation during the development of Arabidopsis trichomes (epidermal hairs). A recessive mutation in the sim locus on chromosome 5 results in clusters of adjacent trichomes that appeared to be morphologically identical 'twins'. Upon closer inspection, the sim mutant was found to produce multicellular trichomes in contrast to the unicellular trichomes produced by wild-type (WT) plants. Mutant trichomes consisting of up to 15 cells have been observed. Scanning electron microscopy of developing sim trichomes suggests that the cell divisions occur very early in the development of mutant trichomes. WT trichome nuclei continue to replicate their DNA after mitosis and cytokinesis have ceased, and as a consequence have a DNA content much greater than 2C. This phenomenon is known as endoreduplication. Individual nuclei of sim trichomes have a reduced level of endoreduplication relative to WT trichome nuclei. Endoreduplication is also reduced in dark-grown sim hypocotyls relative to WT, but not in light-grown hypocotyls. Double mutants of sim with either of two other mutants affecting endoreduplication, triptychon (try) and glabra3 (gl3) are consistent with a function for SIM in endoreduplication. SIM may function as a repressor of mitosis in the endoreduplication cell cycle. Additionally, the relatively normal morphology of multicellular sim trichomes indicates that trichome morphogenesis can occur relatively normally even when the trichome precursor cell continues to divide. The sim mutant phenotype also has implications for the evolution of multicellular trichomes. PMID:10952891

  6. Glandular odontogenic cyst: A diagnostic dilemma.

    PubMed

    Shah, Amisha A; Sangle, Amit; Bussari, Smita; Koshy, Ajit V

    2016-01-01

    Glandular odontogenic cyst (GOC) is a rare and uncommon jaw bone cyst of odontogenic origin described in 1987 by Gardener et al. as a distinct entity. It is a cyst having an unpredictable, potentially aggressive behavior, and has the propensity to grow in large size with relatively high recurrence rate. It poses a diagnostic challenge as it can be clinically and histopathologically confused with lateral periodontal cyst, botryoid odontogenic cyst, radicular and residual cysts with mucous metaplasia, and low-grade mucoepidermoid carcinoma. The present case report describes GOC in both male and female patients with intra-oral swelling following extraction of 36 and 46, respectively. Careful histopathological examination is needed to diagnose GOC, and a careful long-term follow-up is advocated. PMID:27134453

  7. Glandular odontogenic cyst: A diagnostic dilemma

    PubMed Central

    Shah, Amisha A.; Sangle, Amit; Bussari, Smita; Koshy, Ajit V.

    2016-01-01

    Glandular odontogenic cyst (GOC) is a rare and uncommon jaw bone cyst of odontogenic origin described in 1987 by Gardener et al. as a distinct entity. It is a cyst having an unpredictable, potentially aggressive behavior, and has the propensity to grow in large size with relatively high recurrence rate. It poses a diagnostic challenge as it can be clinically and histopathologically confused with lateral periodontal cyst, botryoid odontogenic cyst, radicular and residual cysts with mucous metaplasia, and low-grade mucoepidermoid carcinoma. The present case report describes GOC in both male and female patients with intra-oral swelling following extraction of 36 and 46, respectively. Careful histopathological examination is needed to diagnose GOC, and a careful long-term follow-up is advocated. PMID:27134453

  8. Glandular odontogenic cyst: A case report

    PubMed Central

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

    2014-01-01

    Glandular odontogenic cysts (GOCs) are rare intrabony solitary or multiloculated cysts of odontogenic origin. The importance of GOCs lies in the fact that they exhibit a propensity for recurrence similar to keratocystic odontogenic tumors and that they may be confused microscopically with central mucoepidermoid carcinoma. Thus, the oral and maxillofacial radiologists play an important role in definitive diagnosis of GOC based on distinctive cases; though they are rare. In large part, this is due to the GOC's complex and frequently non-specific histopathology. This report describes a case of GOC occurrence in the posterior mandibular ramus region in a 17-year-old female, which is a rare combination of site, age, and gender for occurrence. PMID:24701462

  9. 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. PMID:23514759

  10. 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

  11. 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.

  12. 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%.

  13. 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

  14. GLABROUS INFLORESCENCE STEMS regulates trichome branching by genetically interacting with SIM in Arabidopsis.

    PubMed

    Sun, Li-Li; Zhou, Zhong-Jing; An, Li-Jun; An, Yan; Zhao, Yong-Qin; Meng, Xiao-Fang; Steele-King, Clare; Gan, Yin-Bo

    2013-07-01

    Arabidopsis trichomes are large branched single cells that protrude from the epidermis. The first morphological indication of trichome development is an increase in nuclear content resulting from an initial cycle of endoreduplication. Our previous study has shown that the C2H2 zinc finger protein GLABROUS INFLORESCENCE STEMS (GIS) is required for trichome initiation in the inflorescence organ and for trichome branching in response to gibberellic acid signaling, although GIS gene does not play a direct role in regulating trichome cell division. Here, we describe a novel role of GIS, controlling trichome cell division indirectly by interacting genetically with a key endoreduplication regulator SIAMESE (SIM). Our molecular and genetic studies have shown that GIS might indireclty control cell division and trichome branching by acting downstream of SIM. A loss of function mutation of SIM signficantly reduced the expression of GIS. Futhermore, the overexpression of GIS rescued the trichome cluster cell phenotypes of sim mutant. The gain or loss of function of GIS had no significant effect on the expression of SIM. These results suggest that GIS may play an indirect role in regulating trichome cell division by genetically interacting with SIM. PMID:23825141

  15. GLABROUS1 overexpression and TRIPTYCHON alter the cell cycle and trichome cell fate in Arabidopsis.

    PubMed Central

    Szymanski, D B; Marks, M D

    1998-01-01

    Cellular competence, initiation cues, and inhibition signals control the distribution of trichomes on the Arabidopsis leaf. The GLABROUS1 (GL1) gene has a dual role in that it is required for trichome initiation, but GL1 overexpression reduces trichome number. We have found that a mutation in the TRIPTYCHON (TRY) gene partially suppresses the GL1 overexpression phenotype but not in a way that indicates that TRY directly controls an epidermal inhibition pathway. Surprisingly, cauliflower mosaic virus 35S::GL1 try plants contain a subclass of trichomes derived from the subepidermal layer. Altered cell cycle control was also detected in 35S::GL1 and try plants. A mutation in TRY led to increased epidermal and mesophyll cell number, a reduction in endoreduplication in the epidermis, and an increase in endoreduplication in trichomes. GL1 overexpression also reduced endoreduplication levels in both the epidermis and trichomes; however, in the presence of try, it synergistically enhanced trichome endoreduplication. Interactions with the COTYLEDON TRICHOME1 (COT1) gene indicate that GL1 and TRY control trichome development and may be involved in cell cycle control during leaf development. PMID:9836744

  16. Trichome cell growth in Arabidopsis thaliana can be derepressed by mutations in at least five genes.

    PubMed Central

    Perazza, D; Herzog, M; Hülskamp, M; Brown, S; Dorne, A M; Bonneville, J M

    1999-01-01

    Leaf trichomes in Arabidopsis are unicellular epidermal hairs with a branched morphology. They undergo successive endoreduplication rounds early during cell morphogenesis. Mutations affecting trichome nuclear DNA content, such as triptychon or glabra3, alter trichome branching. We isolated new mutants with supernumerary trichome branches, which fall into three unlinked complementation groups: KAKTUS and the novel loci, POLYCHOME and RASTAFARI. They map to chromosomes IV, II, and V, respectively. The trichomes of these mutants presented an increased DNA content, although to a variable extent. The spindly-5 mutant, which displays a constitutive gibberellin response, also produces overbranched trichomes containing more nuclear DNA. We analyzed genetic interactions using double mutants and propose that two independent pathways, defined by SPINDLY and TRIPTYCHON, act to limit trichome growth. KAKTUS and POLYCHOME might have redundant actions mediating gibberellin control via SPINDLY. The overall leaf polysomaty was not notably affected by these mutations, suggesting that they affect the control of DNA synthesis in a tissue- or cell type-specific manner. Wild-type tetraploids also produce overbranched trichomes; they displayed a shifted polysomaty in trichomes and in the whole leaf, suggesting a developmental program controlling DNA increases via the counting of endoreduplication rounds. PMID:10224275

  17. Trichome cell growth in Arabidopsis thaliana can be derepressed by mutations in at least five genes.

    PubMed

    Perazza, D; Herzog, M; Hülskamp, M; Brown, S; Dorne, A M; Bonneville, J M

    1999-05-01

    Leaf trichomes in Arabidopsis are unicellular epidermal hairs with a branched morphology. They undergo successive endoreduplication rounds early during cell morphogenesis. Mutations affecting trichome nuclear DNA content, such as triptychon or glabra3, alter trichome branching. We isolated new mutants with supernumerary trichome branches, which fall into three unlinked complementation groups: KAKTUS and the novel loci, POLYCHOME and RASTAFARI. They map to chromosomes IV, II, and V, respectively. The trichomes of these mutants presented an increased DNA content, although to a variable extent. The spindly-5 mutant, which displays a constitutive gibberellin response, also produces overbranched trichomes containing more nuclear DNA. We analyzed genetic interactions using double mutants and propose that two independent pathways, defined by SPINDLY and TRIPTYCHON, act to limit trichome growth. KAKTUS and POLYCHOME might have redundant actions mediating gibberellin control via SPINDLY. The overall leaf polysomaty was not notably affected by these mutations, suggesting that they affect the control of DNA synthesis in a tissue- or cell type-specific manner. Wild-type tetraploids also produce overbranched trichomes; they displayed a shifted polysomaty in trichomes and in the whole leaf, suggesting a developmental program controlling DNA increases via the counting of endoreduplication rounds. PMID:10224275

  18. Maize leaf trichomes represent an entry point of infection for Fusarium species.

    PubMed

    Nguyen, Thi Thanh Xuan; Dehne, Heinz-Wilhelm; Steiner, Ulrike

    2016-08-01

    Fifteen day old maize seedlings were inoculated with Fusarium graminearum, Fusarium proliferatum, and Fusarium verticillioides. More than 90 % F. proliferatum and F. verticillioides conidia and 50 % of F. graminearum formed one germ tube whereas the other 50 % of F. graminearum conidia formed two to three germ tubes. The germ tubes of F. graminearum conidia were longer than those of F. proliferatum and F. verticillioides. The three species of Fusarium infected bi-cellular trichomes by adhering and growing along the trichomes or by attaching to the cap cell of the trichomes 48 h after inoculation. Hyphae penetrated into the trichomes at the base, the side or at the top of the cap cells. The hyphae colonized the cap cells and then spread to base cells. Prickle trichomes were infected 72 h after inoculation. The hyphae either wrapped around prickle trichomes or formed a mass of hyphae around the top of prickle trichomes or formed appressorium. Macro trichomes were infected by F. graminearum 7 d after inoculation. Following penetration, the fungus spread to adjacent epidermal cells and to the subcuticle. This investigation provides the first assessment of F. graminearum, F. proliferatum, and F. verticillioides infection via trichomes of maize leaves. PMID:27521623

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

    PubMed Central

    Pattanaik, Sitakanta; Patra, Barunava; Singh, Sanjay Kumar; Yuan, Ling

    2014-01-01

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

  20. 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 ...

  1. Effects of leaf and bract trichomes on trash content and quality of ginned lint

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spinning efficiency and yarn quality is improved for bales with reduced trash content. Some cotton varieties have been characterized as having smoother leaves (low trichome density) and fewer bract trichomes, and it has been shown that cotton harvested from these varieties are picked with lower tra...

  2. Molecular basis of natural variation and environmental control of trichome patterning.

    PubMed

    Hauser, Marie-Theres

    2014-01-01

    Trichomes are differentiated epidermal cells on above ground organs of nearly all land plants. They play important protective roles as structural defenses upon biotic attacks such as herbivory, oviposition and fungal infections, and against abiotic stressors such as drought, heat, freezing, excess of light, and UV radiation. The pattern and density of trichomes is highly variable within natural population suggesting tradeoffs between traits positively affecting fitness such as resistance and the costs of trichome production. The spatial distribution of trichomes is regulated through a combination of endogenous developmental programs and external signals. This review summarizes the current understanding on the molecular basis of the natural variation and the role of phytohormones and environmental stimuli on trichome patterning. PMID:25071803

  3. Organized F-actin is essential for normal trichome morphogenesis in Arabidopsis.

    PubMed Central

    Szymanski, D B; Marks, M D; Wick, S M

    1999-01-01

    Actin microfilaments form a three-dimensional cytoskeletal network throughout the cell and constitute an essential throughway for organelle and vesicle transport. Development of Arabidopsis trichomes, unicellular structures derived from the epidermis, is being used as a genetic system in which to study actin-dependent growth in plant cells. The present study indicates that filamentous actin (F-actin) plays an important role during Arabidopsis trichome morphogenesis. For example, immunolocalization of actin filaments during trichome morphogenesis identified rearrangements of the cytoskeletal structure during the development of the mature cell. Moreover, pharmacological experiments indicate that there are distinct requirements for actin- and microtubule-dependent function during trichome morphogenesis. The F-actin-disrupting drug cytochalasin D does not affect the establishment of polarity during trichome development; however, maintenance and coordination of the normal pattern of cell growth are very sensitive to this drug. In contrast, oryzalin, an agent that depolymerizes microtubules, severely inhibits cell polarization. Furthermore, cytochalasin D treatment phenocopies a known class of mutations that cause distorted trichome morphology. Results of an analysis of cell shape and microfilament structure in wild-type, mutant, and drug-treated trichomes are consistent with a role for actin in the maintenance and coordination of an established growth pattern. PMID:10590162

  4. A regulatory gene induces trichome formation and embryo lethality in tomato

    PubMed Central

    Yang, Changxian; Zhang, Junhong; Luo, Zhidan; Gong, Pengjuan; Zhang, Chanjuan; Wang, Taotao; Zhang, Yuyang; Lu, Yong'en; Ye, Zhibiao

    2011-01-01

    Trichomes are universal biological structures originating from the aerial epidermis, which serve as an excellent model to study plant differentiation at the cell level. Although the pathway regulating trichome formation in the Rosids has been well characterized, only very recently a few genes were identified for trichome initiation in the Asterids. In this study, we cloned Woolly (Wo), essential for trichome formation in tomato. Transgenic experiments revealed that the woolly phenotype is caused by the mutation in Wo which encodes a homeodomain protein containing a bZIP motif and a START domain. We identified three alleles of Wo and found that each allele contains a missense mutation, which respectively results in an amino acid substitution at the C terminus. Microarray and expression analysis showed that the expression of a B-type cyclin gene, SlCycB2, is possibly regulated by Wo, which also participates in trichome formation. Suppression of Wo or SlCycB2 expression by RNAi decreased the number of type I trichomes, and direct protein–protein interaction was detected between them, implying that both proteins may work together in the regulation of this type of trichome formation. Cytological observation and Wo transcript analysis in the developing seeds showed that embryo development was also correlated with Wo. PMID:21730153

  5. Glandular Odontogenic Cyst of Mandible: A Rare Entity

    PubMed Central

    Mittal, Ankur; Kaur, Gursheen; Sood, Neena

    2015-01-01

    Glandular odontogenic cyst (GOC) is a rare developmental odontogenic cyst. It is a slow growing and asymptomatic swelling, usually affecting middle aged men and has tendency to reoccur. Here, we report a case of GOC in the anterior portion of mandible diagnosed by histopathology. PMID:26813085

  6. 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. PMID:26683710

  7. Glandular dose in breast computed tomography with synchrotron radiation

    NASA Astrophysics Data System (ADS)

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

    2016-01-01

    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.

  8. [The glandular odontogenic cyst--a rare entity].

    PubMed

    Brauer, H U; Manegold-Brauer, G

    2014-05-01

    In this short communication, the very rare glandular odontogenic cyst (GOC) is presented as an independent entity. The GOC is a jawbone cyst of the maxilla and mandible. The typical radiological and histopathological characteristics of the GOC are described. Furthermore, differential diagnoses, current treatment options and the recurrence rates of this of entity are discussed. PMID:24633391

  9. How is Cd Incorporated in Biominerals Eliminated by Tobacco Trichomes?

    NASA Astrophysics Data System (ADS)

    Hokura, Akiko

    In tobacco plants, elimination of Zn and Cd via the production of Ca-containing grains at the top of leaf hairs, called trichomes, is a potent detoxification mechanism. When tobacco plants were grown in a nutrient solution containing an amount of Cd and low Ca supplement, most of the grains were oblong-shaped and low-Cd-substituted calcite. When exposed to the same amount of Cd and high Ca supplement, grains were more abundant and diverse in compositions, and in total more Cd was eliminated. Most grains in the high Ca/Cd experiment were round-shaped and composed predominantly of Cd-substituted vaterite, a usually metastable calcium carbonate polymorph, and subordinate calcite.

  10. 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. PMID:26438788

  11. Foliar trichome-aided formaldehyde uptake in the epiphytic Tillandsia velutina and its response to formaldehyde pollution.

    PubMed

    Li, Peng; Pemberton, Robert; Zheng, Guiling

    2015-01-01

    Epiphytic Tillandsia (Bromeliaceae) species have been found to be efficient biomonitors of atmospheric heavy metals and persistent organic pollutants, but have not been used to monitor or remove the primary indoor atmospheric pollutant formaldehyde (FA). The absorptive capacity of Tillandsia trichomes is well-established, but potential secondary effects of foliar trichomes on gas exchange remain unclear. Our study investigated whether Tillandsia species can absorb FA efficiently and if the leaf trichomes function to improve FA uptake, using Tillandsia velutina. Plants with intact trichomes, decreased FA concentration by 48.42% in 12 h from 1060 μg m(-3) to 546.67 μg m(-3), while FA concentration decreased only by 22.51% in the plants without trichomes. Moreover, the more trichomes removed from the leaves, the lower the capability of FA uptake per unit leaf area, which suggested that T. velutina was capable of absorbing a large amount of FA via the leaves and specialized trichomes facilitated the whole leaf tissue FA absorption. In addition, all plants exposed to FA were chloric, had a reduction in measured leaf chlorophyll, and an increment in permeability of plasma membranes. However, plants in which trichomes had been removed declined or increased more quickly than plants with intact trichomes, indicating Tillandsia leaf trichomes also give the leaves some protection against this toxin. PMID:25150968

  12. Proteomic analysis of the medicinal plant Artemisia annua: Data from leaf and trichome extracts.

    PubMed

    Bryant, Laura; Patole, Chhaya; Cramer, Rainer

    2016-06-01

    This article contains raw and processed data related to research published by Bryant et al.[1]. Data was obtained by MS-based proteomics, analysing trichome-enriched, trichome-depleted and whole leaf samples taken from the medicinal plant Artemisia annua and searching the acquired MS/MS data against a recently published contig database [2] and other genomic and proteomic sequence databases for comparison. The processed data shows that an order-of-magnitude more proteins have been identified from trichome-enriched Artemisia annua samples in comparison to previously published data. Proteins known to have a role in the biosynthesis of artemisinin and other highly abundant proteins were found which imply additional enzymatically driven processes occurring within the trichomes that are significant for the biosynthesis of artemisinin. PMID:26977431

  13. Proteomic analysis of the medicinal plant Artemisia annua: Data from leaf and trichome extracts

    PubMed Central

    Bryant, Laura; Patole, Chhaya; Cramer, Rainer

    2016-01-01

    This article contains raw and processed data related to research published by Bryant et al.[1]. Data was obtained by MS-based proteomics, analysing trichome-enriched, trichome-depleted and whole leaf samples taken from the medicinal plant Artemisia annua and searching the acquired MS/MS data against a recently published contig database [2] and other genomic and proteomic sequence databases for comparison. The processed data shows that an order-of-magnitude more proteins have been identified from trichome-enriched Artemisia annua samples in comparison to previously published data. Proteins known to have a role in the biosynthesis of artemisinin and other highly abundant proteins were found which imply additional enzymatically driven processes occurring within the trichomes that are significant for the biosynthesis of artemisinin. PMID:26977431

  14. 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.

  15. 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. PMID:19494250

  16. 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.

  17. Mean glandular dose in a breast screening programme

    NASA Astrophysics Data System (ADS)

    Galván, H. A.; Pérez-Badillo, M. P.; Villaseñor, Y.

    2012-10-01

    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 "Quality assurance programme for digital mammography", 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.

  18. 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

  19. 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

  20. Detecting uterine glandular lesions: Role of cervical cytology

    PubMed Central

    Bansal, Baneet; Gupta, Parikshaa; Gupta, Nalini; Rajwanshi, Arvind; Suri, Vanita

    2016-01-01

    Background: The sensitivity of cervical cytology for detection of glandular lesions is reported to be low. We conducted this study to assess the diagnostic accuracy of cervical Papanicolaou (Pap) smears for uterine glandular lesions and to compare the diagnostic utility of conventional and liquid-based cytology (LBC) smears for glandular lesions. Materials and Methods: Archived histopathology records of all cases reported as endocervical and endometrial adenocarcinoma in the study period were identified and the available corresponding Pap smears (in preceding 1 year) were retrieved. In addition, the Pap smears reported as glandular cell abnormalities (GCA) during the same study period were retrieved. The overall prevalence of GCA, sensitivity, and specificity of Pap smears for the detection of GCA was calculated. The diagnostic accuracy of conventional and LBC smears for the diagnosis of GCA was also compared. Results: The prevalence of GCA in our study was 0.32%. The overall specificity of Pap smears for the diagnosis of GCA was 60.8%, this was not significantly different between conventional and LBC smears (P = 0.4). The overall sensitivity of Pap smears for the detection of GCA was 41.8%; LBC smears had significantly better sensitivity as compared to conventional smears for the detection of endometrial as compared to endocervical adenocarcinoma (P < 0.05). Conclusions: The prevalence of GCA in Pap smears is low. The specificity of Pap smears, for diagnosis of GCA, was found to be moderate. However, the overall sensitivity of Pap smears for the detection of GCA was low, though better for LBC as compared to conventional smears. PMID:27014363

  1. Calcium promotes cadmium elimination as vaterite grains by tobacco trichomes

    NASA Astrophysics Data System (ADS)

    Isaure, Marie-Pierre; Sarret, Géraldine; Harada, Emiko; Choi, Yong-Eui; Marcus, Matthew A.; Fakra, Sirine C.; Geoffroy, Nicolas; Pairis, Sébastien; Susini, Jean; Clemens, Stephan; Manceau, Alain

    2010-10-01

    In tobacco plants, elimination of Zn and Cd via the production of Ca-containing grains at the top of leaf hairs, called trichomes, is a potent detoxification mechanism. This study examines how Cd is incorporated in these biominerals, and how calcium growth supplement modifies their nature. Scanning electron microscopy coupled with energy dispersive X-ray microanalysis (SEM-EDX), microfocused X-ray diffraction (μ-XRD), and microfocused X-ray absorption near edge structure (μ-XANES) spectroscopy were used to image the morphology of the grains, identify the crystallized mineral phases, and speciate Cd, respectively. The mineralogy of the grains and chemical form of Cd varied with the amount of Ca. When tobacco plants were grown in a nutrient solution containing 25 μM Cd and low Ca supplement (Ca/Cd = 11 mol ratio), most of the grains were oblong-shaped and low-Cd-substituted calcite. When exposed to the same amount of Cd and high Ca supplement (Ca/Cd = 131 mol ratio), grains were more abundant and diverse in compositions, and in total more Cd was eliminated. Most grains in the high Ca/Cd experiment were round-shaped and composed predominantly of Cd-substituted vaterite, a usually metastable calcium carbonate polymorph, and subordinate calcite. Calcium oxalate and a Ca amorphous phase were detected occasionally in the two treatments, but were devoid of Cd. The biomineralization of cadmium and implications of results for Cd exposure of smokers and phytoremediation are discussed.

  2. 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. PMID:26842602

  3. Comparative structural profiling of trichome specialized metabolites in tomato (Solanum lycopersicum) and S. habrochaites: acylsugar profiles revealed by UHPLC/MS and NMR.

    PubMed

    Ghosh, Banibrata; Westbrook, Thomas C; Jones, A Daniel

    2014-01-01

    Many plants accumulate large quantities of specialized metabolites in secretory glandular trichomes (SGTs), which are specialized epidermal cells. In the genus Solanum, SGTs store a diverse collection of glucose and sucrose esters. Profiling of extracts from two accessions (LA1777 and LA1392) of Solanum habrochaites using ultra-high performance liquid chromatography-mass spectrometry (UHPLC/MS) revealed wide acylsugar diversity, with up to 11 isomers annotated for each individual elemental formula. These isomers arise from differences in ester chain lengths and their positions of substitution or branching. Since fragment ion masses were not sufficient to distinguish all isomers, 24 acylsucroses were purified from S. habrochaites accessions and cultivated tomato (Solanum lycopersicum M82) and characterized using NMR spectroscopy. Two-dimensional NMR spectra yielded assignments of positions of substitution of specific acyl groups, and locations of branching. The range of substitution was wider than reported earlier, and in contrast to previous reports, tetra- and penta-acylsucroses were substituted at position 2 with acyl groups other than acetate. Because UHPLC/MS fails to yield sufficient information about structure diversity, and quantitative NMR of acylsugar mixtures is confounded by structural redundancy, the strategic combination of NMR and UHPLC/MS provides a powerful approach for profiling a class of metabolites with great structural diversity across genotypes. PMID:24772058

  4. 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). PMID:25757729

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

    PubMed Central

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

    2013-01-01

    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. PMID:23576783

  6. 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.

  7. 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. PMID:26470072

  8. 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. PMID:25767057

  9. Adhesion and splash dispersal of Salmonella enterica Typhimurium on tomato leaflets: effects of rdar morphotype and trichome density.

    PubMed

    Cevallos-Cevallos, Juan M; Gu, Ganyu; Danyluk, Michelle D; van Bruggen, Ariena H C

    2012-11-01

    Salmonella enterica strains with rdar (red dry and rough) and saw (smooth and white) morphotypes have previously been associated with tomato outbreaks but the dispersal mechanisms of these morphotypes are still poorly understood. In this study, Salmonella adhesion was distinguished from attachment by comparing different contact periods. Initial adhesion of rdar and saw morphotypes of Salmonella was compared in relation to tomato plants with different leaf trichome densities. Trichome densities were increased or reduced by treatment with jasmonic or salicylic acid, respectively. The overall effect of Salmonella morphotype and trichome density on splash dispersal was assessed in a rain simulator and correlated to cell hydrophobicity and initial adhesion. The presence of the rdar morphotype increased initial adhesion at high trichome densities but not at low trichome densities. Attachment of the rdar strain occurred after 30s contact time regardless of trichome density. Splash dispersal was slightly further for the saw morphotype than the rdar morphotype of S. enterica at all trichome densities. Salmonella cells of both morphotypes survived significantly better on the surface of high trichome density leaflets. PMID:23141646

  10. Estimation of mean glandular dose for mammography of augmented breasts

    NASA Astrophysics Data System (ADS)

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

    2000-11-01

    The standard quantity used to relate breast surface exposure to radiation risk is the mean dose received by the radiation sensitive tissue contained within the female breast, the mean glandular dose (MGD). At present, little is known about the MGD received by women with breast implants as there is no technique available to facilitate its calculation. The present work has involved modification of the conventional method for MGD estimation to make it applicable to women with augmented breasts. The technique was used to calculate MGDs for a cohort of 80 women with breast implants, which were compared with similar data calculated for a total of 1258 non-augmented women. Little difference was found in median MGD at low compressed breast thickness. At high breast thickness, however, the MGDs received by women with augmented breasts were found to be considerably lower than those relating to their non-augmented counterparts.

  11. Recurrent Glandular Odontogenic Cyst of Maxilla- A Case Report

    PubMed Central

    Jafarian, Amir Hosein; Rahpeyma, Amin; Khajehahmadi, Saeedeh

    2015-01-01

    The glandular odontogenic cyst (GOC) is a rare lesion with odontogenic origin. It shows a propensity for recurrence revealed in 30% of all case. This investigation reports a case of recurrent GOC in a 35-year-old female in the anterior region of the maxilla, which is uncommon and discusses about IHC finding, surgical methods, and differential diagnosis. Under general anesthesia, peripheral bone ostectomy via large round bur for removal of remaining epithelium of the cyst wall was done. Finally liquid nitrogen was used to remaining bone. This article recommends that soft tissue adjacent to the cortical bone perforation should be excised, as well as peripheral bone ostectomy by large round bur for removal of remaining epithelium of the cyst and liquid nitrogen application to the bony cavity. Because of high recurrence rate of the lesion close follow up of the patients is needed. PMID:26351478

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2016-03-01

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

  14. 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

  15. 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. PMID:18975119

  16. 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.

  17. 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.

  18. 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.

  19. When defense backfires: Detrimental effect of a plant’s protective trichomes on an insect beneficial to the plant

    PubMed Central

    Eisner, Thomas; Eisner, Maria; Hoebeke, E. Richard

    1998-01-01

    The plant Mentzelia pumila (family Loasaceae) has leaves and stems densely covered with tiny hooked trichomes. The structures entrap and kill insects and therefore are most probably protective. But they are also maladaptive in that they incapacitate a coccinellid beetle (Hippodamia convergens) that preys upon an aphid enemy (Macrosiphum mentzeliae) of the plant. The adaptive benefit provided by the trichomes is evidently offset by a cost. PMID:9539750

  20. [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. PMID:26084157

  1. The Trihelix Transcription Factor GTL1 Regulates Ploidy-Dependent Cell Growth in the Arabidopsis Trichome[W][OA

    PubMed Central

    Breuer, Christian; Kawamura, Ayako; Ichikawa, Takanari; Tominaga-Wada, Rumi; Wada, Takuji; Kondou, Youichi; Muto, Shu; Matsui, Minami; Sugimoto, Keiko

    2009-01-01

    Leaf trichomes in Arabidopsis thaliana develop through several distinct cellular processes, such as patterning, differentiation, and growth. Although recent studies have identified several key transcription factors as regulating early patterning and differentiation steps, it is still largely unknown how these regulatory proteins mediate subsequent trichome development, which is accompanied by rapid cell growth and branching. Here, we report a novel trichome mutation in Arabidopsis, which in contrast with previously identified mutants, increases trichome cell size without altering its overall patterning or branching. We show that the corresponding gene encodes a GT-2-LIKE1 (GTL1) protein, a member of the trihelix transcription factor family. GTL1 is present within the nucleus during the postbranching stages of trichome development, and its loss of function leads to an increase in the nuclear DNA content only in trichomes that have completed branching. Our data further demonstrate that the gtl1 mutation modifies the expression of several cell cycle genes and partially rescues the ploidy defects in the cyclin-dependent kinase inhibitor mutant siamese. Taken together, this study provides the genetic evidence for the requirement of transcriptional regulation in the repression of ploidy-dependent plant cell growth as well as for an involvement of GTL trihelix proteins in this regulation. PMID:19717615

  2. Trichomes of tobacco excrete zinc as zinc-substituted calciumcarbonate and other zinc-containing compounds

    SciTech Connect

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

    2006-01-01

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

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

    PubMed

    Cardoso-Gustavson, P; Davis, A R

    2015-01-01

    Reabsorption is a phase of nectar dynamics that occurs concurrently with secretion; it has been described in floral nectaries that exude nectar through stomata or unicellular trichomes, but has not yet been recorded in extrafloral glands. Apparently, nectar reabsorption does not occur in multicellular secretory trichomes (MST) due to the presence of lipophilic impregnations - which resemble Casparian strips - in the anticlinal walls of the stalk cells. It has been assumed that these impregnations restrict solute movement within MST to occur unidirectionally and exclusively by the symplast, thereby preventing nectar reflux toward the underlying nectary tissues. We hypothesised that reabsorption is absent in nectaries possessing MST. The fluorochrome lucifer yellow (LYCH) was applied to standing nectar of two floral and extrafloral glands of distantly related species, and then emission spectra from nectary sections were systematically analysed using confocal microscopy. Passive uptake of LYCH via the stalk cells to the nectary tissues occurred in all MST examined. Moreover, we present evidence of nectar reabsorption in extrafloral nectaries, demonstrating that LYCH passed the stalk cells of MST, although it did not reach the deepest nectary tissues. Identical (control) experiments performed with neutral red (NR) demonstrated no uptake of this stain by actively secreting MST, whereas diffusion of NR did occur in plasmolysed MST of floral nectaries at the post-secretory phase, indicating that nectar reabsorption by MST is governed by stalk cell physiology. Interestingly, non-secretory trichomes failed to reabsorb nectar. The role of various nectary components is discussed in relation to the control of nectar reabsorption by secretory trichomes. PMID:24987788

  4. Chlorsulfuron modifies biosynthesis of acyl Acid substituents of sucrose esters secreted by tobacco trichomes.

    PubMed

    Kandra, L; Wagner, G J

    1990-11-01

    Sucrose esters and duvatrienediol diterpenes are principal constituents formed in and secreted outside head cells of trichomes occurring on surfaces of Nicotiana tabacum. Using trichome-bearing epidermal peels prepared from midveins of N. tabacum cv T.I. 1068 leaves, we found that chlorsulfuron reduced and modified radiolabeling of sucrose ester acyl acids derived from branched-chain amino acid metabolism. The herbicide did not effect formation and exudation of diterpenes which are products of isoprenoid metabolism. Treatment with 1.0 micromolar chlorsulfuron affected 8.5- and 6.3-fold reductions in radiolabeling of methylvaleryl and methylbutyryl groups of sucrose esters, respectively, and concomitant increases of 9- and 9.8-fold in radiolabeling of straight chain valeryl and butyryl groups, respectively. These results and others indicate that inhibition of acetolactate synthase causes an accumulation of 2-oxo-butyric acid that is utilized by enzymes common to Leu biosynthesis to form 2-oxo-valeric acid. Coenzyme A (CoA) activation of this keto acid gives rise to butyryl CoA, which is utilized to form butyryl containing sucrose esters. Alternatively, reutilization of 2-oxo-valeric acid by the same enzymes followed by CoA activation leads to valeryl containing sucrose esters. We propose that in trichome secretory cells synthase, isomerase and dehydrogenase enzymes which catalyze Leu synthesis/degredation in most tissues, convert iso-branched, anteiso-branched and straight-chain keto acids in the formation of sucrose ester acyl groups. PMID:16667871

  5. Chlorsulfuron Modifies Biosynthesis of Acyl Acid Substituents of Sucrose Esters Secreted by Tobacco Trichomes

    PubMed Central

    Kandra, Lili; Wagner, George J.

    1990-01-01

    Sucrose esters and duvatrienediol diterpenes are principal constituents formed in and secreted outside head cells of trichomes occurring on surfaces of Nicotiana tabacum. Using trichome-bearing epidermal peels prepared from midveins of N. tabacum cv T.I. 1068 leaves, we found that chlorsulfuron reduced and modified radiolabeling of sucrose ester acyl acids derived from branched-chain amino acid metabolism. The herbicide did not effect formation and exudation of diterpenes which are products of isoprenoid metabolism. Treatment with 1.0 micromolar chlorsulfuron affected 8.5- and 6.3-fold reductions in radiolabeling of methylvaleryl and methylbutyryl groups of sucrose esters, respectively, and concomitant increases of 9- and 9.8-fold in radiolabeling of straight chain valeryl and butyryl groups, respectively. These results and others indicate that inhibition of acetolactate synthase causes an accumulation of 2-oxo-butyric acid that is utilized by enzymes common to Leu biosynthesis to form 2-oxo-valeric acid. Coenzyme A (CoA) activation of this keto acid gives rise to butyryl CoA, which is utilized to form butyryl containing sucrose esters. Alternatively, reutilization of 2-oxo-valeric acid by the same enzymes followed by CoA activation leads to valeryl containing sucrose esters. We propose that in trichome secretory cells synthase, isomerase and dehydrogenase enzymes which catalyze Leu synthesis/degredation in most tissues, convert iso-branched, anteiso-branched and straight-chain keto acids in the formation of sucrose ester acyl groups. PMID:16667871

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

    PubMed Central

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

    2008-01-01

    Tomosynthesis of the breast is currently a topic of intense interest as a logical next step in the evolution of digital mammography. This study reports on the computation of glandular radiation dose in digital tomosynthesis of the breast. Previously, glandular dose estimations in tomosynthesis have been performed using data from studies of radiation dose in conventional planar mammography. This study evaluates, using Monte Carlo methods, the normalized glandular dose (DgN) to the breast during a tomosynthesis study, and characterizes its dependence on breast size, tissue composition, and x-ray spectrum. The conditions during digital tomosynthesis imaging of the breast were simulated using a computer program based on the Geant4 toolkit. With the use of simulated breasts of varying size, thickness and tissue composition, the DgN to the breast tissue was computed for varying x-ray spectra and tomosynthesis projection angle. Tomosynthesis projections centered about both the cranio-caudal (CC) and medio-lateral oblique (MLO) views were simulated. For each projection angle, the ratio of the glandular dose for that projection to the glandular dose for the zero degree projection was computed. This ratio was denoted the relative glandular dose (RGD) coefficient, and its variation under different imaging parameters was analyzed. Within mammographic energies, the RGD was found to have a weak dependence on glandular fraction and x-ray spectrum for both views. A substantial dependence on breast size and thickness was found for the MLO view, and to a lesser extent for the CC view. Although RGD values deviate substantially from unity as a function of projection angle, the RGD averaged over all projections in a complete tomosynthesis study varies from 0.91 to 1.01. The RGD results were fit to mathematical functions and the resulting equations are provided. PMID:17278508

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

    SciTech Connect

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

    2007-01-15

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

  8. Endometrial Expression of Steroidogenic Factor 1 Promotes Cystic Glandular Morphogenesis.

    PubMed

    Vasquez, Yasmin M; Wu, San-Pin; Anderson, Matthew L; Hawkins, Shannon M; Creighton, Chad J; Ray, Madhumita; Tsai, Sophia Y; Tsai, Ming-Jer; Lydon, John P; DeMayo, Francesco J

    2016-05-01

    Epigenetic silencing of steroidogenic factor 1 (SF1) is lost in endometriosis, potentially contributing to de novo local steroidogenesis favoring inflammation and growth of ectopic endometrial tissue. In this study, we examine the impact of SF1 expression in the eutopic uterus by a novel mouse model that conditionally expresses SF1 in endometrium. In vivo SF1 expression promoted the development of enlarged endometrial glands and attenuated estrogen and progesterone responsiveness. Endometriosis induction by autotransplantation of uterine tissue to the mesenteric membrane resulted in the increase in size of ectopic lesions from SF1-expressing mice. By integrating the SF1-dependent transcriptome with the whole genome binding profile of SF1, we identified uterine-specific SF1-regulated genes involved in Wingless and Progesterone receptor-Hedgehog-Chicken ovalbumin upstream promoter transcription factor II signaling for gland development and epithelium-stroma interaction, respectively. The present results indicate that SF1 directly contributes to the abnormal uterine gland morphogenesis, an inhibition of steroid hormone signaling and activation of an immune response, in addition to previously postulated estrogen production. PMID:27018534

  9. Cell Wall Maturation of Arabidopsis Trichomes Is Dependent on Exocyst Subunit EXO70H4 and Involves Callose Deposition1[OPEN

    PubMed Central

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

    2015-01-01

    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. PMID:25767057

  10. T. cacao Transcriptome Sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To compliment the T. cacao genome sequencing initiative and to build a reference set of expressed genes for functional studies, a broad and state-of-the-art approach to transcriptome sequencing is underway. Using newly optimized methods, transcriptome sequencing libraries were prepared from RNA of o...

  11. 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.

  12. A trichome-specific linoleate lipoxygenase expressed during pyrethrin biosynthesis in pyrethrum.

    PubMed

    Ramirez, Aldana M; Yang, Ting; Bouwmeester, Harro J; Jongsma, Maarten A

    2013-10-01

    The lipid precursor alcohols of pyrethrins-jasmolone, pyrethrolone and cinerolone-have been proposed as sharing parts of the oxylipin pathway with jasmonic acid. This implies that one of the first committed steps of pyrethrin biosynthesis is catalyzed by a lipoxygenase, catalyzing the hydroperoxidation of linolenic acid at position 13. Previously, we showed that the expression and activity of chrysanthemyl diphosphate synthase (TcCDS), the enzyme catalyzing the first committed step in the biosynthesis of the acid moiety of pyrethrins, is trichome-specific and developmentally regulated in flowers. In the present study we characterized the expression pattern of 25 lipoxygenase EST contigs, and subsequently carried out the molecular cloning of two pyrethrum lipoxygenases, TcLOX1 and TcLOX2, that have a similar pattern to TcCDS. Only recombinant TcLOX1 catalyzed the peroxidation of the linolenic acid substrate. Just as TcCDS, TcLOX1, are exclusively expressed in trichomes. Phylogenetic analysis showed that the enzyme shared the highest homology with chloroplast-localized 13-type-lipoxygenases that are involved in maintaining basal levels of jasmonate. PMID:23893337

  13. 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.

  14. [About a case of a recurrent glandular cardiac myxoma in a child].

    PubMed

    Meurgey, Alexandra; Henaine, Roland; Bouvagnet, Patrice; Chalabreysse, Lara

    2016-06-01

    Primary cardiac tumors are extremely rare and mainly benign. The majority of these are myxomas (40%). Myxoma are generally sporadic tumors which occur most commonly in adult females between 30 and 40 years, and are seldom found in the paediatric population (5%). Seven percent are associated with igenetic diseases. We report the case of an eight-year-old boy presenting a recurrent glandular cardiac myxoma. In 2011, he presented a deterioration of the general state. An echocardiography highlighted a left atrial mass on the interatrial septum, with a pedicular insertion. On the microscope, it consisted of a proliferation of stellate cells isolated or clustered in rudimentary vessels in a myxoid stroma presenting haemorrhage changes. These cells expressed CD34 and calretinine. Glandular elements without atypia were clustered within the myxomatous proliferation. They expressed cytokeratin (CK) 7. Surgical resection was macroscopically complete. In 2014, the boy had a sudden neurological deficit during a football match. An echocardiography revealed a recurrence at the same location. The lesion was excised and addressed in several fragments. Classical myxoma was associated with glands without atypia. This last component expressed CKAE1/AE3 and CK7. Ki67 index of proliferation was low. The surgical reintervention was macroscopically complete. The final diagnosis was glandular cardiac myxoma. A genetic survey was conducted, showing the presence of Carney complex. This is the first description in the litterature of a recurrent glandular cardiac myxoma occuring in a child. PMID:27234518

  15. Hypercalcemic encephalopathy in a patient on anti-TB treatment for glandular tuberculosis.

    PubMed

    Abraham, G; Sadasivam, P B; Gaspar, J H; Isphani, N; Lawrence, R

    1992-08-01

    An 84 years old male patient presented with hypercalcemic encephalopathy and mild azotemia while on anti-tuberculous treatment for glandular tuberculosis. He recovered fully during treatment with hydration, intravenous frusemide and oral prednisolone while continuing on the antituberculous therapy. PMID:1308493

  16. Automatic glandular and tubule region segmentation in histological grading of breast cancer

    NASA Astrophysics Data System (ADS)

    Nguyen, Kien; Barnes, Michael; Srinivas, Chukka; Chefd'hotel, Christophe

    2015-03-01

    In the popular Nottingham histologic score system for breast cancer grading, the pathologist analyzes the H and E tissue slides and assigns a score, in the range of 1-3, for tubule formation, nuclear pleomorphism and mitotic activity in the tumor regions. The scores from these three factors are added to give a final score, ranging from 3-9 to grade the cancer. Tubule score (TS), which reflects tubular formation, is a value in 1-3 given by manually estimating the percentage of glandular regions in the tumor that form tubules. In this paper, given an H and E tissue image representing a tumor region, we propose an automated algorithm to detect glandular regions and detect the presence of tubules in these regions. The algorithm first detects all nuclei and lumen candidates in the input image, followed by identifying tumor nuclei from the detected nuclei and identifying true lumina from the lumen candidates using a random forest classifier. Finally, it forms the glandular regions by grouping the closely located tumor nuclei and lumina using a graph-cut-based method. The glandular regions containing true lumina are considered as the ones that form tubules (tubule regions). To evaluate the proposed method, we calculate the tubule percentage (TP), i.e., the ratio of the tubule area to the total glandular area for 353 H and E images of the three TSs, and plot the distribution of these TP values. This plot shows the clear separation among these three scores, suggesting that the proposed algorithm is useful in distinguishing images of these TSs.

  17. 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…

  18. 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

  19. 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

  20. 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.

  1. Mineral nutrient uptake from prey and glandular phosphatase activity as a dual test of carnivory in semi-desert plants with glandular leaves suspected of carnivory

    PubMed Central

    Płachno, Bartosz Jan; Adamec, Lubomír; Huet, Hervé

    2009-01-01

    Background and Aims Ibicella lutea and Proboscidea parviflora are two American semi-desert species of glandular sticky plants that are suspected of carnivory as they can catch small insects. The same characteristics might also hold for two semi-desert plants with glandular sticky leaves from Israel, namely Cleome droserifolia and Hyoscyamus desertorum. The presence of proteases on foliar hairs, either secreted by the plant or commensals, detected using a simple test, has long been considered proof of carnivory. However, this test does not prove whether nutrients are really absorbed from insects by the plant. To determine the extent to which these four species are potentially carnivorous, hair secretion of phosphatases and uptake of N, P, K and Mg from fruit flies as model prey were studied in these species and in Roridula gorgonias and Drosophyllum lusitanicum for comparison. All species examined possess morphological and anatomical adaptations (hairs or emergences secreting sticky substances) to catch and kill small insects. Methods The presence of phosphatases on foliar hairs was tested using the enzyme-labelled fluorescence method. Dead fruit flies were applied to glandular sticky leaves of experimental plants and, after 10–15 d, mineral nutrient content in their spent carcasses was compared with initial values in intact flies after mineralization. Key Results Phosphatase activity was totally absent on Hyoscyamus foliar hairs, a certain level of activity was usually found in Ibicella, Proboscidea and Cleome, and a strong response was found in Drosophyllum. Roridula exhibited only epidermal activity. However, only Roridula and Drosophyllum took up nutrients (N, P, K and Mg) from applied fruit flies. Conclusions Digestion of prey and absorption of their nutrients are the major features of carnivory in plants. Accordingly, Roridula and Drosophyllum appeared to be fully carnivorous; by contrast, all other species examined are non-carnivorous as they did not meet

  2. 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.

  3. Glandular mast cells with distinct phenotype are highly elevated in chronic rhinosinusitis with nasal polyps

    PubMed Central

    Takabayashi, Tetsuji; Kato, Atsushi; Peters, Anju T.; Suh, Lydia A.; Carter, Roderick; Norton, James; Grammer, Leslie C.; Tan, Bruce K.; Chandra, Rakesh K.; Conley, David B.; Kern, Robert C.; Fujieda, Shigeharu; Schleimer, Robert P.

    2012-01-01

    Background Although chronic rhinosinusitis with nasal polyps (CRSwNP) is characterized by Th2 inflammation, the role of mast cells is poorly understood. Objective The objective of this study was to investigate the presence, localization and phenotype of mast cells in patients with chronic rhinosinusitis (CRS). Methods We collected nasal tissue and nasal lavage fluid from patients with CRS and control subjects. We analyzed mRNA for the mast cell proteases tryptase, chymase and carboxypeptidase A3 (CPA3), using real-time PCR, and measured mast cell protease proteins using ELISA, immunohistochemistry, and immunofluorescence. Results Tryptase mRNA was significantly increased in nasal polyps (NPs) from patients with CRSwNP (P < .001) compared with uncinate tissue (UT) from patients with CRS or control subjects. Tryptase protein was also elevated in NPs and in nasal lavage fluids from patients with CRSwNP. Immnohistochemistry showed increased numbers of mast cells in epithelium and glands but not within the lamina propria in NPs. The mast cells detected in epithelium in NPs were characterized by expression of tryptase and CPA3 but not chymase. Mast cells expressing all three proteases were abundant within glandular epithelium of NPs but were not found in normal glandular structures. Conclusion: Herein we demonstrate a unique localization of mast cells within glandular epithelium of NPs, and show that NPs mast cells have distinct phenotypes that vary by tissue location. Glandular mast cells and the diverse subsets of mast cells detected may contribute to the pathogenesis of CRSwNP. PMID:22534535

  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. PMID:23528863

  5. 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. PMID:11997469

  6. Examination of equine glandular stomach lesions for bacteria, including Helicobacter spp by fluorescence in situ hybridisation

    PubMed Central

    2010-01-01

    Background The equine glandular stomach is commonly affected by erosion and ulceration. The aim of this study was to assess whether bacteria, including Helicobacter, could be involved in the aetiology of gastric glandular lesions seen in horses. Results Stomach lesions, as well as normal appearing mucosa were obtained from horses slaughtered for human consumption. All samples were tested for urease activity using the Pyloritek® assay, while mucosal bacterial content was evaluated using Fluorescence In Situ Hybridisation. In selected sub samples, bacteria characterisation was pursued further by cloning and sequencing. Mucosal lesions were found in 36/63 stomachs and included hyperplastic rugae, polypoid structures and focal erosions. None of the samples were tested positive for urease activity or for FISH using the Helicobacter genus specific probe. In samples of lesions, as well as normal samples, clones with 99% similarities to Lactobacillus salivarius and Sarcina ventriculi were found. Escherichia like bacterium clones and Enterococcus clones were demonstrated in one focal erosion. Based on a phylogenetic tree these clones had 100% similarity to Escherichia fergusonii and Enterococcus faecium. The Enterococcus were found colonising the mucosal surface, while E. fergusonii organisms were also demonstrated intraepithelial. Conclusion Gastric Helicobacter spp. could not be verified as being involved in lesions of the glandular stomach of the horse. Since E. fergusonii has been described as an emerging pathogen in both humans and animals, the finding of this bacterium in gastric erosion warrants further clarification to whether gastric infection with this type bacterium is important for horses. PMID:20298612

  7. Mixed squamous cell and glandular papilloma of the lung resembling early adenocarcinoma: A case report

    PubMed Central

    Abe, Jiro; Ito, Shigemi; Takahashi, Satomi; Sato, Ikuro; Tanaka, Ryota; Sato, Taku; Okazaki, Toshimasa

    2016-01-01

    Introduction An extremely rare case of mixed squamous cell and glandular papilloma of the lung is reported. The correlation between the radiological and the pathological features as well as the clinical pitfall in making a diagnosis is discussed. Presentation of case An asymptomatic 68-year-old female with a cigarette smoking habit presented with a small nodule in her peripheral lung. A wedge resection was performed though it failed on-site diagnosis which was instead obtained following pathological scrutiny. The postsurgical course was excellent with no recurrence of disease. Discussion A small ground glass nodule gradually enlarged and transformed to a partially solid nodule a year and a half later. This transformation falsely made us suspect an early adenocarcinoma development. Eventually, the extremely rare subtype of pulmonary papilloma, with biphasic glandular and squamous cells, had been demonstrated to obstruct the peripheral bronchiole; and the adjoining alveoli had filled with a large volume of mucus. These pathological features seemed to have constituted the inner solid portion and the marginal ground glass portion respectively in the CT images, mimicking invasive lepidic adenocarcinoma. Conclusion Both pre- and intra-operative diagnoses are difficult mainly because of the rareness of the disease, however, mixed squamous cell and glandular papilloma may be considered in case the presence of primary adenocarcinoma is not validated. PMID:27141302

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

    PubMed

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

    2015-07-01

    In the image quality assessment for digital breast tomosynthesis (DBT), a breast phantom with an average percentage of 50 % glandular tissue is seldom used, which may not be representative of the breast tissue composition of the women undergoing such examination. This work aims at studying the effect of the glandular composition of the breast on the image quality taking into consideration different sizes of lesions. Monte Carlo simulations were performed using the state-of-the-art computer program PENELOPE to validate the image acquisition system of the DBT equipment as well as to calculate the mean glandular dose for each projection image and for different breast compositions. The integrated PENELOPE imaging tool (PenEasy) was used to calculate, in mammography, for each clinical detection task the X-ray energy that maximises the figure of merit. All the 2D cranial-caudal projections for DBT were simulated and then underwent the reconstruction process applying the Simultaneous Algebraic Reconstruction Technique. Finally, through signal-to-noise ratio analysis, the image quality in DBT was assessed. PMID:25836692

  9. Glandular object based tumor morphometry in H&E biopsy samples for prostate cancer prognosis

    NASA Astrophysics Data System (ADS)

    Fogarasi, Stephen I.; Khan, Faisal M.; Pang, Ho-Yuen H.; Mesa-Tejada, Ricardo; Donovan, Michael J.; Fernandez, Gerardo

    2011-03-01

    Morphological and architectural characteristics of primary prostate tissue compartments, such as epithelial nuclei (EN) and cytoplasm, provide critical information for cancer diagnosis, prognosis and therapeutic response prediction. The subjective and variable Gleason grade assessed by expert pathologists in Hematoxylin and Eosin (H&E) stained specimens has been the standard for prostate cancer diagnosis and prognosis. We propose a novel morphometric, glandular object-oriented image analysis approach for the robust quantification of H&E prostate biopsy images. We demonstrate the utility of features extracted through the proposed method in predicting disease progression post treatment in a multi-institution cohort of 1027 patients. The biopsy based features were univariately predictive for clinical response post therapy; with concordance indexes (CI) <= 0.4 or >= 0.6. In multivariate analysis, a glandular object feature quantifying tumor epithelial cells not directly associated with an intact tumor gland was selected in a model incorporating preoperative clinical data, protein biomarker and morphological imaging features. The model achieved a CI of 0.73 in validation, which was significantly higher than a CI of 0.69 for the standard multivariate model based solely on clinical features currently used in clinical practice. This work presents one of the first demonstrations of glandular object based morphological features in the H&E stained biopsy specimen to predict disease progression post primary treatment. Additionally, it is the largest scale study of the efficacy and robustness of the proposed features in prostate cancer prognosis.

  10. HD-Zip Proteins GL2 and HDG11 Have Redundant Functions in Arabidopsis Trichomes, and GL2 Activates a Positive Feedback Loop via MYB23[W

    PubMed Central

    Khosla, Aashima; Paper, Janet M.; Boehler, Allison P.; Bradley, Amanda M.; Neumann, Titus R.; Schrick, Kathrin

    2014-01-01

    The class IV homeodomain leucine zipper transcription factor GLABRA2 (GL2) acts in a complex regulatory circuit that regulates the differentiation of trichomes in Arabidopsis thaliana. We describe a genetic interaction with HOMEODOMAIN GLABROUS11 (HDG11), previously identified as a negative regulator of trichome branching. gl2 hdg11 double mutants display enhanced trichome cell-type differentiation defects. Transgenic expression of HDG11 using the GL2 promoter partially suppresses gl2 trichome phenotypes. Vice versa, expression of GL2 under the control of its native promoter partially complements hdg11 ectopic branching. Since gl2 hdg11 and gl2 myb23 double mutants and the triple mutant display similar trichome differentiation defects, we investigated a connection to the R2R3-MYB transcription factor MYB23. We show that MYB23 transcript levels are significantly reduced in shoots from gl2 mutants and that GL2 can drive the expression of a MYB23-promoter fusion to green fluorescent protein. Yeast one-hybrid, chromatin immunoprecipitation, and in planta reporter gene experiments indicate that an L1-box in the MYB23 promoter acts as a GL2 binding site. Taken together, our findings reveal a functional redundancy between GL2 and HDG11, two homeodomain leucine zipper transcription factors previously thought to mediate opposing functions in trichome morphogenesis. A model is proposed in which GL2 transcript levels are maintained through a positive feedback loop involving GL2 activation of MYB23. PMID:24824485

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

    PubMed

    Sarret, Géraldine; Harada, Emiko; Choi, Yong-Eui; Isaure, Marie-Pierre; Geoffroy, Nicolas; Fakra, Sirine; Marcus, Matthew A; Birschwilks, Mandy; Clemens, Stephan; Manceau, Alain

    2006-07-01

    Tobacco (Nicotiana tabacum L. cv Xanthi) plants were exposed to toxic levels of zinc (Zn). Zn exposure resulted in toxicity signs in plants, and these damages were partly reduced by a calcium (Ca) supplement. Confocal imaging of intracellular Zn using Zinquin showed that Zn was preferentially accumulated in trichomes. Exposure to Zn and Zn + Ca increased the trichome density and induced the production of Ca/Zn mineral grains on the head cells of trichomes. These grains were aggregates of submicrometer-sized crystals and poorly crystalline material and contained Ca as major element, along with subordinate amounts of Zn, manganese, potassium, chlorine, phosphorus, silicon, and magnesium. Micro x-ray diffraction revealed that the large majority of the grains were composed essentially of metal-substituted calcite (CaCO3). CaCO3 polymorphs (aragonite and vaterite) and CaC2O4 (Ca oxalate) mono- and dihydrate also were identified, either as an admixture to calcite or in separate grains. Some grains did not diffract, although they contained Ca, suggesting the presence of amorphous form of Ca. The presence of Zn-substituted calcite was confirmed by Zn K-edge micro-extended x-ray absorption fine structure spectroscopy. Zn bound to organic compounds and Zn-containing silica and phosphate were also identified by this technique. The proportion of Zn-substituted calcite relative to the other species increased with Ca exposure. The production of Zn-containing biogenic calcite and other Zn compounds through the trichomes is a novel mechanism involved in Zn detoxification. This study illustrates the potential of laterally resolved x-ray synchrotron radiation techniques to study biomineralization and metal homeostasis processes in plants. PMID:16731580

  12. [Cytophysiology of the glandular lobe of the corpora cardiaca: ergastoplasmic granules and their significance].

    PubMed

    Lafon-Cazal, M; Michel, R

    1977-01-01

    The number of ergastoplasmic granules in the glandular lobe of the corpora cardiaca is counted in Locusta migratoria migratorioides R. and F. and Schistocerca gregaria Forsk., male adults of different ages, grouped or isolated, having flown or not, and reared in various conditions of hygrometry and temperature. A good correlation was found between the number of ergastoplasmic granules and the utilization of the adipokinetic hormone. Ergastoplasmic granules may représent an original mechanism of hormonal storage used in view of heavy metabolic requirements. PMID:615543

  13. Transcriptomics using axolotls.

    PubMed

    Voss, S Randal; Athippozhy, Antony; Woodcock, M Ryan

    2015-01-01

    Microarray and RNA-sequencing technology now exists for the characterization of the Ambystoma mexicanum transcriptome. With sufficient replication, these tools give the opportunity to truly investigate gene expression in a variety of experimental paradigms. Analysis of data from the Amby002 array and RNA-sequencing technology can identify genes that change expression levels in concert with each other, which in turn may reveal mechanisms associated with biological processes and molecular functions. PMID:25740496

  14. Cancer Reduces Transcriptome Specialization

    PubMed Central

    Martínez, Octavio; Reyes-Valdés, M. Humberto; Herrera-Estrella, Luis

    2010-01-01

    A central goal of cancer biology is to understand how cells from this family of genetic diseases undergo specific morphological and physiological changes and regress to a de-regulated state of the cell cycle. The fact that tumors are unable to perform most of the specific functions of the original tissue led us to hypothesize that the degree of specialization of the transcriptome of cancerous tissues must be less than their normal counterparts. With the aid of information theory tools, we analyzed four datasets derived from transcriptomes of normal and tumor tissues to quantitatively test the hypothesis that cancer reduces transcriptome specialization. Here, we show that the transcriptional specialization of a tumor is significantly less than the corresponding normal tissue and comparable with the specialization of dedifferentiated embryonic stem cells. Furthermore, we demonstrate that the drop in specialization in cancerous tissues is largely due to a decrease in expression of genes that are highly specific to the normal organ. This approach gives us a better understanding of carcinogenesis and offers new tools for the identification of genes that are highly influential in cancer progression. PMID:20454660

  15. Toad Glandular Secretions and Skin Extractions as Anti-Inflammatory and Anticancer Agents

    PubMed Central

    Tan, C. K.; Hashimi, Saeed M.; Zulfiker, Abu Hasanat Md.; Wei, Ming Q.

    2014-01-01

    Toad glandular secretions and skin extractions contain many natural agents which may provide a unique resource for novel drug development. The dried secretion from the auricular and skin glands of Chinese toad (Bufo bufo gargarizans) is named Chansu, which has been used in Traditional Chinese Medicine (TCM) for treating infection and inflammation for hundreds of years. The sterilized hot water extraction of dried toad skin is named Huachansu (Cinobufacini) which was developed for treating hepatitis B virus (HBV) and several types of cancers. However, the mechanisms of action of Chansu, Huachansu, and their constituents within are not well reported. Existing studies have suggested that their anti-inflammation and anticancer potential were via targeting Nuclear Factor (NF)-κB and its signalling pathways which are crucial hallmarks of inflammation and cancer in various experimental models. Here, we review some current studies of Chansu, Huachansu, and their compounds in terms of their use as both anti-inflammatory and anticancer agents. We also explored the potential use of toad glandular secretions and skin extractions as alternate resources for treating human cancers in combinational therapies. PMID:24734105

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

    PubMed

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

    2015-09-01

    Epithelial glandular differentiation in dedifferentiated chondrosarcoma has not been described. Our patient was a 64-year-old man with a history of prostate cancer status post-radiation and hormonal therapy. On screening bone scan, he was found to have increased uptake in his right femoral shaft. Biopsy revealed intermediate-grade conventional chondrosarcoma. Subsequent femoral resection was remarkable for an intermediate-grade chondrosarcomatous component juxtaposed to an area composed of anastomosing nests and cords of malignant epithelial cells showing nuclear atypia and increased mitotic activity. A fibroblastic-appearing spindle cell population was intimately associated with the epithelial cells. The epithelial cells labeled with 34bE12, AE1/AE3, EMA, and Vimentin (both spindled and epithelial components) while being negative for prostate-specific antigen, prostate specific acid phosphatase, cytokeratin 20, thyroid transcription factor-1, and CDX2. The patient developed local recurrence 9 months after the initial resection but has had no metastatic disease and consistently undetectable prostate-specific antigen levels. Deep parallel sequencing of the dedifferentiated component showed a nonsynonymous mutation at exon 4 of IDH1 gene at codon R132 leading to a substitution of arginine, with serine confirming glandular differentiation in dedifferentiated chondrosarcoma. PMID:26198745

  17. A polynomial hyperelastic model for the mixture of fat and glandular tissue in female breast.

    PubMed

    Calvo-Gallego, Jose L; Martínez-Reina, Javier; Domínguez, Jaime

    2015-09-01

    In the breast of adult women, glandular and fat tissues are intermingled and cannot be clearly distinguished. This work studies if this mixture can be treated as a homogenized tissue. A mechanical model is proposed for the mixture of tissues as a function of the fat content. Different distributions of individual tissues and geometries have been tried to verify the validity of the mixture model. A multiscale modelling approach was applied in a finite element model of a representative volume element (RVE) of tissue, formed by randomly assigning fat or glandular elements to the mesh. Both types of tissues have been assumed as isotropic, quasi-incompressible hyperelastic materials, modelled with a polynomial strain energy function, like the homogenized model. The RVE was subjected to several load cases from which the constants of the polynomial function of the homogenized tissue were fitted in the least squares sense. The results confirm that the fat volume ratio is a key factor in determining the properties of the homogenized tissue, but the spatial distribution of fat is not so important. Finally, a simplified model of a breast was developed to check the validity of the homogenized model in a geometry similar to the actual one. PMID:25950862

  18. Further Studies on Barretts Mucosa in Baboons: Metaplastic Glandular Cells Produce Sialomucin

    PubMed Central

    RUBIO, CARLOS A.; OWSTON, MICHAEL; ORREGO, ABIEL; DICK, EDWARD J.

    2012-01-01

    Background In humans and in baboons, protracted gastro-esophageal reflux (GER) transforms the squamous-lined esophagus into columnar-lined (that is Barrett's mucosa, BM). Alcian blue stain (AB) is used to evidence sialomucin-producing goblet cells in human BM. Aim To assess the frequency and distribution of sialomucin-producing cells in BM in baboons. Materials and Methods Sections from 137 consecutive baboon esophagi were alternatively stained with hematoxylin-eosin (H&E) and with AB (pH 2.5), without counterstain. Results Out of 137 baboons, 131 (95.6%) had BM. Columnar and intramucosal glandular cells produced sialomucin in all 131 of these animals. Many BM cells were ballooned and filled with sialomucins, despite goblet cells not being found in H&E sections. Conclusion In humans, protracted GER is a disease requiring medication that may lead to BM; AB stains mainly goblet cells and occasional columnar cells in BM. In baboons, in contrast, BM is a natural postnatal process of adaptation to GER, triggered by regurgitation and rumination. AB stains all columnar and intra-mucosal glandular cells. Sialomucin-overstuffed cells were more frequent and larger in baboons than in humans. The extra load of sialomucin in BM might be an integrated part of the postnatal life-long process of adaptation to regurgitation and rumination in baboons. PMID:21036729

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

    SciTech Connect

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

    2014-06-15

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

  20. Unexpected roles for ancient proteins: flavone 8-hydroxylase in sweet basil trichomes is a Rieske-type, PAO-family oxygenase.

    PubMed

    Berim, Anna; Park, Jeong-Jin; Gang, David R

    2014-11-01

    Most elucidated hydroxylations in plant secondary metabolism are catalyzed by oxoglutarate- or cytochrome P450-dependent oxygenases. Numerous hydroxylations still evade clarification, suggesting that they might be performed by alternative enzyme types. Here, we report the identification of the flavone 8-hydroxylase (F8H) in sweet basil (Ocimum basilicum L.) trichomes as a Rieske-type oxygenase. Several features of the F8H activity in trichome protein extracts helped to differentiate it from a cytochrome P450-catalyzed reaction and identify candidate genes in the basil trichome EST database. The encoded ObF8H proteins share approximately 50% identity with Rieske-type protochlorophyllide a oxygenases (PTC52) from higher plants. Homology cloning and DNA blotting revealed the presence of several PTC52-like genes in the basil genome. The transcripts of the candidate gene designated ObF8H-1 are strongly enriched in trichomes compared to whole young leaves, indicating trichome-specific expression. The full-length ObF8H-1 protein possesses a predicted N-terminal transit peptide, which directs green fluorescent protein at least in part to chloroplasts. The F8H activity in crude trichome protein extracts correlates well with the abundance of ObF8H peptides. The purified recombinant ObF8H-1 displays high affinity for salvigenin and is inactive with other tested flavones except cirsimaritin, which is 8-hydroxylated with less than 0.2% relative activity. The efficiency of in vivo 8-hydroxylation by engineered yeast was improved by manipulation of protein subcellular targeting. blast searches showed that occurrence of several PTC52-like genes is rather common in sequenced plant genomes. The discovery of ObF8H suggests that Rieske-type oxygenases may represent overlooked candidate catalysts for oxygenations in specialized plant metabolism. PMID:25139498

  1. Viability of dried vegetative trichomes, formation of akinetes and heterocysts and akinete germination in some blue-green algae under water stress.

    PubMed

    Agrawal, S C; Singh, V

    1999-01-01

    Almost all dried vegetative trichomes ofAnabaena iyengarii, Westiellopsis prolifica andNostochopsis lobatus died within 1 h, while those ofOscillatoria acuminata retained viability to some extent for 1 d under similar storage conditions. The viability of dried vegetative trichomes ofO. acuminata decreased about equally on storage at 20 degrees C in the light or in the dark, but dropped rapidly at 12 and 0 degrees C in the dark. Vegetative trichomes ofA. iyengarii, N. lobatus andW. prolifica were more sensitive to frost than those ofO. acuminata, and this correlated with their low resistance to desiccation because both types of exposure involved osmotic stress. Both dried and wet akinetes ofA. iyengarii, W. prolifica andN. lobatus were about equally viable when stored at 20 degrees C in the light or the dark or at 12 and 0 degrees C in the dark, but their germination ability decreased on storage at 0 degrees C. The water stress imposed on growing vegetative trichomes either in high-agar media or in NaCl-supplemented liquid media reduced the survival ofO. acuminata trichomes, decreased or totally suppressed akinete and heterocyst formation and akinete germination inA. iyengarii, W. prolifica andN. lobatus. The sensitivity decreased in the sequenceA. iyengarii Trichomes ofO. acuminata became broader when grown in 0.5-0.8 mol/L NaCl-supplemented media, probably due to polyol accumulation, and they also developed a thin sheath-like structure. PMID:18461490

  2. Incidence of anti-intermediate filament antibody in serum samples of students with suspected glandular fever.

    PubMed Central

    Kataaha, P K; Holborow, E J; Edwards, J M

    1985-01-01

    Serum samples from 40 students with suspected infectious mononucleosis were tested for the presence of antibodies to intermediate filaments (AIFA) of the cytoskeleton. Twenty had antibodies to the Epstein-Barr virus capsid antigen before their illness, and during it their sera remained negative by the Paul-Bunnell test. The other 20 patients did not have antibodies to the Epstein-Barr virus capsid antigen before their illness and seroconverted during the illness. These patients (true infectious mononucleosis group) developed positive Paul-Bunnell tests. Sera from normal subjects (blood donors) were also tested for AIFA. AIFA was present in titres greater than 1/10 in 80% of the infectious mononucleosis group (mean titre 1/40-1/80), 10% of the Paul-Bunnell negative glandular fever group, and 8.5% of the normal blood donors. PMID:2982922

  3. PTEN Phosphatase-Independent Maintenance of Glandular Morphology in a Predictive Colorectal Cancer Model System1

    PubMed Central

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

    2013-01-01

    Organotypic models may provide mechanistic insight into colorectal cancer (CRC) morphology. Three-dimensional (3D) colorectal gland formation is regulated by phosphatase and tensin homologue deleted on chromosome 10 (PTEN) coupling of cell division cycle 42 (cdc42) to atypical protein kinase C (aPKC). This study investigated PTEN phosphatase-dependent and phosphatase-independent morphogenic functions in 3D models and assessed translational relevance in human studies. Isogenic PTEN-expressing or PTEN-deficient 3D colorectal cultures were used. In translational studies, apical aPKC activity readout was assessed against apical membrane (AM) orientation and gland morphology in 3D models and human CRC. We found that catalytically active or inactive PTEN constructs containing an intact C2 domain enhanced cdc42 activity, whereas mutants of the C2 domain calcium binding region 3 membrane-binding loop (M-CBR3) were ineffective. The isolated PTEN C2 domain (C2) accumulated in membrane fractions, but C2 M-CBR3 remained in cytosol. Transfection of C2 but not C2 M-CBR3 rescued defective AM orientation and 3D morphogenesis of PTEN-deficient Caco-2 cultures. The signal intensity of apical phospho-aPKC correlated with that of Na+/H+ exchanger regulatory factor-1 (NHERF-1) in the 3D model. Apical NHERF-1 intensity thus provided readout of apical aPKC activity and associated with glandular morphology in the model system and human colon. Low apical NHERF-1 intensity in CRC associated with disruption of glandular architecture, high cancer grade, and metastatic dissemination. We conclude that the membrane-binding function of the catalytically inert PTEN C2 domain influences cdc42/aPKC-dependent AM dynamics and gland formation in a highly relevant 3D CRC morphogenesis model system. PMID:24348097

  4. Glandular Proteome Identifies Antiprotease Cystatin C as a Critical Modulator of Airway Hydration and Clearance.

    PubMed

    Evans, T Idil Apak; Joo, Nam Soo; Keiser, Nicholas W; Yan, Ziying; Tyler, Scott R; Xie, Weiliang; Zhang, Yulong; Hsiao, Jordy J; Cho, Hyung-Ju; Wright, Michael E; Wine, Jeffrey J; Engelhardt, John F

    2016-04-01

    Defects in the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel lead to viscous secretions from submucosal glands that cannot be properly hydrated and cleared by beating cilia in cystic fibrosis (CF) airways. The mechanisms by which CFTR, and the predominant epithelial sodium channel (ENaC), control the hydration and clearance of glandular secretions remain unclear. We used a proteomics approach to characterize the proteins contained in CF and non-CF submucosal gland fluid droplets and found that differentially regulated proteases (cathepsin S and H) and their antiprotease (cystatin C) influenced the equilibration of fluid on the airway surface and tracheal mucociliary clearance (MCC). Contrary to prevailing models of airway hydration and clearance, cystatin C, or raising the airway surface liquid (ASL) pH, inhibited cathepsin-dependent ENaC-mediated fluid absorption and raised the height of ASL, and yet decreased MCC velocity. Importantly, coupling of both CFTR and ENaC activities were required for effective MCC and for effective ASL height equilibration after volume challenge. Cystatin C-inhibitable cathepsins controlled initial phases of ENaC-mediated fluid absorption, whereas CFTR activity was required to prevent ASL dehydration. Interestingly, CF airway epithelia absorbed fluid more slowly owing to reduced cysteine protease activity in the ASL but became abnormally dehydrated with time. Our findings demonstrate that, after volume challenge, pH-dependent protease-mediated coupling of CFTR and ENaC activities are required for rapid fluid equilibration at the airway surface and for effective MCC. These findings provide new insights into how glandular fluid secretions may be equilibrated at the airway surface and how this process may be impaired in CF. PMID:26334941

  5. Comparison of mammography sensitivity after reduction mammoplasty targeting the glandular and fat tissue

    PubMed Central

    Çakır, Murat; Küçükkartallar, Tevfik; Tekin, Ahmet; Selimoğlu, Nebil; Poyraz, Necdet; Belviranlı, Mehmet Metin; Kartal, Adil

    2015-01-01

    Objective: Mammography may have some limitations in the diagnosis and screening of breast cancer for women who have previously undergone breast reduction surgery. This study aimed to investigate how the structural defects in the breast tissue formed by postoperative changes are reflected on mammography. Material and Methods: The records of patients who had previously undergone breast reduction surgery and who were requested to undergo mammography for breast cancer screening by the general surgery clinic were retrospectively studied. The patients’ ages, surgical procedures, postoperative follow-up periods, amount of removed material, and histopathological and mammographic results were studied. The patients were classified into 3 groups: those older than 40 years who underwent reduction mammoplasty targeting predominantly the glandular tissue (group 1), those younger than 40 years who underwent reduction mammoplasty targeting predominantly the fat tissue (group 2), and those older than 40 years who were diagnosed with breast hypertrophy and were not operated (group 3). Results: The mean follow-up period of the patients was 6 (2–10) years. The mean value of resected tissue was 1120 g (680–2070) in group 1 and 1220 g (720–1980) in group 2. The mean age at the time of surgery was 45 (40–70) years for group 1 and 35 (24–40) years for group 2. All patients in group 1 were classified in Breast Imaging-Reporting and Data System (BI-RADS) category 1–2; 28 patients in group 2 were classified in BI-RADS 1–2, 4 were classified in BI-RADS 3, and 8 were classified in BI-RADS 0. In group 3, 35 patients were classified in BI-RADS 1–2, 4 were classified in BI-RADS 3, and 1 was classified in BI-RADS 0. Conclusion: We believe that breast reduction surgery targeting predominantly the glandular tissue in patients older than 40 years increases mammographic sensitivity. PMID:26170752

  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. Epigenetic alteration of Wnt pathway antagonists in progressive glandular neoplasia of the lung

    PubMed Central

    Licchesi, Julien D.F.; Westra, William H.; Hooker, Craig M.; Machida, Emi O.; Baylin, Stephen B.; Herman, James G.

    2008-01-01

    Background: Atypical adenomatous hyperplasia (AAH) is now recognized as a precursor lesion from which lung adenocarcinomas arise and thus represents an ideal target for studying the early genetic and epigenetic alterations associated with lung tumorigenesis such as alterations of the Wnt pathway. Methods: We assessed the level of Wnt signaling activity in lung cancer cell lines by determining the level of active β-catenin and determined the level of expression of Wnt antagonists APC, DKK1, DKK3, LKB1, SFRP1, 2, 4, 5, WIF1 and RUNX3 using reverse transcription–polymerase chain reaction. Using multiplex nested methylation-specific polymerase chain reaction, we analyzed promoter region methylation of these genes in resected lung tissue in the histopathologic sequence of glandular neoplasia (normal lung parenchyma, low-grade and high-grade AAH, adenocarcinoma). Results: The majority of non-small cell lung cancer cell lines (11 of 16, 69%) have evidence of active Wnt signaling and silencing of Wnt antagonists correlated with promoter hypermethylation. Promoter region methylation of Wnt antagonists was common in primary lung adenocarcinoma and there was a significant increase in the frequency of methylation for Wnt antagonist genes and the number of genes methylated with each stage of tumorigenesis (test for rend P ≤ 0.01). Additionally, odds ratios for promoter hypermethylation of individual or multiple Wnt antagonist genes and adenocarcinomas were statistically significantly elevated and ranged between 3.64 and 48.17. Conclusion: These results show that gene silencing of Wnt antagonists by promoter hypermethylation occurs during the earliest stages of glandular neoplasia of the lung and accumulates with progression toward malignancy. PMID:18308762

  8. 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

  9. Optimizing the anode-filter combination in the sense of image quality and average glandular dose in digital mammography

    NASA Astrophysics Data System (ADS)

    Varjonen, Mari; Strömmer, Pekka

    2008-03-01

    This paper presents the optimized image quality and average glandular dose in digital mammography, and provides recommendations concerning anode-filter combinations in digital mammography, which is based on amorphous selenium (a-Se) detector technology. The full field digital mammography (FFDM) system based on a-Se technology, which is also a platform of tomosynthesis prototype, was used in this study. X-ray tube anode-filter combinations, which we studied, were tungsten (W) - rhodium (Rh) and tungsten (W) - silver (Ag). Anatomically adaptable fully automatic exposure control (AAEC) was used. The average glandular doses (AGD) were calculated using a specific program developed by Planmed, which automates the method described by Dance et al. Image quality was evaluated in two different ways: a subjective image quality evaluation, and contrast and noise analysis. By using W-Rh and W-Ag anode-filter combinations can be achieved a significantly lower average glandular dose compared with molybdenum (Mo) - molybdenum (Mo) or Mo-Rh. The average glandular dose reduction was achieved from 25 % to 60 %. In the future, the evaluation will concentrate to study more filter combinations and the effect of higher kV (>35 kV) values, which seems be useful while optimizing the dose in digital mammography.

  10. 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.

  11. Orchestration of microtubules and the actin cytoskeleton in trichome cell shape determination by a plant-unique kinesin

    PubMed Central

    Tian, Juan; Han, Libo; Feng, Zhidi; Wang, Guangda; Liu, Weiwei; Ma, Yinping; Yu, Yanjun; Kong, Zhaosheng

    2015-01-01

    Microtubules (MTs) and actin filaments (F-actin) function cooperatively to regulate plant cell morphogenesis. However, the mechanisms underlying the crosstalk between these two cytoskeletal systems, particularly in cell shape control, remain largely unknown. In this study, we show that introduction of the MyTH4-FERM tandem into KCBP (kinesin-like calmodulin-binding protein) during evolution conferred novel functions. The MyTH4 domain and the FERM domain in the N-terminal tail of KCBP physically bind to MTs and F-actin, respectively. During trichome morphogenesis, KCBP distributes in a specific cortical gradient and concentrates at the branching sites and the apexes of elongating branches, which lack MTs but have cortical F-actin. Further, live-cell imaging and genetic analyses revealed that KCBP acts as a hub integrating MTs and actin filaments to assemble the required cytoskeletal configuration for the unique, polarized diffuse growth pattern during trichome cell morphogenesis. Our findings provide significant insights into the mechanisms underlying cytoskeletal regulation of cell shape determination. DOI: http://dx.doi.org/10.7554/eLife.09351.001 PMID:26287478

  12. The human mitochondrial transcriptome

    PubMed Central

    Mercer, Tim R.; Neph, Shane; Dinger, Marcel E.; Crawford, Joanna; Smith, Martin A.; Shearwood, Anne-Marie J.; Haugen, Eric; Bracken, Cameron P.; Rackham, Oliver; Stamatoyannopoulos, John A.; Filipovska, Aleksandra; Mattick, John S.

    2011-01-01

    Summary The human mitochondrial genome comprises a distinct genetic system transcribed as precursor polycistronic transcripts that are subsequently cleaved to generate individual mRNAs, tRNAs and rRNAs. Here we provide a comprehensive analysis of the human mitochondrial transcriptome across multiple cell lines and tissues. Using directional deep sequencing and parallel analysis of RNA ends, we demonstrate wide variation in mitochondrial transcript abundance and precisely resolve transcript processing and maturation events. We identify previously undescribed transcripts, including small RNAs, and observe the enrichment of several nuclear RNAs in mitochondria. Using high-throughput in vivo DNaseI footprinting, we establish the global profile of DNA-binding protein occupancy across the mitochondrial genome at single nucleotide resolution, revealing regulatory features at mitochondrial transcription initiation sites and functional insights into disease-associated variants. This integrated analysis of the mitochondrial transcriptome reveals unexpected complexity in the regulation, expression, and processing of mitochondrial RNA, and provides a resource for future studies of mitochondrial function (accessed at mitochondria.matticklab.com). PMID:21854988

  13. Gel-based and gel-free proteomic analysis of Nicotiana tabacum trichomes identifies proteins involved in secondary metabolism and in the (a)biotic stress response.

    PubMed

    Van Cutsem, Emmanuel; Simonart, Géraldine; Degand, Hervé; Faber, Anne-Marie; Morsomme, Pierre; Boutry, Marc

    2011-02-01

    Nicotiana tabacum leaves are covered by trichomes involved in the secretion of large amounts of secondary metabolites, some of which play a major role in plant defense. However, little is known about the metabolic pathways that operate in these structures. We undertook a proteomic analysis of N. tabacum trichomes in order to identify their protein complement. Efficient trichome isolation was obtained by abrading frozen leaves. After homogenization, soluble proteins and a microsomal fraction were prepared by centrifugation. Gel-based and gel-free proteomic analyses were then performed. 2-DE analysis of soluble proteins led to the identification of 1373 protein spots, which were digested and analyzed by MS/MS, leading to 680 unique identifications. Both soluble proteins and microsomal fraction were analyzed by LC MALDI-MS/MS after trypsin digestion, leading to 858 identifications, many of which had not been identified after 2-DE, indicating that the two methods complement each other. Many enzymes putatively involved in secondary metabolism were identified, including enzymes involved in the synthesis of terpenoid precursors and in acyl sugar production. Several transporters were also identified, some of which might be involved in secondary metabolite transport. Various (a)biotic stress response proteins were also detected, supporting the role of trichomes in plant defense. PMID:21268273

  14. Ectopic expression of R3 MYB transcription factor gene OsTCL1 in Arabidopsis, but not rice, affects trichome and root hair formation.

    PubMed

    Zheng, Kaijie; Tian, Hainan; Hu, Qingnan; Guo, Hongyan; Yang, Li; Cai, Ling; Wang, Xutong; Liu, Bao; Wang, Shucai

    2016-01-01

    In Arabidopsis, a MYB-bHLH-WD40 (MBW) transcriptional activator complex activates the homeodomain protein gene GLABRA2 (GL2), leading to the promotion of trichome formation and inhibition of root hair formation. The same MBW complex also activates single-repeat R3 MYB genes. R3 MYBs in turn, play a negative feedback role by competing with R2R3 MYB proteins for binding bHLH proteins, thus blocking the formation of the MBW complex. By BLASTing the rice (Oryza sativa) protein database using the entire amino acid sequence of Arabidopsis R3 MYB transcription factor TRICHOMELESS1 (TCL1), we found that there are two genes in rice genome encoding R3 MYB transcription factors, namely Oryza sativa TRICHOMELESS1 (OsTCL1) and OsTCL2. Expressing OsTCL1 in Arabidopsis inhibited trichome formation and promoted root hair formation, and OsTCL1 interacted with GL3 when tested in Arabidopsis protoplasts. Consistent with these observations, expression levels of GL2, R2R3 MYB transcription factor gene GLABRA1 (GL1) and several R3 MYB genes were greatly reduced, indicating that OsTCL1 is functional R3 MYB. However, trichome and root hair formation in transgenic rice plants overexpressing OsTCL1 remained largely unchanged, and elevated expression of OsGL2 was observed in the transgenic rice plants, indicating that rice may use different mechanisms to regulate trichome formation. PMID:26758286

  15. Ectopic expression of R3 MYB transcription factor gene OsTCL1 in Arabidopsis, but not rice, affects trichome and root hair formation

    PubMed Central

    Zheng, Kaijie; Tian, Hainan; Hu, Qingnan; Guo, Hongyan; Yang, Li; Cai, Ling; Wang, Xutong; Liu, Bao; Wang, Shucai

    2016-01-01

    In Arabidopsis, a MYB-bHLH-WD40 (MBW) transcriptional activator complex activates the homeodomain protein gene GLABRA2 (GL2), leading to the promotion of trichome formation and inhibition of root hair formation. The same MBW complex also activates single-repeat R3 MYB genes. R3 MYBs in turn, play a negative feedback role by competing with R2R3 MYB proteins for binding bHLH proteins, thus blocking the formation of the MBW complex. By BLASTing the rice (Oryza sativa) protein database using the entire amino acid sequence of Arabidopsis R3 MYB transcription factor TRICHOMELESS1 (TCL1), we found that there are two genes in rice genome encoding R3 MYB transcription factors, namely Oryza sativa TRICHOMELESS1 (OsTCL1) and OsTCL2. Expressing OsTCL1 in Arabidopsis inhibited trichome formation and promoted root hair formation, and OsTCL1 interacted with GL3 when tested in Arabidopsis protoplasts. Consistent with these observations, expression levels of GL2, R2R3 MYB transcription factor gene GLABRA1 (GL1) and several R3 MYB genes were greatly reduced, indicating that OsTCL1 is functional R3 MYB. However, trichome and root hair formation in transgenic rice plants overexpressing OsTCL1 remained largely unchanged, and elevated expression of OsGL2 was observed in the transgenic rice plants, indicating that rice may use different mechanisms to regulate trichome formation. PMID:26758286

  16. 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.

  17. 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

  18. Phylogenomics Using Transcriptome Data.

    PubMed

    Cannon, Johanna Taylor; Kocot, Kevin Michael

    2016-01-01

    This chapter presents a generalized protocol for conducting phylogenetic analyses using large-scale molecular datasets, specifically using transcriptome data from the Illumina sequencing platform. The general molecular lab bench protocol consists of RNA extraction, cDNA synthesis, and sequencing, in this case via Illumina. After sequences have been obtained, bioinformatics methods are used to assemble raw reads, identify coding regions, and categorize sequences from different species into groups of orthologous genes (OGs). The specific OGs to be used for phylogenetic inference are selected using a custom shell script. Finally, the selected orthologous groups are concatenated into a supermatrix. Generalized methods for phylogenomic inference using maximum likelihood and Bayesian inference software are presented. PMID:27460370

  19. 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

  20. Anguillid herpesvirus 1 transcriptome.

    PubMed

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

    2012-09-01

    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

  1. 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.

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

    PubMed Central

    Joachims, Michelle L.; Leehan, Kerry M.; Lawrence, Christina; Pelikan, Richard C.; Moore, Jacen S.; Pan, Zijian; Rasmussen, Astrid; Radfar, Lida; Lewis, David M.; Grundahl, Kiely M.; Kelly, Jennifer A.; Wiley, Graham B.; Shugay, Mikhail; 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

  3. 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. PMID:26033492

  4. Mixed squamous cell and glandular papilloma of the lung: a case study and literature review.

    PubMed

    Inamura, Kentaro; Kumasaka, Toshio; Furuta, Reiko; Shimada, Kei; Hiyama, Noriko; Furuhata, Yoshiaki; Tanaka, Isao; Takemura, Tamiko

    2011-04-01

    Mixed squamous cell and glandular papilloma (mixed papilloma) of the lung is an extremely rare neoplasm, with only 10 cases reported so far in the English literature. We present a case study of endobronchial mixed papilloma with immunohistochemical and etiological investigations. A 49-year-old male with a smoking history complained of hemoptysis, presented with a lung mass closely adjacent to large vessels in the computed tomography findings, and underwent lobectomy. The 3.0-cm sized polypoid tumor was histologically diagnosed as endobronchial mixed papilloma. Immunohistochemically, intracellular mucin was positive for MUC5AC, which is expressed in tracheobronchial goblet cells. CAM5.2 and CK19 were diffusely positive, indicating that the tumor originated from the columnar epithelium by squamous metaplasia. CEA and CA19-9 were focally positive. A human papillomavirus (HPV) investigation with in situ hybridization using a wide spectrum probe and a newly-developed PCR system did not detect any HPV infection. Including this case with a detailed HPV investigation, all of the reported cases of mixed papilloma were HPV-negative, and a literature review including newly-reported cases indicated a high frequency of smoking in such cases. Endobronchial mixed papillomas might have a smoking-related etiology. PMID:21418399

  5. Glandular Odontogenic Cyst: Report of Two Cases and Review of Literature

    PubMed Central

    Sherlin, Herald J.; Ramalingam, Karthikeyan; Natesan, Anuja; Premkumar, Priya; Ramani, Pratibha; Chandrasekar, Thiruvengadam

    2009-01-01

    Glandular odontogenic cyst (GOC) is an uncommon jaw bone cyst of odontogenic origin described in 1987 by Gardner et al. It is a cyst having an unpredictable and potentially aggressive behaviour. It also has the propensity to grow to a large size and tendency to recur with only 111 cases having been reported thus far. The first case occurred in a 42-year-old female and presented as a localized swelling extending from 19 to 29 regions. There was a history of traumatic injury at the site. There was evidence of bicortical expansion and radiographs revealed a multilocular radiolucency. The second case occurred in a 21-year-old male, as a large swelling in the mandible and radiograph revealed radiolucency in the region. On histopathological examination, these lesions were diagnosed as GOC. It was concluded that, two cases submitted by us correlate with the existing literature that GOC’s affect more commonly in the middle age group, having predilection for mandible and that trauma could be a precipitating factor for its occurrence. The increased recurrence rates can be due to its intrinsic biological behavior, multilocularity of the cyst, and incomplete removal of the lining following conservative treatment. PMID:19644539

  6. Ultrastructure of posterior sternal glands of Macrotermes annandalei (Silvestri): new members of the sexual glandular set found in termites (Insecta).

    PubMed

    Quennedey, André; Peppuy, Alexis; Courrent, Annie; Robert, Alain; Everaerts, Claude; Bordereau, Christian

    2004-12-01

    In female alates of Macrotermes annandalei, two types of abdominal glands are involved in the secretion of sex pheromone. Tergal glands are found at the anterior margin of tergites 6-10 and posterior sternal glands (PSGs) are located at the anterior margin of sternites 6-7. The cytological features of both types of glands are quite similar. The fine structural organization of PSGs is studied more precisely and described for the first time. The glandular cuticle is pitted with narrow apertures corresponding to the openings of numerous subcuticular pouches. Several Class 3 glandular units open in each pouch. One canal cell and one secretory cell make an individual glandular unit. The canal cell is enlarged apically and is connected with the other canal cells to form a common pouch. Based on the structural features found in these glands, we propose a common secretory process for PSGs and tergal glands. During the physiological maturation of alates inside the nest, secretory vesicles amass in the cytoplasm of secretory cells, while large intercellular spaces collapse the cuticular pouches. At the time of dispersal flight, pouches are filled with the content of secretory vesicles while intercellular spaces are sharply reduced. After calling behavior, no secretion remains in the glands and pouches collapse again, while secretory cells are drastically reduced in size. The structure and the secretory processes of PSGs and tergal glands are compared to those of abdominal sexual glands known in termites. PMID:15487007

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

    SciTech Connect

    Pignatelli, M.; Bodmer, W.F. )

    1988-08-01

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

  8. 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

  9. 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

  10. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  12. Normalized mean glandular dose computation from mammography using GATE: a validation study

    NASA Astrophysics Data System (ADS)

    Myronakis, Marios E.; Zvelebil, Marketa; Darambara, Dimitra G.

    2013-04-01

    Mean glandular dose (MGD) is the figure of merit to assess breast dose after a mammographic acquisition. The use of normalized MGD obtained from Monte Carlo computations with measured incident air kerma determines the MGD delivered to patients. The Geant4 Application for Tomographic Emission (GATE) toolkit is a modern Monte Carlo application specifically designed for medical imaging systems modelling. Although there is an increasing number of publications using GATE worldwide for a wide range of medical imaging and therapeutic applications, there is currently no means to obtain normalized MGD. In this work, the GATE toolkit is extended, through the development of two new modules, to provide normalized MGD information for compressed breast phantoms based on simple geometries. The normalized MGD values were validated against published work and provided results at half value layers lower than 0.3 and greater than 0.6 mmAl. In addition, the skin thickness and composition were considered. Normalized MGD was computed after substitution of the adipose layer surrounding the standard breast phantom with skin tissue and the relative difference is reported. Spectrum generation was facilitated by further development of previously published work by other authors. Validation of the new GATE extension showed good agreement with published data and can be used to assess breast dose from mammographic as well as more complex x-ray imaging techniques. Changing skin thickness and composition revealed substantial changes in normalized MGD specifically for compressed breast thickness different than 5 cm and a possible revision of the structure of the standard breast model may be necessary.

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

    PubMed

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

    2015-10-21

    For the evaluation of the average glandular dose (AGD) in digital mammography (DM) and digital breast tomosynthesis (DBT) phantoms simulating standard model breasts are used. These phantoms consist of slabs of polymethyl methacrylate (PMMA) or a combination of PMMA and polyethylene (PE). In the last decades the automatic exposure control (AEC) increased in complexity and became more sensitive to (local) differences in breast composition. The question is how well the AGD estimated using these simple dosimetry phantoms agrees with the average patient AGD. In this study the AGDs for both dosimetry phantoms and for patients have been evaluated for 5 different x-ray systems in DM and DBT modes. It was found that the ratios between patient and phantom AGD did not differ considerably using both dosimetry phantoms. These ratios averaged over all breast thicknesses were 1.14 and 1.15 for the PMMA and PMMA-PE dosimetry phantoms respectively in DM mode and 1.00 and 1.02 in the DBT mode. These ratios were deemed to be sufficiently close to unity to be suitable for dosimetry evaluation in quality control procedures. However care should be taken when comparing systems for DM and DBT since depending on the AEC operation, ratios for particular breast thicknesses may differ substantially (0.83-1.96). Although the predictions of both phantoms are similar we advise the use of PMMA  +  PE slabs for both DM and DBT to harmonize dosimetry protocols and avoid any potential issues with the use of spacers with the PMMA phantoms. PMID:26407015

  14. 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

  15. Normalized mean glandular dose computation from mammography using GATE: a validation study.

    PubMed

    Myronakis, Marios E; Zvelebil, Marketa; Darambara, Dimitra G

    2013-04-01

    Mean glandular dose (MGD) is the figure of merit to assess breast dose after a mammographic acquisition. The use of normalized MGD obtained from Monte Carlo computations with measured incident air kerma determines the MGD delivered to patients. The Geant4 Application for Tomographic Emission (GATE) toolkit is a modern Monte Carlo application specifically designed for medical imaging systems modelling. Although there is an increasing number of publications using GATE worldwide for a wide range of medical imaging and therapeutic applications, there is currently no means to obtain normalized MGD. In this work, the GATE toolkit is extended, through the development of two new modules, to provide normalized MGD information for compressed breast phantoms based on simple geometries. The normalized MGD values were validated against published work and provided results at half value layers lower than 0.3 and greater than 0.6 mmAl. In addition, the skin thickness and composition were considered. Normalized MGD was computed after substitution of the adipose layer surrounding the standard breast phantom with skin tissue and the relative difference is reported. Spectrum generation was facilitated by further development of previously published work by other authors. Validation of the new GATE extension showed good agreement with published data and can be used to assess breast dose from mammographic as well as more complex x-ray imaging techniques. Changing skin thickness and composition revealed substantial changes in normalized MGD specifically for compressed breast thickness different than 5 cm and a possible revision of the structure of the standard breast model may be necessary. PMID:23475310

  16. Glandular odontogenic cyst – Literature review and report of a paediatric case

    PubMed Central

    Faisal, Mohammad; Ahmad, Syed Ansar; Ansari, Uzma

    2015-01-01

    Glandular odontogenic cyst (GOC) is an extremely rare lesion occurring in the jawbones. The present paper is a review of 181 cases of GOCs reported in English literature, since it was first reported by Padayache and Van Wyk in 1987. Mandible was involved in 130 cases and maxilla in 51 cases. Anterior mandible was the most common area of involvement. Radiographic appearance was that of a unilocular radiolucency in 98 of 176 reported cases. Rest presented as multilocular radiolucency. Cortical expansion was observed in 136 of the 180 reported cases while cortex breach or perforation was seen in 81 cases. The treatment of choice was that of minor procedures that included enucleation with or without curettage, peripheral ostectomy, cryotherapy, etc. in 157 of the total 177 reported cases. Marginal jaw resection, segmental mandibulectomy etc. was reported in 20 cases. Although minor surgical procedures were the treatment of choice in most studies, two major studies of Kaplan et al. and Fowler et al. involving 111 and 46 cases, recorded a recurrence rate of 35.9 and 19.6%, respectively. The age range was between 11 and 82 years. The respective mean age of patients in the above mentioned studies was 45.7 for Kaplan's and 51 years for Fowler's whereas in our study, the mean age was 45.9 years. Very rarely does GOC presents itself in a paediatric patient. The paper also reports a case of an 11-year-old child whose histopathogy came out to be a case of a GOC. PMID:26587384

  17. Quantitative bacterial transcriptomics with RNA-seq

    PubMed Central

    Creecy, James P.; Conway, Tyrrell

    2014-01-01

    RNA sequencing has emerged as the premier approach to study bacterial transcriptomes. While the earliest published studies analyzed the data qualitatively, the data are readily digitized and lend themselves to quantitative analysis. High-resolution RNA sequence (RNA-seq) data allows transcriptional features (promoters, terminators, operons, etc.) to be pinpointed on any bacterial transcriptome. Once the transcriptome is mapped, the activity of transcriptional features can be quantified. Here we highlight how quantitative transcriptome analysis can reveal biological insights and briefly discuss some of the challenges to be faced by the field of bacterial transcriptomics in the near future. PMID:25483350

  18. A WD40 Repeat Protein from Medicago truncatula Is Necessary for Tissue-Specific Anthocyanin and Proanthocyanidin Biosynthesis But Not for Trichome Development1[W][OA

    PubMed Central

    Pang, Yongzhen; Wenger, Jonathan P.; Saathoff, Katie; Peel, Gregory J.; Wen, Jiangqi; Huhman, David; Allen, Stacy N.; Tang, Yuhong; Cheng, Xiaofei; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S.; Sumner, Lloyd W.; Marks, M. David; Dixon, Richard A.

    2009-01-01

    WD40 repeat proteins regulate biosynthesis of anthocyanins, proanthocyanidins (PAs), and mucilage in the seed and the development of trichomes and root hairs. We have cloned and characterized a WD40 repeat protein gene from Medicago truncatula (MtWD40-1) via a retrotransposon-tagging approach. Deficiency of MtWD40-1 expression blocks accumulation of mucilage and a range of phenolic compounds, including PAs, epicatechin, other flavonoids, and benzoic acids, in the seed, reduces epicatechin levels without corresponding effects on other flavonoids in flowers, reduces isoflavone levels in roots, but does not impair trichome or root hair development. MtWD40-1 is expressed constitutively, with highest expression in the seed coat, where its transcript profile temporally parallels those of PA biosynthetic genes. Transcript profile analysis revealed that many genes of flavonoid biosynthesis were down-regulated in a tissue-specific manner in M. truncatula lines harboring retrotransposon insertions in the MtWD40-1 gene. MtWD40-1 complemented the anthocyanin, PA, and trichome phenotypes of the Arabidopsis (Arabidopsis thaliana) transparent testa glabrous1 mutant. We discuss the function of MtWD40-1 in natural product formation in M. truncatula and the potential use of the gene for engineering PAs in the forage legume alfalfa (Medicago sativa). PMID:19710231

  19. A WD40 repeat protein from Medicago truncatula is necessary for tissue-specific anthocyanin and proanthocyanidin biosynthesis but not for trichome development.

    PubMed

    Pang, Yongzhen; Wenger, Jonathan P; Saathoff, Katie; Peel, Gregory J; Wen, Jiangqi; Huhman, David; Allen, Stacy N; Tang, Yuhong; Cheng, Xiaofei; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S; Sumner, Lloyd W; Marks, M David; Dixon, Richard A

    2009-11-01

    WD40 repeat proteins regulate biosynthesis of anthocyanins, proanthocyanidins (PAs), and mucilage in the seed and the development of trichomes and root hairs. We have cloned and characterized a WD40 repeat protein gene from Medicago truncatula (MtWD40-1) via a retrotransposon-tagging approach. Deficiency of MtWD40-1 expression blocks accumulation of mucilage and a range of phenolic compounds, including PAs, epicatechin, other flavonoids, and benzoic acids, in the seed, reduces epicatechin levels without corresponding effects on other flavonoids in flowers, reduces isoflavone levels in roots, but does not impair trichome or root hair development. MtWD40-1 is expressed constitutively, with highest expression in the seed coat, where its transcript profile temporally parallels those of PA biosynthetic genes. Transcript profile analysis revealed that many genes of flavonoid biosynthesis were down-regulated in a tissue-specific manner in M. truncatula lines harboring retrotransposon insertions in the MtWD40-1 gene. MtWD40-1 complemented the anthocyanin, PA, and trichome phenotypes of the Arabidopsis (Arabidopsis thaliana) transparent testa glabrous1 mutant. We discuss the function of MtWD40-1 in natural product formation in M. truncatula and the potential use of the gene for engineering PAs in the forage legume alfalfa (Medicago sativa). PMID:19710231

  20. Induced resistance in groundnut by jasmonic acid and salicylic acid through alteration of trichome density and oviposition by Helicoverpa armigera (Lepidoptera: Noctuidae)

    PubMed Central

    War, Abdul Rashid; Hussain, Barkat; Sharma, Hari C.

    2013-01-01

    Jasmonic acid (JA) and salicylic acid (SA) are important phytohormones involved in plant resistance against insect herbivory and pathogen infection. Application of JA and SA induces several defensive traits in plants. Here we investigated the effect of JA and SA on trichome density in five groundnut genotypes [ICGV 86699, ICGV 86031, ICG 2271, ICG 1697 (resistant) and JL 24 (susceptible)]. The effect of JA- and SA-induced resistance on the oviposition behaviour of Helicoverpa armigera on different groundnut genotypes was also studied. Pre-treatment with JA increased numbers of trichomes in the insect-resistant genotypes, ICGV 86699, ICGV 86031, ICG 2271, and ICG 1697. The induction was greater at 10 days after treatment. Jasmonic acid- and SA-treated plants showed a substantial effect on the oviposition behaviour of H. armigera. Jasmonic acid application and herbivory reduced the number of eggs laid by H. armigera in all the groundnut genotypes tested. However, a greater reduction was recorded on plants pre-treated with JA. More egg laying was recorded in JL 24 in all the treatments as compared to the insect-resistant genotypes. These results suggested that pre-treatment with JA increased trichome density in groundnut plants, which conferred antixenosis for oviposition by H. armigera.

  1. ‘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

  2. Transcriptomics and disease vector control

    PubMed Central

    2010-01-01

    Next-generation sequencing can be used to compare transcriptomes under different conditions. A study in BMC Genomics applies this approach to investigating the effects of exposure to a range of xenobiotics on changes in gene expression in the larvae of Aedes aegypti, the mosquito vector of dengue fever. See research article http://www.biomedcentral.com/1471-2164/11/216 PMID:20525113

  3. 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

  4. 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

  5. Glandular neoplasms of the urachus: a report of 55 cases emphasizing mucinous cystic tumors with proposed classification.

    PubMed

    Amin, Mahul B; Smith, Steven C; Eble, John N; Rao, Priya; Choi, William W L; Tamboli, Pheroze; Young, Robert H

    2014-08-01

    Published experience remains limited for glandular neoplasms of the urachus, especially mucinous cystic tumors. We reviewed 55 glandular urachal neoplasms to evaluate their clinical features and histopathologic spectrum and to devise a classification system for the mucinous cystic forms. Within the 55 cases studied, we observed 2 groups with differing clinical, gross, and histopathologic features. The first group, invasive, noncystic adenocarcinomas (n=24), had clinicopathologic features in accord with the known spectrum of urachal adenocarcinoma (mean age 50 y, female:male ratio 1.7, with recurrence or death from disease in 9/16 cases over a 45 mo mean follow-up). The second group, mucinous cystic tumors (n=31), morphologically resembled mucinous cystic tumors of the ovary and appeared classifiable by the same approach (mean age 47 y, female:male ratio 1.4) and included mucinous cystadenoma (n=4), mucinous cystic tumor of low malignant potential (n=22, including 2 cases with intraepithelial carcinoma), and mucinous cystadenocarcinoma with microscopic (n=4) or frank invasion (n=1). Follow-up information was available for 13 patients with mucinous cystic tumors (mean 41 mo); we observed no local recurrence or distant metastasis. This experience suggests that there is a distinct group of glandular, cystic tumors of the urachus that is classifiable in a manner similar to ovarian neoplasms and that has a favorable prognosis after complete excision. As with cystic neoplasms of other organs, rigorous sampling is recommended to identify potentially small foci of carcinoma that could be missed by inadequate sampling. Accordingly, classification based on methods other than complete surgical excision may be hazardous. PMID:25025366

  6. Effect of heat shock on the chilling sensitivity of trichomes and petioles of African violet (Saintpaulia ionantha).

    PubMed

    Saltveit, Mikal E.; Hepler, Peter K.

    2004-05-01

    Chilling at 6 degrees C caused an immediate cessation of protoplasmic streaming in trichomes from African violets (Saintpaulia ionantha), and a slower aggregation of chloroplasts in the cells. Streaming slowly recovered upon warming to 20 degrees C, reaching fairly stable rates after 4, 15, 25 and 35 min for tissue chilled for 2 min and for 2, 14 and 24 h, respectively. The rate of ion leakage from excised petioles into an isotonic 0.2 M mannitol solution increased after 12 h of chilling and reached a maximum after 3 days of chilling. A heat shock at 45 degrees C for 6 min reduced chilling-induced rates of ion leakage from excised 1-cm petiole segments by over 50%, namely to levels near that from non-chilled control tissue. Heat-shock treatments themselves had no effect on the rate of ion leakage from non-chilled petiole segments. Protoplasmic streaming was stopped by 1 min of heat shock at 45 degrees C, but slowly recovered to normal levels after about 30 min Chloroplasts aggregation was prevented by a 1 or 2 min 45 degrees C heat-shock treatment administered 1.5 h before chilling, but heat-shock treatments up to 6 min only slightly delayed the reduction in protoplasmic streaming caused by chilling. Tradescantia virginiana did not exhibit symptoms associated with chilling injury in sensitive species (i.e. cessation of protoplasmic streaming in stamen hairs and increased ion leakage from leaf tissue). PMID:15086815

  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. PMID:22095147

  8. Serum placental-type alkaline phosphatase activity in women with squamous and glandular malignancies of the reproductive tract.

    PubMed Central

    Ind, T E; Iles, R K; Carter, P G; Lowe, D G; Shepherd, J H; Hudson, C N; Chard, T

    1994-01-01

    AIM--To investigate serum placental-type alkaline phosphatase (PLAP-type) activities in women with squamous and glandular malignancies of the reproductive tract using an immunoradiometric assay. METHODS--PLAP-type immunoreactivity was measured in 180 women with non-ovarian malignancies of the reproductive tract and the values were compared with those from 334 controls. The cases comprised 18 vulval, nine vaginal, 103 cervical, 46 endometrial, and five fallopian tube cancers. RESULTS--Serum PLAP-type activities were no different from controls in patients with squamous cell tumours. Women with adenocarcinoma of the cervix, endometrium, and fallopian tube had increased values: women with endometrial cancer had a median value nearly four times greater than that of controls. There was no direct correlation between PLAP-type activities and stage of disease in patients with endometrial cancer, but values reverted to normal after treatment. CONCLUSIONS--Serum PLAP-type measurements are of no value in the management of patients with squamous cell tumours of the female reproductive tract. Raised activities can, however, be found in glandular tumours, in particular endometrial cancer where serum PLAP-type measurements may be of value in predicting remission. PMID:7829680

  9. Integration of co-localized glandular morphometry and protein biomarker expression in immunofluorescent images for prostate cancer prognosis

    NASA Astrophysics Data System (ADS)

    Scott, Richard; Khan, Faisal M.; Zeineh, Jack; Donovan, Michael; Fernandez, Gerardo

    2015-03-01

    Immunofluorescent (IF) image analysis of tissue pathology has proven to be extremely valuable and robust in developing prognostic assessments of disease, particularly in prostate cancer. There have been significant advances in the literature in quantitative biomarker expression as well as characterization of glandular architectures in discrete gland rings. However, while biomarker and glandular morphometric features have been combined as separate predictors in multivariate models, there is a lack of integrative features for biomarkers co-localized within specific morphological sub-types; for example the evaluation of androgen receptor (AR) expression within Gleason 3 glands only. In this work we propose a novel framework employing multiple techniques to generate integrated metrics of morphology and biomarker expression. We demonstrate the utility of the approaches in predicting clinical disease progression in images from 326 prostate biopsies and 373 prostatectomies. Our proposed integrative approaches yield significant improvements over existing IF image feature metrics. This work presents some of the first algorithms for generating innovative characteristics in tissue diagnostics that integrate co-localized morphometry and protein biomarker expression.

  10. Transcriptomics of the human endometrium.

    PubMed

    Díaz-Gimeno, Patricia; Ruíz-Alonso, Maria; Blesa, David; Simón, Carlos

    2014-01-01

    During the mid-secretory phase, the endometrium acquires the receptive phenotype, which corresponds to the only period throughout the endometrial cycle in which embryo implantation is viable. Endometrial receptivity is a crucial process and even more important in Assisted Reproductive Technologies (ART) where embryo-endometrial synchronization is coordinated through embryo transfer timing. Over the last decade, transcriptomic analyses performed on the human endometrium have shown that specific genomic signatures can be used to successfully phenotype different phases of the menstrual cycle including the receptive stage, independently of the histological appereance of the endometrial tissue. In this paper, we review current evidence demonstrating that endometrial transcriptomics objectively identifies the implantation window in a personalized manner, opening the field for the diagnosis of the endometrial factor in ART and moving to stratified medicine at this level, using microarray technology and soon high-throughput next generation sequencing coupled with functional and systems genomics approach. PMID:25023678

  11. 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

  12. Computer vision for image-based transcriptomics.

    PubMed

    Stoeger, Thomas; Battich, Nico; Herrmann, Markus D; Yakimovich, Yauhen; Pelkmans, Lucas

    2015-09-01

    Single-cell transcriptomics has recently emerged as one of the most promising tools for understanding the diversity of the transcriptome among single cells. Image-based transcriptomics is unique compared to other methods as it does not require conversion of RNA to cDNA prior to signal amplification and transcript quantification. Thus, its efficiency in transcript detection is unmatched by other methods. In addition, image-based transcriptomics allows the study of the spatial organization of the transcriptome in single cells at single-molecule, and, when combined with superresolution microscopy, nanometer resolution. However, in order to unlock the full power of image-based transcriptomics, robust computer vision of single molecules and cells is required. Here, we shortly discuss the setup of the experimental pipeline for image-based transcriptomics, and then describe in detail the algorithms that we developed to extract, at high-throughput, robust multivariate feature sets of transcript molecule abundance, localization and patterning in tens of thousands of single cells across the transcriptome. These computer vision algorithms and pipelines can be downloaded from: https://github.com/pelkmanslab/ImageBasedTranscriptomics. PMID:26014038

  13. Tricks to translating TB transcriptomics.

    PubMed

    Deffur, Armin; Wilkinson, Robert J; Coussens, Anna K

    2015-05-01

    Transcriptomics and other high-throughput methods are increasingly applied to questions relating to tuberculosis (TB) pathogenesis. Whole blood transcriptomics has repeatedly been applied to define correlates of TB risk and has produced new insight into the late stage of disease pathogenesis. In a novel approach, authors of a recently published study in Science Translational Medicine applied complex data analysis of existing TB transcriptomic datasets, and in vitro models, in an attempt to identify correlates of protection in TB, which are crucially required for the development of novel TB diagnostics and therapeutics to halt this global epidemic. Utilizing latent TB infection (LTBI) as a surrogate of protection, they identified IL-32 as a mediator of interferon gamma (IFNγ)-vitamin D dependent antimicrobial immunity and a marker of LTBI. Here, we provide a review of all TB whole-blood transcriptomic studies to date in the context of identifying correlates of protection, discuss potential pitfalls of combining complex analyses originating from such studies, the importance of detailed metadata to interpret differential patient classification algorithms, the effect of differing circulating cell populations between patient groups on the interpretation of resulting biomarkers and we decipher weighted gene co-expression network analysis (WGCNA), a recently developed systems biology tool which holds promise of identifying novel pathway interactions in disease pathogenesis. In conclusion, we propose the development of an integrated OMICS platform and open access to detailed metadata, in order for the TB research community to leverage the vast array of OMICS data being generated with the aim of unraveling the holy grail of TB research: correlates of protection. PMID:26046091

  14. 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

  15. The Immunophilin-Interacting Protein AtFIP37 from Arabidopsis Is Essential for Plant Development and Is Involved in Trichome Endoreduplication1

    PubMed Central

    Vespa, Laurent; Vachon, Gilles; Berger, Frédéric; Perazza, Daniel; Faure, Jean-Denis; Herzog, Michel

    2004-01-01

    The FKBP12 (FK506-binding protein 12 kD) immunophilin interacts with several protein partners in mammals and is a physiological regulator of the cell cycle. In Arabidopsis, only one specific partner of AtFKBP12, namely AtFIP37 (FKBP12 interacting protein 37 kD), has been identified but its function in plant development is not known. We present here the functional analysis of AtFIP37 in Arabidopsis. Knockout mutants of AtFIP37 show an embryo-lethal phenotype that is caused by a strong delay in endosperm development and embryo arrest. AtFIP37 promoter::β-glucuronidase reporter gene constructs show that the gene is expressed during embryogenesis and throughout plant development, in undifferentiating cells such as meristem or embryonic cells as well as highly differentiating cells such as trichomes. A translational fusion with the enhanced yellow fluorescent protein indicates that AtFIP37 is a nuclear protein localized in multiple subnuclear foci that show a speckled distribution pattern. Overexpression of AtFIP37 in transgenic lines induces the formation of large trichome cells with up to six branches. These large trichomes have a DNA content up to 256C, implying that these cells have undergone extra rounds of endoreduplication. Altogether, these data show that AtFIP37 is critical for life in Arabidopsis and implies a role for AtFIP37 in the regulation of the cell cycle as shown for FKBP12 and TOR (target of rapamycin) in mammals. PMID:15047892

  16. 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. PMID:26071533

  17. 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. PMID:26348995

  18. Using Transcriptomics to Understand the Wheat Genome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Wheat (Triticum aestivum L.) is one of the most important food crops in the world, and transcriptomics studies of this crop promise to reveal the expression dynamics of genes that control many agriculturally important traits. In this review of wheat transcriptomics research, the current status of tr...

  19. 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

  20. Transcriptome sequencing goals, assembly, and assessment.

    PubMed

    Wheat, Christopher W; Vogel, Heiko

    2011-01-01

    Transcriptome sequencing provides quick, direct access to the mRNA. With this information, one can design primers for PCR of thousands of different genes, SNP markers, probes for microarrays and qPCR, or just use the sequence data itself in comparative studies. Transcriptome sequencing, while getting cheaper, is still an expensive endeavor, with an examination of data quality and its assembly infrequently performed in depth. Here, we outline many of the important issues we think need consideration when starting a transcriptome sequencing project. We also walk the reader through a detailed analysis of an example transcriptome dataset, highlighting the importance of both within-dataset analysis and comparative inferences. Our hope is that with greater attention focused upon assessing assembly performance, advances in transcriptome assembly will increase as prices continue to drop and new technologies, such as Illumina sequencing, start to be used. PMID:22065435

  1. Digital breast tomosynthesis and digital mammography: A comparison of figures of merit for various average glandular doses

    NASA Astrophysics Data System (ADS)

    Kim, Ye-seul; Park, Hye-Suk; Park, SuJin; Kim, Hee-Joung; Choi, Jae-Gu; Choi, Young-Wook; Park, Jun-Ho; Lee, Jae-Jun

    2013-05-01

    Previous studies on the application of tomosynthesis to breast imaging have demonstrated the potential of digital breast tomosynthesis (DBT). DBT can improve the specificity of digital mammography (DM) through improved marginal visibility of lesions and early breast cancer detection for women with dense breasts. To investigate possible improvements in the accuracy of lesion detection with DBT systems as compared to DM, we conducted a quantitative evaluation by using simulated lesions embedded in a breast phantom. A prototype DBT and dedicated DM system were used in this study. For the DBT system, the average glandular dose (AGD) was calculated using a formalism that was a simple extension of mammography dosimetry. The DBT and the DM images were acquired with average glandular doses (AGDs) ranging from 1 to 4 mGy. To analyze the results objectively, we calculated metrics for in-plane lesion visibility in the form of the contrast-to-noise ratio for the in-focus plane from the DBT reconstruction image and from the craniocaudal (CC) image from the DM system. The imaging performance of DBT was quantitatively compared with that of DM in terms of the figure of merit. Although the DM showed better results in terms of the contrast-to-noise ratio (CNR) of the mass due to the reduced overlapping of tissue and lesion, an increase in breast thickness of over 3 cm increased the CNR of the mass with the DBT system. For microcalcification detection, the DBT system showed significantly higher CNR than the DM system and gave better predictions of the microcalcification size. We compared the performances of the DM and the DBT systems for various AGDs and breast thicknesses. In conclusion, the results indicate that the DBT systems can play an important role in the detection of masses or microcalcifications without severe compression.

  2. 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. PMID:25695723

  3. Cell proliferation, DNA repair, and p53 function are not required for programmed death of prostatic glandular cells induced by androgen ablation.

    PubMed Central

    Berges, R R; Furuya, Y; Remington, L; English, H F; Jacks, T; Isaacs, J T

    1993-01-01

    Androgen ablation induces programmed death of androgen-dependent prostatic glandular cells, resulting in fragmentation of their genomic DNA and the cells themselves into apoptotic bodies. Twenty percent of prostatic glandular cells undergo programmed death per day between day 2 and 5 after castration. During this same period, < 1% of prostatic glandular cells enter the S phase of the cell cycle, documenting that > 95% of these die in G0. During the programmed death of these G0 glandular cells, a futile DNA repair process is induced secondary to the DNA fragmentation. This futile DNA repair is not required, however, since inhibition of this process by > 90% with an appropriately timed hydroxy-urea dosing regimen had no effect upon the extent of the programmed death of these cells after castration. Likewise, p53 gene expression is not required since the same degree of cell death occurred in prostates and seminal vesicles after castration of wild-type and p53-deficient mice. PMID:8415631

  4. Transcriptomic changes in brain development

    PubMed Central

    Dillman, Allissa A.; Cookson, Mark R.

    2015-01-01

    The transcriptome changes hugely during development of the brain. Whole genes, alternate exons and single base pair changes related to RNA editing all show differences between embryonic and mature brain. Collectively, these changes control proteomic diversity as the brain develops. Additionally, there are many changes in non-coding RNAs (miRNA and lncRNA) that interact with mRNA to influence the overall transcriptional landscape. Here we will discuss what is known about such changes in brain development, particularly focussing on high throughput approaches and how those can be used to infer mechanisms by which gene expression is controlled in the brain as it matures. PMID:25172477

  5. 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. PMID:26291785

  6. Increased secretion of glandular-kallikrein in the bronchial washings induced by intravenous injection of leukotriene C4 in guinea-pigs.

    PubMed Central

    Jin, H. Y.; Katori, M.; Majima, M.; Sunahara, N.

    1992-01-01

    1. Intravenous administration of leukotriene C4 (LTC4) and LTD4 (1-10 nmol kg-1) caused a dose-dependent increase in secretion of glandular-kallikrein in the bronchial washings of guinea-pigs, as measured by cleavage of a synthetic substrate and the formation of kinin. LTC4 was more potent than LTD4 and pilocarpine was much less potent than peptide leukotrienes on a molecular basis. 2. The increases in levels of glandular-kallikrein in the bronchial washings that were induced by LTC4 (3 nmol kg-1, i.v.) were almost completely inhibited by pretreatment with an antagonist of leukotrienes (ONO-1078), with an antagonist of thromboxane (S-1452), with an inhibitor of thromboxane synthetase (OKY-046), with indomethacin, with atropine or with scopolamine. These results indicate that the LTC4-induced increase in levels of glandular-kallikrein may have been mediated by the formation of thromboxane and the release of acetylcholine. 3. The increases in levels of glandular-kallikrein in the bronchial washings induced by STA2 (20 pmol kg-1, i.v.), a stable analogue of thromboxane A2, were completely blocked by pretreatment with atropine, whereas increases induced by pilocarpine (41 mumol kg-1, i.v.) were not blocked by pretreatment with indomethacin, although such increases were inhibited by atropine. This result indicates that secretion of kallikrein stimulated by LTC4 may have been mediated by the successive formation of thromboxane A2 and release of acetylcholine. 4. Intravenous administration of bradykinin (3-30 nmol kg-1) caused a dose-dependent increase in levels of glandular-kallikrein in the bronchial washings. This increase was completely inhibited by pretreatment with atropine, with indomethacin or with an antagonist of thromboxane.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1628150

  7. The Olfactory Transcriptomes of Mice

    PubMed Central

    Ibarra-Soria, Ximena; Levitin, Maria O.; Saraiva, Luis R.; Logan, Darren W.

    2014-01-01

    The olfactory (OR) and vomeronasal receptor (VR) repertoires are collectively encoded by 1700 genes and pseudogenes in the mouse genome. Most OR and VR genes were identified by comparative genomic techniques and therefore, in many of those cases, only their protein coding sequences are defined. Some also lack experimental support, due in part to the similarity between them and their monogenic, cell-specific expression in olfactory tissues. Here we use deep RNA sequencing, expression microarray and quantitative RT-PCR in both the vomeronasal organ and whole olfactory mucosa to quantify their full transcriptomes in multiple male and female mice. We find evidence of expression for all VR, and almost all OR genes that are annotated as functional in the reference genome, and use the data to generate over 1100 new, multi-exonic, significantly extended receptor gene annotations. We find that OR and VR genes are neither equally nor randomly expressed, but have reproducible distributions of abundance in both tissues. The olfactory transcriptomes are only minimally different between males and females, suggesting altered gene expression at the periphery is unlikely to underpin the striking sexual dimorphism in olfactory-mediated behavior. Finally, we present evidence that hundreds of novel, putatively protein-coding genes are expressed in these highly specialized olfactory tissues, and carry out a proof-of-principle validation. Taken together, these data provide a comprehensive, quantitative catalog of the genes that mediate olfactory perception and pheromone-evoked behavior at the periphery. PMID:25187969

  8. The Frankia alni symbiotic transcriptome.

    PubMed

    Alloisio, Nicole; Queiroux, Clothilde; Fournier, Pascale; Pujic, Petar; Normand, Philippe; Vallenet, David; Médigue, Claudine; Yamaura, Masatoshi; Kakoi, Kentaro; Kucho, Ken-ichi

    2010-05-01

    The actinobacteria Frankia spp. are able to induce the formation of nodules on the roots of a large spectrum of actinorhizal plants, where they convert dinitrogen to ammonia in exchange for plant photosynthates. In the present study, transcriptional analyses were performed on nitrogen-replete free-living Frankia alni cells and on Alnus glutinosa nodule bacteria, using whole-genome microarrays. Distribution of nodule-induced genes on the genome was found to be mostly over regions with high synteny between three Frankia spp. genomes, while nodule-repressed genes, which were mostly hypothetical and not conserved, were spread around the genome. Genes known to be related to nitrogen fixation were highly induced, nif (nitrogenase), hup2 (hydrogenase uptake), suf (sulfur-iron cluster), and shc (hopanoids synthesis). The expression of genes involved in ammonium assimilation and transport was strongly modified, suggesting that bacteria ammonium assimilation was limited. Genes involved in particular in transcriptional regulation, signaling processes, protein drug export, protein secretion, lipopolysaccharide, and peptidoglycan biosynthesis that may play a role in symbiosis were also identified. We also showed that this Frankia symbiotic transcriptome was highly similar among phylogenetically distant plant families Betulaceae and Myricaceae. Finally, comparison with rhizobia transcriptome suggested that F. alni is metabolically more active in symbiosis than rhizobia. PMID:20367468

  9. 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

  10. The olfactory transcriptomes of mice.

    PubMed

    Ibarra-Soria, Ximena; Levitin, Maria O; Saraiva, Luis R; Logan, Darren W

    2014-09-01

    The olfactory (OR) and vomeronasal receptor (VR) repertoires are collectively encoded by 1700 genes and pseudogenes in the mouse genome. Most OR and VR genes were identified by comparative genomic techniques and therefore, in many of those cases, only their protein coding sequences are defined. Some also lack experimental support, due in part to the similarity between them and their monogenic, cell-specific expression in olfactory tissues. Here we use deep RNA sequencing, expression microarray and quantitative RT-PCR in both the vomeronasal organ and whole olfactory mucosa to quantify their full transcriptomes in multiple male and female mice. We find evidence of expression for all VR, and almost all OR genes that are annotated as functional in the reference genome, and use the data to generate over 1100 new, multi-exonic, significantly extended receptor gene annotations. We find that OR and VR genes are neither equally nor randomly expressed, but have reproducible distributions of abundance in both tissues. The olfactory transcriptomes are only minimally different between males and females, suggesting altered gene expression at the periphery is unlikely to underpin the striking sexual dimorphism in olfactory-mediated behavior. Finally, we present evidence that hundreds of novel, putatively protein-coding genes are expressed in these highly specialized olfactory tissues, and carry out a proof-of-principle validation. Taken together, these data provide a comprehensive, quantitative catalog of the genes that mediate olfactory perception and pheromone-evoked behavior at the periphery. PMID:25187969

  11. Plant transcriptomes reveal hidden guests.

    PubMed

    Zhu, Jiao; Wang, Guirong; Pelosi, Paolo

    2016-06-01

    With the wide adoption of transcriptome sequencing an ever increasing amount of information is becoming available, together with spurious data originating from contamination. We show that sometimes errors and inaccuracy can turn beneficial, revealing insect and arthropod pests when analysing plant transcriptomes. We have found a large number of soluble olfactory proteins, odorant-binding proteins (OBPs) and chemosensory proteins (CSPs), in plant databases, likely due to contamination by guest insects. In fact, both classes of proteins are only expressed in insects, with few CSPs also present in other arthropods. In addition, we found many sequences of the Niemann-Pick (Npc2) family, proteins dedicated to cholesterol transport in vertebrates and hypothesised to be involved in chemical communication in insects, but absent in plants. In several cases we were able to trace down members of the three classes of proteins to the insect or arthopod species responsible for contamination. Our work suggests that genes found in plants and recognised as contaminants can be turned into useful information to investigate plant-insect relationships or to identify new sequences from insects species not yet investigated. PMID:27130825

  12. 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

  13. 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

  14. Altered gut transcriptome in spondyloarthropathy

    PubMed Central

    Laukens, D; Peeters, H; Cruyssen, B V; Boonefaes, T; Elewaut, D; De Keyser, F; Mielants, H; Cuvelier, C; Veys, E M; Knecht, K; Van Hummelen, P; Remaut, E; Steidler, L; De Vos, M; Rottiers, P

    2006-01-01

    Background Intestinal inflammation is a common feature of spondyloarthropathy (SpA) and Crohn's disease. Inflammation is manifested clinically in Crohn's disease and subclinically in SpA. However, a fraction of patients with SpA develops overt Crohn's disease. Aims To investigate whether subclinical gut lesions in patients with SpA are associated with transcriptome changes comparable to those seen in Crohn's disease and to examine global gene expression in non‐inflamed colon biopsy specimens and screen patients for differentially expressed genes. Methods Macroarray analysis was used as an initial genomewide screen for selecting a comprehensive set of genes relevant to Crohn's disease and SpA. This led to the identification of 2625 expressed sequence tags that are differentially expressed in the colon of patients with Crohn's disease or SpA. These clones, with appropriate controls (6779 in total), were used to construct a glass‐based microarray, which was then used to analyse colon biopsy specimens from 15 patients with SpA, 11 patients with Crohn's disease and 10 controls. Results 95 genes were identified as differentially expressed in patients with SpA having a history of subclinical chronic gut inflammation and also in patients with Crohn's disease. Principal component analysis of this filtered set of genes successfully distinguished colon biopsy specimens from the three groups studied. Patients with SpA having subclinical chronic gut inflammation cluster together and are more related to those with Crohn's disease. Conclusion The transcriptome in the intestine of patients with SpA differs from that of controls. Moreover, these gene changes are comparable to those seen in patients with Crohn's disease, confirming initial clinical observations. On the basis of these findings, new (genetic) markers for detection of early Crohn's disease in patients with SpA can be considered. PMID:16476712

  15. Modeling skewness in human transcriptomes.

    PubMed

    Casellas, Joaquim; Varona, Luis

    2012-01-01

    Gene expression data are influenced by multiple biological and technological factors leading to a wide range of dispersion scenarios, although skewed patterns are not commonly addressed in microarray analyses. In this study, the distribution pattern of several human transcriptomes has been studied on free-access microarray gene expression data. Our results showed that, even in previously normalized gene expression data, probe and differential expression within probe effects suffer from substantial departures from the commonly assumed symmetric gaussian distribution. We developed a flexible mixed model for non-competitive microarray data analysis that accounted for asymmetric and heavy-tailed (Student's t distribution) dispersion processes. Random effects for gene expression data were modeled under asymmetric Student's t distributions where the asymmetry parameter (λ) took values from perfect symmetry (λ = 0) to right- (λ>0) or left-side (λ>0) over-expression patterns. This approach was applied to four free-access human data sets and revealed clearly better model performance when comparing with standard approaches accounting for traditional symmetric gaussian distribution patterns. Our analyses on human gene expression data revealed a substantial degree of right-hand asymmetry for probe effects, whereas differential gene expression addressed both symmetric and left-hand asymmetric patterns. Although these results cannot be extrapolated to all microarray experiments, they highlighted the incidence of skew dispersion patterns in human transcriptome; moreover, we provided a new analytical approach to appropriately address this biological phenomenon. The source code of the program accommodating these analytical developments and additional information about practical aspects on running the program are freely available by request to the corresponding author of this article. PMID:22701729

  16. Comparative transcriptomics of early dipteran development

    PubMed Central

    2013-01-01

    Background Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). Results We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. Conclusions We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies). PMID:23432914

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

    PubMed Central

    Johnson, Abby L.; Zinser, Glendon M.

    2014-01-01

    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. PMID:25139050

  18. Tissue expression of glandular kallikrein and its response to 17 beta-estradiol in the acclimatized carp.

    PubMed

    Haussmann, Denise; Vidal, Rene; Figueroa, Jaime

    2006-06-01

    Cyprinus carpio skeletal muscle kallikrein was isolated to apparent homogeneity, and a polyclonal antiserum against the purified protein was generated. Glandular kallikrein expression and tissue distribution were assessed using both Western blots and immunohistochemistry. A 39-kDa protein was detected in skeletal muscle, the gill, kidney, and pituitary gland, where an additional 72-kDa immunoreactive band was observed. Immunohistochemistry revealed immunoreactive kallikrein in the intermuscle tissue, epithelial gill cells, apical portion of distal and proximal tubular cells in the kidney, mucus and epithelial cells of the skin, intestinal tube, and prolactin-producing cells of the pituitary gland. In addition, the effect of 17beta-estradiol on kallikrein expression was analyzed in three different tissues of winter- and summer-acclimatized male carps. A 2.5-fold (p<0.05) increase in kallikrein immunoreactivity due to estrogen treatment was observed in winter-acclimatized carp muscle, but not in summer-acclimatized fish. In contrast, the gill responded differently, since a 2-fold (p<0.05) increase was found only in summer-acclimatized carps. Kallikrein immunoreactivity in the kidney increased both in summer- (2.5 fold) and in winter-acclimatized carps (1.5 fold). The signals obtained demonstrate the existence of tissue-specific variable responses to estrogen treatment in vivo, between winter and summer-acclimatized carp. PMID:16849838

  19. 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

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

    PubMed

    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

  2. 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. PMID:14521517

  3. The transcriptome of cerebral ischemia

    PubMed Central

    VanGilder, Reyna L.; Huber, Jason D.; Rosen, Charles L.; Barr, Taura L.

    2015-01-01

    The molecular causality and response to stroke is complex. Yet, much of the literature examining the molecular response to stroke has focused on targeted pathways that have been well-characterized. Consequently, our understanding of stroke pathophysiology has made little progress by way of clinical therapeutics since tissue plasminogen activator was approved for treatment nearly a decade ago. The lack of clinical translation is in part due to neuron-focused studies, preclinical models of cerebral ischemia and the paradoxical nature of neuro-inflammation. With the evolution of the Stroke Therapy Academic Industry Roundtable criteria streamlining research efforts and broad availability of genomic technologies, the ability to decipher the molecular fingerprint of ischemic stroke is on the horizon. This review highlights preclinical microarray findings of the ischemic brain, discusses the transcriptome of cerebral preconditioning and emphasizes the importance of further characterizing the role of the neurovascular unit and peripheral white blood cells in mediating stroke damage and repair within the penumbra. PMID:22381515

  4. [Transcriptome analysis of Dunaliella viridis].

    PubMed

    Zhu, Shuaiqi; Gong, Yifu; Hang, Yuqing; Liu, Hao; Wang, Heyu

    2015-08-01

    In order to understand the gene information, function, haloduric pathway (glycerolipid metabolism) and related key genes for Dunaliella viridis, we used Illumina HiSeqTM 2000 high-throughput sequencing technology to sequence its transcriptome. Trinity soft was used to assemble the data to form transcripts. Based on the Clusters of Orthologous Groups (COG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG ) databases, we carried out functional annotation and classification, pathway annotation, and the opening reading fragment (ORF) sequence prediction of transcripts. The key genes in the glycerolipid metabolism were analyzed. The results suggested that 81,593 transcripts were found, and 77,117 ORF sequences were predicted, accounting for 94.50% of all transcripts. COG classification results showed that 16,569 transcripts were assigned to 24 categories. GO classification annotated 76,436 transcripts. The number of transcripts for biologcial processes was 30,678, accounting for 40.14% of all transcripts. KEGG pathway analysis showed that 26,428 transcripts were annotated to 317 pathways, and 131 pathways were related to metabolism, accounting for 41.32% of all annotated pathways. Only one transcript was annotated as coding the key enzyme dihydroxyacetone kinase involved in the glycerolipid pathway. This enzyme could be related to glycerol biosynthesis under salt stress. This study further improved the gene information and laid the foundation of metabolic pathway research for Dunaliella viridis. PMID:26266786

  5. 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

  6. Comparative transcriptome analysis of four prymnesiophyte algae.

    PubMed

    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

  7. 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

  8. 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. PMID:25458215

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

    PubMed Central

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

    2012-01-01

    Δ9-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. PMID:22802619

  11. 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

  12. Virtual clinical trials using inserted pathology in clinical images: investigation of assumptions for local glandularity and noise

    NASA Astrophysics Data System (ADS)

    Rashidnasab, Alaleh; Elangovan, Premkumar; Mackenzie, Alistair; Dance, David R.; Young, Kenneth C.; Bosmans, Hilde; Wells, Kevin

    2015-03-01

    Virtual clinical trials have been proposed as a viable alternative to clinical trials for testing and comparing the performance of breast imaging systems. One of the main simulation methodologies used in virtual trials employs clinical images of patients in which simulated models of cancer are inserted using a physics-based template multiplication technique. The purpose of this work is to investigate two assumptions commonly considered in this simulation approach: Firstly, given the absence of useful depth information in a clinical situation, an average measure of the local breast glandularity is commonly used as an estimate of the breast composition at the insertion site; secondly, it is also assumed that any change in the relative noise in the image at the insertion site, after insertion of a mass, is negligible. In order to test the validity of these assumptions, spheres representing idealised masses and anthropomorphic computational breast phantoms with perfect prior knowledge of local tissue composition and distribution were used. Results from several region of interest (ROI) insertions demonstrated a lack of variation obtained in contrast with insertion depth using the template multiplication insertion method as compared to the true depth-wise variation contrast values obtained from voxel replacement in a heterogeneous phantom. It was also found that the amount of noise is underestimated by insertion of spherical masses using template multiplication method by 8% - 29% compared to voxel replacement for the test conditions. This resulted in up to 12% variation in contrast-to-noise-ratio (CNR) values between template multiplication and voxel replacement methods.

  13. Human papillomavirus prevalence and type-distribution in cervical glandular neoplasias: Results from a European multinational epidemiological study.

    PubMed

    Holl, Katsiaryna; Nowakowski, Andrzej M; Powell, Ned; McCluggage, W Glenn; Pirog, Edyta C; Collas De Souza, Sabrina; Tjalma, Wiebren A; Rosenlund, Mats; Fiander, Alison; Castro Sánchez, Maria; Damaskou, Vasileia; Joura, Elmar A; Kirschner, Benny; Koiss, Robert; O'Leary, John; Quint, Wim; Reich, Olaf; Torné, Aureli; Wells, Michael; Rob, Lukas; Kolomiets, Larisa; Molijn, Anco; Savicheva, Alevtina; Shipitsyna, Elena; Rosillon, Dominique; Jenkins, David

    2015-12-15

    Cervical glandular neoplasias (CGN) present a challenge for cervical cancer prevention due to their complex histopathology and difficulties in detecting preinvasive stages with current screening practices. Reports of human papillomavirus (HPV) prevalence and type-distribution in CGN vary, providing uncertain evidence to support prophylactic vaccination and HPV screening. This study [108288/108290] assessed HPV prevalence and type-distribution in women diagnosed with cervical adenocarcinoma in situ (AIS, N = 49), adenosquamous carcinoma (ASC, N = 104), and various adenocarcinoma subtypes (ADC, N = 461) from 17 European countries, using centralised pathology review and sensitive HPV testing. The highest HPV-positivity rates were observed in AIS (93.9%), ASC (85.6%), and usual-type ADC (90.4%), with much lower rates in rarer ADC subtypes (clear-cell: 27.6%; serous: 30.4%; endometrioid: 12.9%; gastric-type: 0%). The most common HPV types were restricted to HPV16/18/45, accounting for 98.3% of all HPV-positive ADC. There were variations in HPV prevalence and ADC type-distribution by country. Age at diagnosis differed by ADC subtype, with usual-type diagnosed in younger women (median: 43 years) compared to rarer subtypes (medians between 57 and 66 years). Moreover, HPV-positive ADC cases were younger than HPV-negative ADC. The six years difference in median age for women with AIS compared to those with usual-type ADC suggests that cytological screening for AIS may be suboptimal. Since the great majority of CGN are HPV16/18/45-positive, the incorporation of prophylactic vaccination and HPV testing in cervical cancer screening are important prevention strategies. Our results suggest that special attention should be given to certain rarer ADC subtypes as most appear to be unrelated to HPV. PMID:26096203

  14. Classification of spatial textures in benign and cancerous glandular tissues by stereology and stochastic geometry using artificial neural networks.

    PubMed

    Mattfeldt, T; Gottfried, H; Schmidt, V; Kestler, H A

    2000-05-01

    Stereology and stochastic geometry can be used as auxiliary tools for diagnostic purposes in tumour pathology. Whether first-order parameters or stochastic-geometric functions are more important for the classification of the texture of biological tissues is not known. In the present study, volume and surface area per unit reference volume, the pair correlation function and the centred quadratic contact density function of epithelium were estimated in three case series of benign and malignant lesions of glandular tissues. The information provided by the latter functions was summarized by the total absolute areas between the estimated curves and their horizontal reference lines. These areas are considered as indicators of deviation of the tissue texture from a completely uncorrelated volume process and from the Boolean model with convex grains, respectively. We used both areas and the first-order parameters for the classification of cases using artificial neural networks (ANNs). Learning vector quantization and multilayer feedforward networks with backpropagation were applied as neural paradigms. Applications included distinction between mastopathy and mammary cancer (40 cases), between benign prostatic hyperplasia and prostatic cancer (70 cases) and between chronic pancreatitis and pancreatic cancer (60 cases). The same data sets were also classified with linear discriminant analysis. The stereological estimates in combination with ANNs or discriminant analysis provided high accuracy in the classification of individual cases. The question of which category of estimator is the most informative cannot be answered globally, but must be explored empirically for each specific data set. Using learning vector quantization, better results could often be obtained than by multilayer feedforward networks with backpropagation. PMID:10810010

  15. 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

  16. 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

  17. 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

  18. 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. PMID:25740926

  19. BUILDING ROBUST TRANSCRIPTOMES WITH MASTER SPLICING FACTORS

    PubMed Central

    Jangi, Mohini; Sharp, Phillip A.

    2014-01-01

    Coherent splicing networks arise from many discrete splicing decisions regulated in unison. Here, we examine the properties of robust, context-specific splicing networks. We propose that a subset of key splicing regulators, or “master splicing factors,” respond to environmental cues to establish and maintain tissue transcriptomes during development. PMID:25417102

  20. 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...

  1. 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...

  2. Transcriptome Encyclopedia of Early Human Development.

    PubMed

    Sahakyan, Anna; Plath, Kathrin

    2016-05-01

    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. PMID:27153491

  3. Dissecting FASD Through the Global Transcriptome

    PubMed Central

    Zhou, Feng C.

    2015-01-01

    The recent study by Stepien, Lussier, Pavlidis, Kobor, and Weinberg demonstrates how prenatal alcohol exposure alters genomic expression far into the adulthood, and also provides a new view about how transcriptions might respond differently upon new environmental challenge. This study also provides a more comprehensive view by filling a gap of the global transcriptome analyses of FASD. PMID:25702586

  4. 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...

  5. The testicular germ cell tumour transcriptome.

    PubMed

    Alagaratnam, S; Lind, G E; Kraggerud, S M; Lothe, R A; Skotheim, R I

    2011-08-01

    Testicular germ cell tumours (TGCTs) are characterized by young age of onset and a complex pattern of histological subtypes. Transcriptomic studies have tried to uncover the gene expression patterns underlying this. Here, we present a systematic review of transcriptome studies of TGCTs of adolescents and young adults and identify genes common across the various studies, both for TGCTs in general as well as the histological subtypes, hence elucidating both transcriptional changes associated with malignant transformation and differentiation patterns. A meta-analysis of this type adds power and significance to the genes thus found, where most studies have included only a limited number of samples. Both known (KRAS, MYCN and TPD52) and novel (CCT6A, IGFBP3 and SALL2) cancer genes are implicated in TGC tumorigenesis. Gene expression patterns characteristic to embryonic stem cells are also found deregulated in TGC tumorigenesis. This is reflected in how pluripotent embryonal carcinoma cells commonly differentiate into a variety of embryonic and extra-embryonic histological types, each with unique transcriptomes. The embryonal carcinomas in particular are found to overexpress pluripotency genes, while gene signatures for seminomas, teratomas and yolk sac tumours were also identified. This underlines the distinctive transcriptomic programme across histological subtypes, especially striking given that the TGCT genome is largely similar across the same subtypes. PMID:21651573

  6. Transcriptome Analysis of the Capra hircus Ovary

    PubMed Central

    Zhao, Zhong Quan; Wang, Li Juan; Sun, Xiao Wei; Zhang, Jiao Jiao; Zhao, Yong Ju; Na, Ri Su; Zhang, Jia Hua

    2015-01-01

    Background Capra hircus is an important economic livestock animal, and therefore, it is necessary to discover transcriptome information about their reproductive performance. In this study, we performed de novo transcriptome sequencing to produce the first transcriptome dataset for the goat ovary using high-throughput sequencing technologies. The result will contribute to research on goat reproductive performance. Method and Results RNA-seq analysis generated more than 38.8 million clean paired end (PE) reads, which were assembled into 80,069 unigenes (mean size = 619 bp). Based on sequence similarity searches, 64,824 (60.6%) genes were identified, among which 29,444 and 11,271 unigenes were assigned to Gene Ontology (GO) categories and Clusters of Orthologous Groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) showed that 27,766 (63.4%) unigenes were mapped to 258 KEGG pathways. Furthermore, we investigated the transcriptome differences of goat ovaries at two different ages using a tag-based digital gene expression system. We obtained a sequencing depth of over 5.6 million and 5.8 million tags for the two ages and identified a large number of genes associated with reproductive hormones, ovulatory cycle and follicle. Moreover, many antisense transcripts and novel transcripts were found; clusters with similar differential expression patterns, enriched GO terms and metabolic pathways were revealed for the first time with regard to the differentially expressed genes. Conclusions The transcriptome provides invaluable new data for a functional genomic resource and future biological research in Capra hircus, and it is essential for the in-depth study of candidate genes in breeding programs. PMID:25822507

  7. The plasticity of the grapevine berry transcriptome

    PubMed Central

    2013-01-01

    Background Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in grapevine by comparing the berry transcriptome in a single clone of the vegetatively-propagated common grapevine species Vitis vinifera cultivar Corvina through 3 consecutive growth years cultivated in 11 different vineyards in the Verona area of Italy. Results Most of the berry transcriptome clustered by year of growth rather than common environmental conditions or viticulture practices, and transcripts related to secondary metabolism showed high sensitivity towards different climates, as confirmed also by metabolomic data obtained from the same samples. When analyzed in 11 vineyards during 1 growth year, the environmentally-sensitive berry transcriptome comprised 5% of protein-coding genes and 18% of the transcripts modulated during berry development. Plastic genes were particularly enriched in ontology categories such as transcription factors, translation, transport, and secondary metabolism. Specific plastic transcripts were associated with groups of vineyards sharing common viticulture practices or environmental conditions, and plastic transcriptome reprogramming was more intense in the year characterized by extreme weather conditions. We also identified a set of genes that lacked plasticity, showing either constitutive expression or similar modulation in all berries. Conclusions Our data reveal candidate genes potentially responsible for the phenotypic plasticity of grapevine and provide the first step towards the characterization of grapevine transcriptome plasticity under different agricultural systems. PMID:23759170

  8. RNA-Seq-Mediated Transcriptome Analysis of a Fiberless Mutant Cotton and Its Possible Origin Based on SNP Markers

    PubMed Central

    Ma, Qifeng; Wu, Man; Pei, Wenfeng; Wang, Xiaoyan; Zhai, Honghong; Wang, Wenkui; Li, Xingli; Zhang, Jinfa; Yu, Jiwen; Yu, Shuxun

    2016-01-01

    As the longest known single-celled trichomes, cotton (Gossypium L.) fibers constitute a classic model system to investigate cell initiation and elongation. In this study, we used a high-throughput transcriptome sequencing technology to identify fiber-initiation-related single nucleotide polymorphism (SNP) markers and differentially expressed genes (DEGs) between the wild-type (WT) Upland cotton (G. hirsutum) Xuzhou 142 and its natural fuzzless-lintless mutant Xuzhou 142 fl. Approximately 700 million high-quality cDNA reads representing over 58 Gb of sequences were obtained, resulting in the identification of 28,610 SNPs—of which 17,479 were novel—from 13,960 expressed genes. Of these SNPs, 50% of SNPs in fl were identical to those of G. barbadense, which suggests the likely origin of the fl mutant from an interspecific hybridization between Xuzhou 142 and an unknown G. barbadense genotype. Of all detected SNPs, 15,555, 12,750, and 305 were classified as non-synonymous, synonymous, and pre-terminated ones, respectively. Moreover, 1,352 insertion/deletion polymorphisms (InDels) were also detected. A total of 865 DEGs were identified between the WT and fl in ovules at −3 and 0 days post-anthesis, with 302 candidate SNPs selected from these DEGs for validation by a high-resolution melting analysis and Sanger sequencing in seven cotton genotypes. The number of genotypic pairwise polymorphisms varied from 43 to 302, indicating that the identified SNPs are reliable. These SNPs should serve as good resources for breeding and genetic studies in cotton. PMID:26990639

  9. RNA-Seq-Mediated Transcriptome Analysis of a Fiberless Mutant Cotton and Its Possible Origin Based on SNP Markers.

    PubMed

    Ma, Qifeng; Wu, Man; Pei, Wenfeng; Wang, Xiaoyan; Zhai, Honghong; Wang, Wenkui; Li, Xingli; Zhang, Jinfa; Yu, Jiwen; Yu, Shuxun

    2016-01-01

    As the longest known single-celled trichomes, cotton (Gossypium L.) fibers constitute a classic model system to investigate cell initiation and elongation. In this study, we used a high-throughput transcriptome sequencing technology to identify fiber-initiation-related single nucleotide polymorphism (SNP) markers and differentially expressed genes (DEGs) between the wild-type (WT) Upland cotton (G. hirsutum) Xuzhou 142 and its natural fuzzless-lintless mutant Xuzhou 142 fl. Approximately 700 million high-quality cDNA reads representing over 58 Gb of sequences were obtained, resulting in the identification of 28,610 SNPs--of which 17,479 were novel--from 13,960 expressed genes. Of these SNPs, 50% of SNPs in fl were identical to those of G. barbadense, which suggests the likely origin of the fl mutant from an interspecific hybridization between Xuzhou 142 and an unknown G. barbadense genotype. Of all detected SNPs, 15,555, 12,750, and 305 were classified as non-synonymous, synonymous, and pre-terminated ones, respectively. Moreover, 1,352 insertion/deletion polymorphisms (InDels) were also detected. A total of 865 DEGs were identified between the WT and fl in ovules at -3 and 0 days post-anthesis, with 302 candidate SNPs selected from these DEGs for validation by a high-resolution melting analysis and Sanger sequencing in seven cotton genotypes. The number of genotypic pairwise polymorphisms varied from 43 to 302, indicating that the identified SNPs are reliable. These SNPs should serve as good resources for breeding and genetic studies in cotton. PMID:26990639

  10. TRICHOME BIREFRINGENCE-LIKE27 affects aluminum sensitivity by modulating the O-acetylation of xyloglucan and aluminum-binding capacity in Arabidopsis.

    PubMed

    Zhu, Xiao Fang; Sun, Ying; Zhang, Bao Cai; Mansoori, Nasim; Wan, Jiang Xue; Liu, Yu; Wang, Zhi Wei; Shi, Yuan Zhi; Zhou, Yi Hua; Zheng, Shao Jian

    2014-09-01

    Xyloglucan (XyG) has been reported to contribute to the aluminum (Al)-binding capacity of the cell wall in Arabidopsis (Arabidopsis thaliana). However, the influence of O-acetylation of XyG, accomplished by the putative O-acetyltransferase TRICHOME BIREFRINGENCE-LIKE27 (TBL27 [AXY4]), on its Al-binding capacity is not known. In this study, we found that the two corresponding TBL27 mutants, axy4-1 and axy4-3, were more Al sensitive than wild-type Columbia-0 plants. TBL27 was expressed in roots as well as in leaves, stems, flowers, and siliques. Upon Al treatment, even within 30 min, TBL27 transcript accumulation was strongly down-regulated. The mutants axy4-1 and axy4-3 accumulated significantly more Al in the root and wall, which could not be correlated with pectin content or pectin methylesterase activity, as no difference in the mutants was observed compared with the wild type when exposed to Al stress. The increased Al accumulation in the wall of the mutants was found to be in the hemicellulose fraction. While the total sugar content of the hemicellulose fraction did not change, the O-acetylation level of XyG was reduced by Al treatment. Taken together, we conclude that modulation of the O-acetylation level of XyG influences the Al sensitivity in Arabidopsis by affecting the Al-binding capacity in the hemicellulose. PMID:25006026

  11. 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

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

    PubMed

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

    2015-06-01

    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

  13. Comparison of N-linked Glycoproteins in Human Whole Saliva, Parotid, Submandibular, and Sublingual Glandular Secretions Identified using Hydrazide Chemistry and Mass Spectrometry.

    PubMed

    Ramachandran, Prasanna; Boontheung, Pinmanee; Pang, Eric; Yan, Weihong; Wong, David T; Loo, Joseph A

    2008-12-01

    INTRODUCTION: Saliva is a body fluid that holds promise for use as a diagnostic fluid for detecting diseases. Salivary proteins are known to be heavily glycosylated and are known to play functional roles in the oral cavity. We identified N-linked glycoproteins in human whole saliva, as well as the N-glycoproteins in parotid, submandibular, and sublingual glandular fluids. MATERIALS AND METHODS: We employed hydrazide chemistry to affinity enrich for N-linked glycoproteins and glycopeptides. PNGase F releases the N-peptides/proteins from the agarose-hydrazide resin, and liquid chromatography-tandem mass spectrometry was used to identify the salivary N-glycoproteins. RESULTS: A total of 156 formerly N-glycosylated peptides representing 77 unique N-glycoproteins were identified in salivary fluids. The total number of N-glycoproteins identified in the individual fluids was: 62, 34, 44, and 53 in whole saliva, parotid fluid, submandibular fluid, and sublingual fluid, respectively. The majority of the N-glycoproteins were annotated as extracellular proteins (40%), and several of the N-glycoproteins were annotated as membrane proteins (14%). A number of glycoproteins were differentially found in submandibular and sublingual glandular secretions. CONCLUSIONS: Mapping the N-glycoproteome of parotid, submandibular, and sublingual saliva is important for a thorough understanding of biological processes occurring in the oral cavity and to realize the role of saliva in the overall health of human individuals. Moreover, identifying glycoproteins in saliva may also be valuable for future disease biomarker studies. PMID:21960768

  14. p40 as a Basal Cell Marker in the Diagnosis of Prostate Glandular Proliferations: A Comparative Immunohistochemical Study with 34betaE12

    PubMed Central

    Brustmann, Hermann

    2015-01-01

    Immunohistochemistry is important for the accurate diagnosis of basal cells in atypical glandular proliferations of the prostate. p40, an isoform of p63, may be an adjunct to a marker panel in this setting. Biopsies of 68 patients were analyzed by immunohistochemistry using antibodies to 34betaE12 and p40. Basal cell staining was classified as negative, partial (<60%), or diffuse (≥60%); irregular staining was defined as discordant staining patterns. In acinar proliferations (N = 41), partial staining for both markers was seen in 42%, and diffuse staining in 46% of reactive cases. An irregular reactivity was noted in one case only (2%). Finally, these lesions were signed out as benign. Acinar proliferations negative for both markers and limited amount of glands (≤4) were termed atypical small acinar proliferations (ASAP). Out of six PIN lesions two cases showed partial, three cases showed diffuse reactivity for both markers, and one case was stained irregular. All cases diagnosed as prostate carcinomas (N = 20) had no evidence of basal cell staining for neither of the markers. p40 expression is closely correlated to 34betaE12 with respect to demonstration of basal cells of prostate glands and may provide further information on the dignity of glandular proliferations of the prostate. PMID:25852959

  15. Analysis of Whole Transcriptome Sequencing Data: Workflow and Software

    PubMed Central

    Yang, In Seok

    2015-01-01

    RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification. PMID:26865842

  16. Applications of new sequencing technologies for transcriptome analysis.

    PubMed

    Morozova, Olena; Hirst, Martin; Marra, Marco A

    2009-01-01

    Transcriptome analysis has been a key area of biological inquiry for decades. Over the years, research in the field has progressed from candidate gene-based detection of RNAs using Northern blotting to high-throughput expression profiling driven by the advent of microarrays. Next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution. PMID:19715439

  17. Analysis of Whole Transcriptome Sequencing Data: Workflow and Software.

    PubMed

    Yang, In Seok; Kim, Sangwoo

    2015-12-01

    RNA is a polymeric molecule implicated in various biological processes, such as the coding, decoding, regulation, and expression of genes. Numerous studies have examined RNA features using whole transcriptome sequencing (RNA-seq) approaches. RNA-seq is a powerful technique for characterizing and quantifying the transcriptome and accelerates the development of bioinformatics software. In this review, we introduce routine RNA-seq workflow together with related software, focusing particularly on transcriptome reconstruction and expression quantification. PMID:26865842

  18. 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

  19. Whole Body Melanoma Transcriptome Response in Medaka

    PubMed Central

    Schartl, Manfred; Shen, Yingjia; Maurus, Katja; Walter, Ron; Tomlinson, Chad; Wilson, Richard K.; Postlethwait, John; Warren, Wesley C.

    2015-01-01

    The incidence of malignant melanoma continues to increase each year with poor prognosis for survival in many relapse cases. To reverse this trend, whole body response measures are needed to discover collaborative paths to primary and secondary malignancy. Several species of fish provide excellent melanoma models because fish and human melanocytes both appear in the epidermis, and fish and human pigment cell tumors share conserved gene expression signatures. For the first time, we have examined the whole body transcriptome response to invasive melanoma as a prelude to using transcriptome profiling to screen for drugs in a medaka (Oryzias latipes) model. We generated RNA-seq data from whole body RNA isolates for controls and melanoma fish. After testing for differential expression, 396 genes had significantly different expression (adjusted p-value <0.02) in the whole body transcriptome between melanoma and control fish; 379 of these genes were matched to human orthologs with 233 having annotated human gene symbols and 14 matched genes that contain putative deleterious variants in human melanoma at varying levels of recurrence. A detailed canonical pathway evaluation for significant enrichment showed the top scoring pathway to be antigen presentation but also included the expected melanocyte development and pigmentation signaling pathway. Results revealed a profound down-regulation of genes involved in the immune response, especially the innate immune system. We hypothesize that the developing melanoma actively suppresses the immune system responses of the body in reacting to the invasive malignancy, and that this mal-adaptive response contributes to disease progression, a result that suggests our whole-body transcriptomic approach merits further use. In these findings, we also observed novel genes not yet identified in human melanoma expression studies and uncovered known and new candidate drug targets for further testing in this malignant melanoma medaka model. PMID

  20. Whole Body Melanoma Transcriptome Response in Medaka.

    PubMed

    Schartl, Manfred; Shen, Yingjia; Maurus, Katja; Walter, Ron; Tomlinson, Chad; Wilson, Richard K; Postlethwait, John; Warren, Wesley C

    2015-01-01

    The incidence of malignant melanoma continues to increase each year with poor prognosis for survival in many relapse cases. To reverse this trend, whole body response measures are needed to discover collaborative paths to primary and secondary malignancy. Several species of fish provide excellent melanoma models because fish and human melanocytes both appear in the epidermis, and fish and human pigment cell tumors share conserved gene expression signatures. For the first time, we have examined the whole body transcriptome response to invasive melanoma as a prelude to using transcriptome profiling to screen for drugs in a medaka (Oryzias latipes) model. We generated RNA-seq data from whole body RNA isolates for controls and melanoma fish. After testing for differential expression, 396 genes had significantly different expression (adjusted p-value <0.02) in the whole body transcriptome between melanoma and control fish; 379 of these genes were matched to human orthologs with 233 having annotated human gene symbols and 14 matched genes that contain putative deleterious variants in human melanoma at varying levels of recurrence. A detailed canonical pathway evaluation for significant enrichment showed the top scoring pathway to be antigen presentation but also included the expected melanocyte development and pigmentation signaling pathway. Results revealed a profound down-regulation of genes involved in the immune response, especially the innate immune system. We hypothesize that the developing melanoma actively suppresses the immune system responses of the body in reacting to the invasive malignancy, and that this mal-adaptive response contributes to disease progression, a result that suggests our whole-body transcriptomic approach merits further use. In these findings, we also observed novel genes not yet identified in human melanoma expression studies and uncovered known and new candidate drug targets for further testing in this malignant melanoma medaka model. PMID

  1. 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

  2. Global meta-analysis of transcriptomics studies.

    PubMed

    Caldas, José; Vinga, Susana

    2014-01-01

    Transcriptomics meta-analysis aims at re-using existing data to derive novel biological hypotheses, and is motivated by the public availability of a large number of independent studies. Current methods are based on breaking down studies into multiple comparisons between phenotypes (e.g. disease vs. healthy), based on the studies' experimental designs, followed by computing the overlap between the resulting differential expression signatures. While useful, in this methodology each study yields multiple independent phenotype comparisons, and connections are established not between studies, but rather between subsets of the studies corresponding to phenotype comparisons. We propose a rank-based statistical meta-analysis framework that establishes global connections between transcriptomics studies without breaking down studies into sets of phenotype comparisons. By using a rank product method, our framework extracts global features from each study, corresponding to genes that are consistently among the most expressed or differentially expressed genes in that study. Those features are then statistically modelled via a term-frequency inverse-document frequency (TF-IDF) model, which is then used for connecting studies. Our framework is fast and parameter-free; when applied to large collections of Homo sapiens and Streptococcus pneumoniae transcriptomics studies, it performs better than similarity-based approaches in retrieving related studies, using a Medical Subject Headings gold standard. Finally, we highlight via case studies how the framework can be used to derive novel biological hypotheses regarding related studies and the genes that drive those connections. Our proposed statistical framework shows that it is possible to perform a meta-analysis of transcriptomics studies with arbitrary experimental designs by deriving global expression features rather than decomposing studies into multiple phenotype comparisons. PMID:24586684

  3. Strategies for transcriptome analysis in nonmodel plants.

    PubMed

    Ward, Judson A; Ponnala, Lalit; Weber, Courtney A

    2012-02-01

    Even with recent reductions in sequencing costs, most plants lack the genomic resources required for successful short-read transcriptome analyses as performed routinely in model species. Several approaches for the analysis of short-read transcriptome data are reviewed for nonmodel species for which the genome of a close relative is used as the reference genome. Two approaches using a data set from Phytophthora-challenged Rubus idaeus (red raspberry) are compared. Over 70000000 86-nt Illumina reads derived from R. idaeus roots were aligned to the Fragaria vesca genome using publicly available informatics tools (Bowtie/TopHat and Cufflinks). Alignment identified 16956 putatively expressed genes. De novo assembly was performed with the same data set and a publicly available transcriptome assembler (Trinity). A BLAST search with a maximum e-value threshold of 1.0 × 10(-3) revealed that over 36000 transcripts had matches to plants and over 500 to Phytophthora. Gene expression estimates from alignment to F. vesca and de novo assembly were compared for raspberry (Pearson's correlation = 0.730). Together, alignment to the genome of a close relative and de novo assembly constitute a powerful method of transcriptome analysis in nonmodel organisms. Alignment to the genome of a close relative provides a framework for differential expression testing if alignments are made to the predefined gene-space of a close relative and de novo assembly provides a more robust method of identifying unique sequences and sequences from other organisms in a system. These methods are considered experimental in nonmodel systems, but can be used to generate resources and specific testable hypotheses. PMID:22301897

  4. The Avian Transcriptome Response to Malaria Infection

    PubMed Central

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

    2015-01-01

    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. PMID:25636457

  5. Comparative analysis of the transcriptomes of Populus

    SciTech Connect

    Tuskan, Gerald A; Davis, John M

    2008-01-01

    Sequencing of the Populus trichocarpa genome creates an opportunity to describe the transcriptome of a woody perennial species and establish an atlas of gene expression. A comparison with the transcriptomes of other species can also define genes that are conserved or diverging in plant species. Here, the transcriptome in vegetative organs of the P. trichocarpa reference genotype Nisqually-1 was characterized. A comparison with Arabidopsis thaliana orthologs was used to distinguish gene functional categories that may be evolving differently in a woody perennial and an annual herbaceous species. A core set of genes expressed in common among vegetative organs was detected, as well as organ-specific genes. Statistical tests identified chromatin domains, where adjacent genes were expressed more frequently than expected by chance. Extensive divergence was detected in the expression patterns of A. thaliana and P. trichocarpa orthologs, but transcription of a small number of genes appeared to have remained conserved in the two species. Despite separation of lineages for over 100 million yr, these results suggest that selection has limited transcriptional divergence of genes associated with some essential functions in A. thaliana and P. trichocarpa. However, extensive remodeling of transcriptional networks indicates that expression regulation may be a key determinant of plant diversity.

  6. The meiotic transcriptome architecture of plants

    PubMed Central

    Dukowic-Schulze, Stefanie; Chen, Changbin

    2014-01-01

    Although a number of genes that play key roles during the meiotic process have been characterized in great detail, the whole process of meiosis is still not completely unraveled. To gain insight into the bigger picture, large-scale approaches like RNA-seq and microarray can help to elucidate the transcriptome landscape during plant meiosis, discover co-regulated genes, enriched processes, and highly expressed known and unknown genes which might be important for meiosis. These high-throughput studies are gaining more and more popularity, but their beginnings in plant systems reach back as far as the 1960's. Frequently, whole anthers or post-meiotic pollen were investigated, while less data is available on isolated cells during meiosis, and only few studies addressed the transcriptome of female meiosis. For this review, we compiled meiotic transcriptome studies covering different plant species, and summarized and compared their key findings. Besides pointing to consistent as well as unique discoveries, we finally draw conclusions what can be learned from these studies so far and what should be addressed next. PMID:24926296

  7. Myosins XI-K, XI-1, and XI-2 are required for development of pavement cells, trichomes, and stigmatic papillae in Arabidopsis

    PubMed Central

    2012-01-01

    Background The positioning and dynamics of vesicles and organelles, and thus the growth of plant cells, is mediated by the acto-myosin system. In Arabidopsis there are 13 class XI myosins which mediate vesicle and organelle transport in different cell types. So far the involvement of five class XI myosins in cell expansion during the shoot and root development has been shown, three of which, XI-1, XI-2, and XI-K, are essential for organelle transport. Results Simultaneous depletion of Arabidopsis class XI myosins XI-K, XI-1, and XI-2 in double and triple mutant plants affected the growth of several types of epidermal cells. The size and shape of trichomes, leaf pavement cells and the elongation of the stigmatic papillae of double and triple mutant plants were affected to different extent. Reduced cell size led to significant size reduction of shoot organs in the case of triple mutant, affecting bolt formation, flowering time and fertility. Phenotype analysis revealed that the reduced fertility of triple mutant plants was caused by delayed or insufficient development of pistils. Conclusions We conclude that the class XI myosins XI-K, XI-1 and XI-2 have partially redundant roles in the growth of shoot epidermis. Myosin XI-K plays more important role whereas myosins XI-1 and XI-2 have minor roles in the determination of size and shape of epidermal cells, because the absence of these two myosins is compensated by XI-K. Co-operation between myosins XI-K and XI-2 appears to play an important role in these processes. PMID:22672737

  8. Biosynthesis of platelet-activating factor in glandular gastric mucosa. Evidence for the involvement of the 'de novo' pathway and modulation by fatty acids.

    PubMed

    Fernandez-Gallardo, S; Gijon, M A; Garcia, M C; Cano, E; Sanchez Crespo, M

    1988-09-15

    The biosynthesis of platelet-activating factor (PAF), a phospholipid autocoid with potent ulcerogenic properties that is produced in secretory exocrine glands by physiological secretagogues, was assessed in microsomal preparations of glandular gastric mucosa. For this purpose, 1-O-alkyl-2-lyso-sn-glycero-3-phosphocholine (lyso-PAF):acetyl-CoA acetyltransferase (EC 2.3.1.67); the enzymes of the 'de novo' pathway: 1-O-alkyl-2-lyso-sn-glycero-3-phosphate (alkyl-lyso-GP):acetyl-CoA acetyltransferase and 1-O-alkyl-2-acetyl-sn-glycerol (alkylacetyl-G):CDP-choline cholinephosphotransferase (EC 2.7.8.16); and some enzymes involved in the catabolism of PAF and lyso-PAF were assayed. Only the enzymes of the 'de novo' pathway and small amounts of PAF acetylhydrolase, phospholipase A2 and a lysophospholipase D acting on either lipids could be detected in the gastric preparations, whereas lyso-PAF:acetyl-CoA acetyltransferase activity was undetectable. The specific activity of alkyl-lyso-GP:acetyl-CoA acetyltransferase in the gastric mucosa was about one-tenth of that found in spleen microsomes and its apparent Km for acetyl-CoA was 454 microM compared with 277 microM in spleen microsomes. Glandular mucosa homogenates contained preformed PAF at a concentration of 2.7 +/- 0.7 ng equivalents of PAF (hexadecyl)/mg of protein. When gastric microsomes were incubated with micromolar concentrations of fatty acids (arachidonic, palmitic and oleic) prior to the assay of dithiothreitol (DTT)-insensitive cholinephosphotransferase, a dose-dependent reduction in the formation of PAF was observed, arachidonic acid being the most potent inhibitor, followed by linoleic acid (only tested on spleen microsomes) and oleic acid. By contrast, 1,2-diolein and phosphatidylcholine (dipalmitoyl) showed no or little effect. These results indicate that glandular gastric mucosa can produce PAF through the 'de novo' pathway, and that fatty acids, especially unsaturated, can reduce that synthesis by

  9. A four-day oral treatment regimen for simultaneous micronucleus analyses in the glandular stomach, colon, and bone marrow of rats.

    PubMed

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

    2013-12-12

    Our aim was to develop a multi-tissue micronucleus (MN) test method for the simultaneous analysis of rat glandular stomach, colon, and bone marrow. We have evaluated the multi-tissue MN test method with a regimen in which rats were administered chemicals orally once per day for four days and the cells of each tissue were collected 24 h after the final dose. The following compounds were studied: N-nitroso-N-methylurea (MNU), 4-nitroquinoline-1-oxide (4NQO), N-methyl-N'-nitro-N-nitrosoguanidine (MNNG), N-methyl-N-nitrosourethane (NMUT), 1,2-dimethylhydrazine 2HCl (DMH), 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine HCl (PhIP), KBrO(3), amaranth (AM), and quercetin (QN). The gastrointestinal tract carcinogens increased the frequencies of micronucleated (MNed) cells in target tissue in a dose-dependent manner: MNU in gastric- and colonic-cells; 4NQO, MNNG, and NMUT in gastric cells; DMH and PhIP in colonic cells. In immature erythrocytes, MNU, 4NQO, DMH, and PhIP increased the frequency of MNed cells but MNNG and NMUT did not. The food additive KBrO(3), which is known to be a renal carcinogen, increased the frequencies of MNed cells in the glandular stomach and bone marrow. The food additive AM and the plant flavonoid QN, which are non-carcinogenic in most studies, did not cause increased MNed cells in any of the three tissues. Our results indicate that this multi-tissue MN test method is useful for the comprehensive evaluation of the genotoxicity of orally administered compounds. PMID:24140632

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

    PubMed Central

    2010-01-01

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

  11. Nemertean toxin genes revealed through transcriptome sequencing.

    PubMed

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

    2014-12-01

    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

  12. 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. PMID:27423230

  13. 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

  14. Transcriptome analysis of embryo maturation in maize

    PubMed Central

    2013-01-01

    Background Maize is one of the most important crops in the world. With the exponentially increasing population and the need for ever increased food and feed production, an increased yield of maize grain (as well as rice, wheat and other grains) will be critical. Maize grain development is understood from the perspective of morphology, hormone responses, and storage reserve accumulation. This includes various studies on gene expression during embryo development and maturation but a global study of gene expression of the embryo has not been possible until recently. Transcriptome analysis is a powerful new tool that can be used to understand the genetic basis of embryo maturation. Results We undertook a transcriptomic analysis of normal maturing embryos at 15, 21 and 27 days after pollination (DAP), of one elite maize germplasm line that was utilized in crosses to transgenic plants. More than 19,000 genes were analyzed by this method and the challenge was to select subsets of genes that are vitally important to embryo development and maturation for the initial analysis. We describe the changes in expression for genes relating to primary metabolic pathways, DNA synthesis, late embryogenesis proteins and embryo storage proteins, shown through transcriptome analysis and confirmed levels of transcription for some genes in the transcriptome using qRT-PCR. Conclusions Numerous genes involved in embryo maturation have been identified, many of which show changes in expression level during the progression from 15 to 27 DAP. An expected array of genes involved in primary metabolism was identified. Moreover, more than 30% of transcripts represented un-annotated genes, leaving many functions to be discovered. Of particular interest are the storage protein genes, globulin-1, globulin-2 and an unidentified cupin family gene. When expressing foreign proteins in maize, the globulin-1 promoter is most often used, but this cupin family gene has much higher expression and may be a

  15. RNAseq versus genome-predicted transcriptomes: a large population of novel transcripts identified in an Illumina-454 Hydra transcriptome

    PubMed Central

    2013-01-01

    Background Evolutionary studies benefit from deep sequencing technologies that generate genomic and transcriptomic sequences from a variety of organisms. Genome sequencing and RNAseq have complementary strengths. In this study, we present the assembly of the most complete Hydra transcriptome to date along with a comparative analysis of the specific features of RNAseq and genome-predicted transcriptomes currently available in the freshwater hydrozoan Hydra vulgaris. Results To produce an accurate and extensive Hydra transcriptome, we combined Illumina and 454 Titanium reads, giving the primacy to Illumina over 454 reads to correct homopolymer errors. This strategy yielded an RNAseq transcriptome that contains 48’909 unique sequences including splice variants, representing approximately 24’450 distinct genes. Comparative analysis to the available genome-predicted transcriptomes identified 10’597 novel Hydra transcripts that encode 529 evolutionarily-conserved proteins. The annotation of 170 human orthologs points to critical functions in protein biosynthesis, FGF and TOR signaling, vesicle transport, immunity, cell cycle regulation, cell death, mitochondrial metabolism, transcription and chromatin regulation. However, a majority of these novel transcripts encodes short ORFs, at least 767 of them corresponding to pseudogenes. This RNAseq transcriptome also lacks 11’270 predicted transcripts that correspond either to silent genes or to genes expressed below the detection level of this study. Conclusions We established a simple and powerful strategy to combine Illumina and 454 reads and we produced, with genome assistance, an extensive and accurate Hydra transcriptome. The comparative analysis of the RNAseq transcriptome with genome-predicted transcriptomes lead to the identification of large populations of novel as well as missing transcripts that might reflect Hydra-specific evolutionary events. PMID:23530871

  16. 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

  17. 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. PMID:23393031

  18. An American mink (Neovison vison) transcriptome.

    PubMed

    Christensen, Knud; Anistoroaei, Razvan

    2014-04-01

    HiSeq2000 Illumina pair-end sequenced transcript data originating from a pool of four different tissues of a wild-type American mink yielded approximately 90 Gb of raw data. Subsequently, unique contigs were assembled by a combined approach using velvet and phrap. Of these assembled contigs, about 136 000 match the dog genome and nearly 30 000 contigs match the human transcriptome at more than 17 000 unique gene locations. Gene annotation for these contigs was performed employing custom-made scripts run in combination with comparative sequence similarity search and alignment in the dog and human genome using blast algorithms. Transcripts representing five genes known to be associated with pigmentation were reliably aligned against large mink genomic contigs derived from BAC clones. Sequence comparison between transcript and genomic data revealed seven SNPs. In this study, we generated and annotated mink transcript sequences representing more than 16 000 known genes. This is the first comprehensive transcriptome for the American mink genome, which will facilitate further development in mink expression profiling studies and provide a good annotation basis in the perspectives of a whole genome sequencing project. The project was deposited at EMBL database with the accession number PRJEB1260. PMID:24444022

  19. 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

  20. The Human Blood Metabolome-Transcriptome Interface

    PubMed Central

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

    2015-01-01

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

  1. 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

  2. The floral transcriptome of Eucalyptus grandis.

    PubMed

    Vining, Kelly J; Romanel, Elisson; Jones, Rebecca C; Klocko, Amy; Alves-Ferreira, Marcio; Hefer, Charles A; Amarasinghe, Vindhya; Dharmawardhana, Palitha; Naithani, Sushma; Ranik, Martin; Wesley-Smith, James; Solomon, Luke; Jaiswal, Pankaj; Myburg, Alexander A; Strauss, Steven H

    2015-06-01

    As a step toward functional annotation of genes required for floral initiation and development within the Eucalyptus genome, we used short read sequencing to analyze transcriptomes of floral buds from early and late developmental stages, and compared these with transcriptomes of diverse vegetative tissues, including leaves, roots, and stems. A subset of 4807 genes (13% of protein-coding genes) were differentially expressed between floral buds of either stage and vegetative tissues. A similar proportion of genes were differentially expressed among all tissues. A total of 479 genes were differentially expressed between early and late stages of floral development. Gene function enrichment identified 158 gene ontology classes that were overrepresented in floral tissues, including 'pollen development' and 'aromatic compound biosynthetic process'. At least 40 floral-dominant genes lacked functional annotations and thus may be novel floral transcripts. We analyzed several genes and gene families in depth, including 49 putative biomarkers of floral development, the MADS-box transcription factors, 'S-domain'-receptor-like kinases, and selected gene family members with phosphatidylethanolamine-binding protein domains. Expanded MADS-box gene subfamilies in Eucalyptus grandis included SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), SEPALLATA (SEP) and SHORT VEGETATIVE PHASE (SVP) Arabidopsis thaliana homologs. These data provide a rich resource for functional and evolutionary analysis of genes controlling eucalypt floral development, and new tools for breeding and biotechnology. PMID:25353719

  3. Macrophage epoxygenase determines a profibrotic transcriptome signature.

    PubMed

    Behmoaras, Jacques; Diaz, Ana Garcia; Venda, Lara; Ko, Jeong-Hun; Srivastava, Prashant; Montoya, Alex; Faull, Peter; Webster, Zoe; Moyon, Ben; Pusey, Charles D; Abraham, David J; Petretto, Enrico; Cook, Terence H; Aitman, Timothy J

    2015-05-15

    Epoxygenases belong to the cytochrome P450 family. They generate epoxyeicosatrienoic acids, which are known to have anti-inflammatory effects, but little is known about their role in macrophage function. By high-throughput sequencing of RNA in primary macrophages derived from rodents and humans, we establish the relative expression of epoxygenases in these cells. Zinc-finger nuclease-mediated targeted gene deletion of the major rat macrophage epoxygenase Cyp2j4 (ortholog of human CYP2J2) resulted in reduced epoxyeicosatrienoic acid synthesis. Cyp2j4(-/-) macrophages have relatively increased peroxisome proliferator-activated receptor-γ levels and show a profibrotic transcriptome, displaying overexpression of a specific subset of genes (260 transcripts) primarily involved in extracellular matrix, with fibronectin being the most abundantly expressed transcript. Fibronectin expression is under the control of epoxygenase activity in human and rat primary macrophages. In keeping with the in vitro findings, Cyp2j4(-/-) rats show upregulation of type I collagen following unilateral ureter obstruction of the kidney, and quantitative proteomics analysis (liquid chromatography-tandem mass spectrometry) showed increased renal type I collagen and fibronectin protein abundance resulting from experimentally induced crescentic glomerulonephritis in these rats. Taken together, these results identify the rat epoxygenase Cyp2j4 as a determinant of a profibrotic macrophage transcriptome that could have implications in various inflammatory conditions, depending on macrophage function. PMID:25840911

  4. New Frontiers in Schistosoma Genomics and Transcriptomics

    PubMed Central

    Nahum, Laila A.; Mourão, Marina M.; Oliveira, Guilherme

    2012-01-01

    Schistosomes are digenean blood flukes of aves and mammals comprising 23 species. Some species are causative agents of human schistosomiasis, the second major neglected disease affecting over 230 million people worldwide. Modern technologies including the sequencing and characterization of nucleic acids and proteins have allowed large-scale analyses of parasites and hosts, opening new frontiers in biological research with potential biomedical and biotechnological applications. Nuclear genomes of the three most socioeconomically important species (S. haematobium, S. japonicum, and S. mansoni) have been sequenced and are under intense investigation. Mitochondrial genomes of six Schistosoma species have also been completely sequenced and analysed from an evolutionary perspective. Furthermore, DNA barcoding of mitochondrial sequences is used for biodiversity assessment of schistosomes. Despite the efforts in the characterization of Schistosoma genomes and transcriptomes, many questions regarding the biology and evolution of this important taxon remain unanswered. This paper aims to discuss some advances in the schistosome research with emphasis on genomics and transcriptomics. It also aims to discuss the main challenges of the current research and to point out some future directions in schistosome studies. PMID:23227308

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

    PubMed Central

    2011-01-01

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

  6. 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

  7. 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

  8. Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes

    PubMed Central

    Nam, Kyoungwoo; Jeong, Heesu; Nam, Jin-Wu

    2016-01-01

    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. PMID:26927182

  9. Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes.

    PubMed

    Nam, Kyoungwoo; Jeong, Heesu; Nam, Jin-Wu

    2016-01-01

    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. PMID:26927182

  10. Comparative transcriptomics across the prokaryotic tree of life.

    PubMed

    Cohen, Ofir; Doron, Shany; Wurtzel, Omri; Dar, Daniel; Edelheit, Sarit; Karunker, Iris; Mick, Eran; Sorek, Rotem

    2016-07-01

    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

  11. 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

  12. JAFFA: High sensitivity transcriptome-focused fusion gene detection.

    PubMed

    Davidson, Nadia M; Majewski, Ian J; Oshlack, Alicia

    2015-01-01

    Genomic instability is a hallmark of cancer and, as such, structural alterations and fusion genes are common events in the cancer landscape. RNA sequencing (RNA-Seq) is a powerful method for profiling cancers, but current methods for identifying fusion genes are optimised for short reads. JAFFA (https://github.com/Oshlack/JAFFA/wiki) is a sensitive fusion detection method that outperforms other methods with reads of 100 bp or greater. JAFFA compares a cancer transcriptome to the reference transcriptome, rather than the genome, where the cancer transcriptome is inferred using long reads directly or by de novo assembling short reads. PMID:26019724

  13. The Kidney Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling

    PubMed Central

    Habuka, Masato; Fagerberg, Linn; Hallström, Björn M.; Kampf, Caroline; Edlund, Karolina; Sivertsson, Åsa; Yamamoto, Tadashi; Pontén, Fredrik; Uhlén, Mathias; Odeberg, Jacob

    2014-01-01

    To understand renal functions and disease, it is important to define the molecular constituents of the various compartments of the kidney. Here, we used comparative transcriptomic analysis of all major organs and tissues in the human body, in combination with kidney tissue micro array based immunohistochemistry, to generate a comprehensive description of the kidney-specific transcriptome and proteome. A special emphasis was placed on the identification of genes and proteins that were elevated in specific kidney subcompartments. Our analysis identified close to 400 genes that had elevated expression in the kidney, as compared to the other analysed tissues, and these were further subdivided, depending on expression levels, into tissue enriched, group enriched or tissue enhanced. Immunohistochemistry allowed us to identify proteins with distinct localisation to the glomeruli (n = 11), proximal tubules (n = 120), distal tubules (n = 9) or collecting ducts (n = 8). Among the identified kidney elevated transcripts, we found several proteins not previously characterised or identified as elevated in kidney. This description of the kidney specific transcriptome and proteome provides a resource for basic and clinical research to facilitate studies to understand kidney biology and disease. PMID:25551756

  14. The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling.

    PubMed

    Habuka, Masato; Fagerberg, Linn; Hallström, Björn M; Kampf, Caroline; Edlund, Karolina; Sivertsson, Åsa; Yamamoto, Tadashi; Pontén, Fredrik; Uhlén, Mathias; Odeberg, Jacob

    2014-01-01

    To understand renal functions and disease, it is important to define the molecular constituents of the various compartments of the kidney. Here, we used comparative transcriptomic analysis of all major organs and tissues in the human body, in combination with kidney tissue micro array based immunohistochemistry, to generate a comprehensive description of the kidney-specific transcriptome and proteome. A special emphasis was placed on the identification of genes and proteins that were elevated in specific kidney subcompartments. Our analysis identified close to 400 genes that had elevated expression in the kidney, as compared to the other analysed tissues, and these were further subdivided, depending on expression levels, into tissue enriched, group enriched or tissue enhanced. Immunohistochemistry allowed us to identify proteins with distinct localisation to the glomeruli (n = 11), proximal tubules (n = 120), distal tubules (n = 9) or collecting ducts (n = 8). Among the identified kidney elevated transcripts, we found several proteins not previously characterised or identified as elevated in kidney. This description of the kidney specific transcriptome and proteome provides a resource for basic and clinical research to facilitate studies to understand kidney biology and disease. PMID:25551756

  15. Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR)

    PubMed Central

    Peng, Xinxia; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Nishida, Andrew; Pipes, Lenore; Bozinoski, Marjan; Thomas, Matthew J.; Kelly, Sara; Weiss, Jeffrey M.; Raveendran, Muthuswamy; Muzny, Donna; Gibbs, Richard A.; Rogers, Jeffrey; Schroth, Gary P.; Katze, Michael G.; Mason, Christopher E.

    2015-01-01

    The non-human primate reference transcriptome resource (NHPRTR, available online at http://nhprtr.org/) aims to generate comprehensive RNA-seq data from a wide variety of non-human primates (NHPs), from lemurs to hominids. In the 2012 Phase I of the NHPRTR project, 19 billion fragments or 3.8 terabases of transcriptome sequences were collected from pools of ∼20 tissues in 15 species and subspecies. Here we describe a major expansion of NHPRTR by adding 10.1 billion fragments of tissue-specific RNA-seq data. For this effort, we selected 11 of the original 15 NHP species and subspecies and constructed total RNA libraries for the same ∼15 tissues in each. The sequence quality is such that 88% of the reads align to human reference sequences, allowing us to compute the full list of expression abundance across all tissues for each species, using the reads mapped to human genes. This update also includes improved transcript annotations derived from RNA-seq data for rhesus and cynomolgus macaques, two of the most commonly used NHP models and additional RNA-seq data compiled from related projects. Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis. PMID:25392405

  16. Transcriptome Sequences Resolve Deep Relationships of the Grape Family

    PubMed Central

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

    2013-01-01

    Previous phylogenetic studies of the grape family (Vitaceae) yielded poorly resolved deep relationships, thus impeding our understanding of the evolution of the family. Next-generation sequencing now offers access to protein coding sequences very easily, quickly and cost-effectively. To improve upon earlier work, we extracted 417 orthologous single-copy nuclear genes from the transcriptomes of 15 species of the Vitaceae, covering its phylogenetic diversity. The resulting transcriptome phylogeny provides robust support for the deep relationships, showing the phylogenetic utility of transcriptome data for plants over a time scale at least since the mid-Cretaceous. The pros and cons of transcriptome data for phylogenetic inference in plants are also evaluated. PMID:24069307

  17. 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...

  18. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.

    PubMed

    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

    2016-02-01

    Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We constructed a cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis of single-cell RNA sequencing. We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. We also analyzed cell type-specific mRNA processing and characterized genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we found that some of our transcriptomic cell types displayed 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

  19. Plant transcriptomics and responses to environmental stress: an overview.

    PubMed

    Imadi, Sameen Ruqia; Kazi, Alvina Gul; Ahanger, Mohammad Abass; Gucel, Salih; Ahmad, Parvaiz

    2015-09-01

    Different stresses include nutrient deficiency, pathogen attack, exposure to toxic chemicals etc. Transcriptomic studies have been mainly applied to only a few plant species including the model plant, Arabidopsis thaliana. These studies have provided valuable insights into the genetic networks of plant stress responses. Transcriptomics applied to cash crops including barley, rice, sugarcane, wheat and maize have further helped in understanding physiological and molecular responses in terms of genome sequence, gene regulation, gene differentiation, posttranscriptional modifications and gene splicing. On the other hand, comparative transcriptomics has provided more information about plant's response to diverse stresses. Thus, transcriptomics, together with other biotechnological approaches helps in development of stress tolerance in crops against the climate change. PMID:26440096

  20. 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

  1. Transcriptomic characterization of fibrolamellar hepatocellular carcinoma.

    PubMed

    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

    2015-11-01

    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

  2. Transcriptomic analyses of Hand2 transgenic embryos.

    PubMed

    Funato, Noriko; Kokubo, Hiroki; Saga, Yumiko

    2016-09-01

    In this article, we further provide the data generated for the previously published research article "Specification of jaw identity by the Hand2 transcription factor." To better understand the downstream genes of the basic helix-loop-helix transcription factor Hand2, we generated double-transgenic mice (Hand2 (NC) ) by intercrossing CAG-floxed CAT-Hand2 mice with Wnt1-Cre mice for conditional activation of Hand2 expression in the neural crest. Altered expression of Hand2 induces transformation of the upper jaw to the lower jaw in Hand2 (NC) mutant mice. This data article provides Tables detailing the differentially expressed genes between wild-type and Hand2 (NC) mutant embryos. The raw array data of our transcriptomes as generated using Affymetrix microarrays are available on the NCBI Gene Expression Omnibus (GEO) browser (Reference number GSE75805). PMID:27408813

  3. The human transcriptome across tissues and individuals

    PubMed Central

    Melé, Marta; Ferreira, Pedro G.; Reverter, Ferran; DeLuca, David S.; Monlong, Jean; Sammeth, Michael; Young, Taylor R.; Goldmann, Jakob M; Pervouchine, Dmitri D.; Sullivan, Timothy J.; Johnson, Rory; Segrè, Ayellet V.; Djebali, Sarah; Niarchou, Anastasia; Wright, Fred A.; Lappalainen, Tuuli; Calvo, Miquel; Getz, Gad; Dermitzakis, Emmanouil T.; Ardlie, Kristin G.; Guigó, Roderic

    2015-01-01

    Transcriptional regulation and posttranscriptional processing underlie many cellular and organismal phenotypes. We used RNA sequence data generated by Genotype-Tissue Expression (GTEx) project to investigate the patterns of transcriptome variation across individuals and tissues. Tissues exhibit characteristic transcriptional signatures that show stability in postmortem samples. These signatures are dominated by a relatively small number of genes—which is most clearly seen in blood—though few are exclusive to a particular tissue and vary more across tissues than individuals. Genes exhibiting high interindividual expression variation include disease candidates associated with sex, ethnicity, and age. Primary transcription is the major driver of cellular specificity, with splicing playing mostly a complementary role; except for the brain, which exhibits a more divergent splicing program. Variation in splicing, despite its stochasticity, may play in contrast a comparatively greater role in defining individual phenotypes. PMID:25954002

  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. MOROKOSHI: Transcriptome Database in Sorghum bicolor

    PubMed Central

    Makita, Yuko; Shimada, Setsuko; Kawashima, Mika; Kondou-Kuriyama, Tomoko; Toyoda, Tetsuro; Matsui, Minami

    2015-01-01

    In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection facilitates the refinement of transcriptional annotation, and accurate transcription start sites help to unravel transcriptional regulation. We constructed a normalized FL-cDNA library from eight growth stages of aerial tissues in Sorghum bicolor and isolated 37,607 clones. These clones were Sanger sequenced from the 5′ and/or 3′ ends and in total 38,981 high-quality expressed sequence tags (ESTs) were obtained. About one-third of the transcripts of known genes were captured as FL-cDNA clone resources. In addition to these, we also annotated 272 novel genes, 323 antisense transcripts and 1,672 candidate isoforms. These clones are available from the RIKEN Bioresource Center. After obtaining accurate annotation of transcriptional units, we performed expression profile analysis. We carried out spikelet-, seed- and stem-specific RNA sequencing (RNA-Seq) analysis and confirmed the expression of 70.6% of the newly identified genes. We also downloaded 23 sorghum RNA-Seq samples that are publicly available and these are shown on a genome browser together with our original FL-cDNA and RNA-Seq data. Using our original and publicly available data, we made an expression profile of each gene and identified the top 20 genes with the most similar expression. In addition, we visualized their relationships in gene co-expression networks. Users can access and compare various transcriptome data from S, bicolor at http://sorghum.riken.jp. PMID:25505007

  6. Integrative analysis of the mouse embryonic transcriptome.

    PubMed

    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

  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. Peroxidase gene discovery from the horseradish transcriptome

    PubMed Central

    2014-01-01

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

  9. The hermit crab's nose—antennal transcriptomics

    PubMed Central

    Groh, Katrin C.; Vogel, Heiko; Stensmyr, Marcus C.; Grosse-Wilde, Ewald; Hansson, Bill S.

    2014-01-01

    In the course of evolution, crustaceans adapted to a large variety of habitats. Probably the most extreme habitat shift was the transition from water to land, which occurred independently in at least five crustacean lineages. This substantial change in life style required adaptations in sensory organs, as the medium conveying stimuli changed in both chemical and physical properties. One important sensory organ in crustaceans is the first pair of antennae, housing their sense of smell. Previous studies on the crustacean transition from water to land focused on morphological, behavioral, and physiological aspects but did not analyze gene expression. Our goal was to scrutinize the molecular makeup of the crustacean antennulae, comparing the terrestrial Coenobita clypeatus and the marine Pagurus bernhardus. We sequenced and analyzed the antennal transcriptomes of two hermit crab species. Comparison to previously published datasets of similar tissues revealed a comparable quality and GO annotation confirmed a highly similar set of expressed genes in both datasets. The chemosensory gene repertoire of both species displayed a similar set of ionotropic receptors (IRs), most of them belonging to the divergent IR subtype. No binding proteins, gustatory receptors (GRs) or insect-like olfactory receptors (ORs) were present. Additionally to their olfactory function, the antennules were equipped with a variety of pathogen defense mechanisms, producing relevant substances on site. The overall similarity of both transcriptomes is high and does not indicate a general shift in genetic makeup connected to the change in habitat. IRs seem to perform the task of olfactory detection in both hermit crab species studied. PMID:24478616

  10. Tumor induction in the glandular stomach of rats after oral administration of a single or a few doses of N-methyl-N'-nitro-N-nitrosoguanidine during the newborn period.

    PubMed

    Sumi, Y; Miyakawa, M

    1978-12-01

    When N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) was orally intubated to conventional newborn rats by the catheter technique, the rats were found with tumors almost exclusively developed in the glandular stomach, mostly until 280 days after the first intubation. Tumor incidence was about 50% in both sexs of rats that survived the intubation of a single dose of MNNG in rats of less than 24 hr after birth and almost 100% in both sexes of rats that survived the intubation of three consecutive daily doses of MNNG on 5th day after birth. Out of 52 rats treated with MNNG, 40.4% developed carcinomas (20 adenocarcinomas and 1 squamous cell carcinoma), three of them having metastatic lesions. The predilective localization of tumors in the glandular, especially fundic, portion of the stomach, might be attributed to the use of newborns and to the catheter technique devised here. PMID:750273

  11. 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

  12. 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

  13. 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

  14. Apoptotic wing degeneration and formation of an altruism-regulating glandular appendage (gemma) in the ponerine ant Diacamma sp. from Japan (Hymenoptera, Formicidae, Ponerinae).

    PubMed

    Gotoh, A; Sameshima, S; Tsuji, K; Matsumoto, T; Miura, T

    2005-02-01

    We here show an example of morphological novelties, which have evolved from insect wings into the specific structures controlling social behaviour in an ant species. Most ant colonies consist of winged queen(s) and wingless workers. In the queenless ponerine ant Diacamma sp. from Japan, however, all female workers have a pair of small thoracic appendages, called "gemmae", which are homologous to the forewings and acts as an organ regulating altruism expression. Most workers, whose gemmae are clipped off by other colony members, become nonreproductive helpers, while only a single individual with complete gemmae becomes functionally reproductive. We examined histologically the development of gemmae, and compared it with that of functional wings in males. Female larvae had well-developed wing discs for both fore- and hindwings. At pupation, however, the wing discs started to evaginate and later degenerate. The hindwing discs completely degenerated, while the degeneration of forewing discs was incomplete, leading to the formation of gemmae. The degeneration process involved apoptotic cell death as confirmed by TUNEL assay. In addition, glandular cells differentiated from the epithelial cells of the forewing buds after completion of pupation. The mechanism of developmental transition from wing to gemma can be regarded as an evolutionary gain of new function, which can be seen in insect appendages and vertebrate limbs. PMID:15647944

  15. 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.

  16. Exposure dose reduction for the high energy spectrum in the photon counting mammography: simulation study based on Japanese breast glandularity and thickness

    NASA Astrophysics Data System (ADS)

    Niwa, Naoko; Yamazaki, Misaki; Kodera, Yoshie; Yamamuro, Mika; Yamada, Kanako; Asai, Yoshiyuki; Yamada, Koji

    2015-03-01

    Recently, digital mammography with a photon counting silicon detector has been developed. With the aim of reducing the exposure dose, we have proposed a new mammography system that uses a cadmium telluride series photon counting detector. In addition, we also propose to use a high energy X-ray spectrum with a tungsten anode. The purpose of this study was assessed that the effectiveness of the high X-ray energy spectrum in terms of image quality using a Monte Carlo simulation. The proposed photon counting system with the high energy X-ray is compared to a conventional flat panel detector system with a Mo/Rh spectrum. The contrast-to-noise ratio (CNR) is calculated from simulation images with the use of breast phantoms. The breast model phantoms differed by glandularity and thickness, which were determined from Japanese clinical mammograms. We found that the CNR values were higher in the proposed system than in the conventional system. The number of photons incident on the detector was larger in the proposed system, so that the noise values was lower in comparison with the conventional system. Therefore, the high energy spectrum yielded the same CNR as using the conventional spectrum while allowing a considerable dose reduction to the breast.

  17. A comparison of mean glandular dose diagnostic reference levels within the all-digital Irish National Breast Screening Programme and the Irish Symptomatic Breast Services.

    PubMed

    O'Leary, Desiree; Rainford, Louise

    2013-03-01

    Data on image quality, compression and radiation dose were collected from symptomatic breast units within the Republic of Ireland. Quantitative and qualitative data were analysed using SPSS. Recommendations of mean glandular dose (MGD) diagnostic reference levels were made at various levels for film-screen and full field digital mammography units to match levels published worldwide. MGDs received by symptomatic breast patients within Ireland are higher than those received in the all-digital Irish Breast Screening service; 55-65 mm breast: 1.75 mGy (screening) vs. 2.4 mGy (symptomatic) at the 95th percentile; various reasons are proposed for the differences. MGDs achieved in the screening service may be lower because of the exacting requirements for radiographer training, characteristics of the patients and equipment quality assurance levels. More precise imaging guidelines, standards and training of symptomatic radiographers performing mammography are suggested to remediate MGDs delivered to the breasts of Irish women attending the symptomatic breast services. PMID:22740646

  18. Glandular kallikreins in the teleost Cyprinus carpio: tissue distribution, possible involvement in prolactin processing, and effect of 17 beta-estradiol in vivo.

    PubMed

    Figueroa, J; Fernández, K; Haussmann, D; Richards, G; Barra, V; Kausel, G

    2002-09-01

    We examined glandular kallikrein (GK), a putative prolactin processing protease, in the teleost Cyprinus carpio. When employing an anti-Centropristis striata GK antibody proteins of 39 kDa in muscle, 52 kDa in gill, 52 kDa in kidney, and two proteins of 46 and 72 kDa in pituitary gland were detected. Immunoreactive kallikreins were recognized in intermuscle cell tissue, epithelial gill cells, apical region of tubular cells, and prolactin producing lactotrophs in pituitary gland, suggesting a osmoregulatory role for this enzyme. We found three prolactin (PRL) variants using anti-tilapia PRL antibodies, in pituitary gland 23 and 16 kDa, and in plasma 23 and 22 kDa forms. Clearly co-localization of GK and PRL in lactotrophs could be demonstrated. In winter-acclimatized male carp, where the pituitary PRL level is low, 17beta-estradiol treatment increased PRL but not GK immunoreactivity. In contrast to GK and PRL co-regulation by estrogen in mammalian pituitary gland, no similar effect on immunoreactive PRL and GK was observed in the ichtyc pituitary. No changes in GK immunostaining occurred in gill or muscle tissue in response to estrogen treatment. These results, taken with the observation of significantly increased GK immunoreactivity in the apical region of kidney tubular cells in estrogen treated male carp, indicate that the regulation of GK expression in pituitary and kidney could be different in fish with respect to mammals. PMID:12392686

  19. Binding sites for iodinated endothelin-1, endothelin-2 and endothelin-3 demonstrated on human uterine glandular epithelial cells by quantitative high-resolution autoradiography.

    PubMed

    Davenport, A P; Cameron, I T; Smith, S K; Brown, M J

    1991-04-01

    Quantitative in-vitro receptor autoradiography has been used to localize and compare the anatomical distribution of binding sites for iodinated endothelins (ET-1, ET-2 and ET-3) in human uterus. Binding sites for the three iodinated isoforms had a similar gross anatomical distribution. The density of binding sites was significantly higher in the endometrium compared with the myometrium and greatest at the endometrial-myometrial junction. In cross-competition experiments, unlabelled ET-1, ET-2, ET-3, sarafotoxin S6b and mouse vasoactive intestinal contractor (1 mumol/l) competed for the binding sites of all the iodinated peptides suggesting that ETs may bind to the same receptor. However, preproendothelin(110-130) (endothelin-like peptide) or preproendothelin(124-130) and other non-endothelin vasoactive peptides tested as a concentration of 1 mumol/l did not compete. Micro-autoradiography revealed that high densities of iodinated ET-1, ET-2 and ET-3 binding sites were localized to glandular epithelial cells and blood vessels with lower levels in the myometrium and vascular smooth muscle, suggesting that these potent vasoactive and proliferative agents could play a role in the control of menstruation. PMID:2030325

  20. Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots

    PubMed Central

    Jayakodi, Murukarthick; Lee, Sang-Choon; Park, Hyun-Seung; Jang, Woojong; Lee, Yun Sun; Choi, Beom-Soon; Nah, Gyoung Ju; Kim, Do-Soon; Natesan, Senthil; Sun, Chao; Yang, Tae-Jin

    2014-01-01

    Background Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results Assemblies were generated from ∼85 million and ∼77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases. We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use. PMID:25379008

  1. 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

  2. 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. PMID

  3. 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

  4. 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.

  5. afterParty: turning raw transcriptomes into permanent resources

    PubMed Central

    2013-01-01

    Background Next-generation DNA sequencing technologies have made it possible to generate transcriptome data for novel organisms quickly and cheaply, to the extent that the effort required to annotate and publish a new transcriptome is greater than the effort required to sequence it. Often, following publication, details of the annotation effort are only available in summary form, hindering subsequent exploitation of the data. To promote best-practice in annotation and to ensure that data remain accessible, we have written afterParty, a web application that allows users to assemble, annotate and publish novel transcriptomes using only a web browser. Results afterParty is a robust web application that implements best-practice transcriptome assembly, annotation, browsing, searching, and visualization. Users can turn a collection of reads (from Roche 454 chemistry) or assembled contigs (from any sequencing chemistry, including Illumina Solexa RNA-Seq) into a searchable, browsable transcriptome resource and quickly make it publicly available. Contigs are functionally annotated based on similarity to known sequences and protein domains. Once assembled and annotated, transcriptomes derived from multiple species or libraries can be compared and searched. afterParty datasets can either be created using the existing afterParty server, or using local instances that can be built easily using a virtual machine. afterParty includes powerful visualization tools for transcriptome dataset exploration and uses a flexible annotation architecture which will allow additional types of annotation to be added in the future. Conclusions afterParty's main use case scenario is one in which a working biologist has generated a large volume of transcribed sequence data and wishes to turn it into a useful resource that has some durability. By reducing the effort, bioinformatics skills, and computational resources needed to annotate and publish a transcriptome, afterParty will facilitate the

  6. 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

  7. Neuropeptide receptor transcriptome reveals unidentified neuroendocrine pathways.

    PubMed

    Yamanaka, Naoki; Yamamoto, Sachie; Zitnan, Dusan; Watanabe, Ken; Kawada, Tsuyoshi; Satake, Honoo; Kaneko, Yu; Hiruma, Kiyoshi; Tanaka, Yoshiaki; Shinoda, Tetsuro; Kataoka, Hiroshi

    2008-01-01

    Neuropeptides are an important class of molecules involved in diverse aspects of metazoan development and homeostasis. Insects are ideal model systems to investigate neuropeptide functions, and the major focus of insect neuropeptide research in the last decade has been on the identification of their receptors. Despite these vigorous efforts, receptors for some key neuropeptides in insect development such as prothoracicotropic hormone, eclosion hormone and allatotropin (AT), remain undefined. In this paper, we report the comprehensive cloning of neuropeptide G protein-coupled receptors from the silkworm, Bombyx mori, and systematic analyses of their expression. Based on the expression patterns of orphan receptors, we identified the long-sought receptor for AT, which is thought to stimulate juvenile hormone biosynthesis in the corpora allata (CA). Surprisingly, however, the AT receptor was not highly expressed in the CA, but instead was predominantly transcribed in the corpora cardiaca (CC), an organ adjacent to the CA. Indeed, by using a reverse-physiological approach, we purified and characterized novel allatoregulatory peptides produced in AT receptor-expressing CC cells, which may indirectly mediate AT activity on the CA. All of the above findings confirm the effectiveness of a systematic analysis of the receptor transcriptome, not only in characterizing orphan receptors, but also in identifying novel players and hidden mechanisms in important biological processes. This work illustrates how using a combinatorial approach employing bioinformatic, molecular, biochemical and physiological methods can help solve recalcitrant problems in neuropeptide research. PMID:18725956

  8. 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. PMID:25124096

  9. Sequencing the AML Genome, Transcriptome, and Epigenome

    PubMed Central

    Mardis, Elaine R.

    2014-01-01

    Leukemia is a disease that develops as a result of changes in the genomes of hematopoietic cells, a fact first appreciated by microscopic examination of the bone marrow cell chromosomes of affected patients. These studies revealed that specific subtypes of leukemia diagnosis correlated with specific chromosomal abnormalities, such as the t(15;17) of acute promyelocytic leukemia1 and the t(9;22) of chronic myeloid leukemia2. Over time, our genomic characterization of hematologic malignancies has moved beyond the resolution of the microscope to that of individual nucleotides in the analysis of whole genome sequencing data using state-of-the-art massively parallel sequencing (MPS) instruments and algorithmic analyses of the resulting data. In addition to studying the genomic sequence alterations that occur in patient’s genomes, these same instruments can decode the methylation landscape of the leukemia genome and the resulting RNA expression landscape of the leukemia transcriptome. Broad correlative analyses can then integrate these three data types to better inform researchers and clinicians about the biology of individual acute myeloid leukemia (AML) cases, facilitating improvements in care and prognosis. PMID:25311738

  10. Ameloblastoma Phenotypes Reflected in Distinct Transcriptome Profiles.

    PubMed

    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

  11. Transcriptome analysis of sarracenia, an insectivorous plant.

    PubMed

    Srivastava, Anuj; Rogers, Willie L; Breton, Catherine M; Cai, Liming; Malmberg, Russell L

    2011-08-01

    Sarracenia species (pitcher plants) are carnivorous plants which obtain a portion of their nutrients from insects captured in the pitchers. To investigate these plants, we sequenced the transcriptome of two species, Sarracenia psittacina and Sarracenia purpurea, using Roche 454 pyrosequencing technology. We obtained 46 275 and 36 681 contigs by de novo assembly methods for S. psittacina and S. purpurea, respectively, and further identified 16 163 orthologous contigs between them. Estimation of synonymous substitution rates between orthologous and paralogous contigs indicates the events of genome duplication and speciation within the Sarracenia genus both occurred ∼2 million years ago. The ratios of synonymous and non-synonymous substitution rates indicated that 491 contigs have been under positive selection (K(a)/K(s) > 1). Significant proportions of these contigs were involved in functions related to binding activity. We also found that the greatest sequence similarity for both of these species was to Vitis vinifera, which is most consistent with a non-current classification of the order Ericales as an asterid. This study has provided new insights into pitcher plants and will contribute greatly to future research on this genus and its distinctive ecological adaptations. PMID:21676972

  12. A transcriptomic atlas of mouse neocortical layers.

    PubMed

    Belgard, T Grant; Marques, Ana C; Oliver, Peter L; Abaan, Hatice Ozel; Sirey, Tamara M; Hoerder-Suabedissen, Anna; García-Moreno, Fernando; Molnár, Zoltán; Margulies, Elliott H; Ponting, Chris P

    2011-08-25

    In the mammalian cortex, neurons and glia form a patterned structure across six layers whose complex cytoarchitectonic arrangement is likely to contribute to cognition. We sequenced transcriptomes from layers 1-6b of different areas (primary and secondary) of the adult (postnatal day 56) mouse somatosensory cortex to understand the transcriptional levels and functional repertoires of coding and noncoding loci for cells constituting these layers. A total of 5,835 protein-coding genes and 66 noncoding RNA loci are differentially expressed ("patterned") across the layers, on the basis of a machine-learning model (naive Bayes) approach. Layers 2-6b are each associated with specific functional and disease annotations that provide insights into their biological roles. This new resource (http://genserv.anat.ox.ac.uk/layers) greatly extends currently available resources, such as the Allen Mouse Brain Atlas and microarray data sets, by providing quantitative expression levels, by being genome-wide, by including novel loci, and by identifying candidate alternatively spliced transcripts that are differentially expressed across layers. PMID:21867878

  13. Transcriptome annotation using tandem SAGE tags

    PubMed Central

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of gene expression (SAGE) can reveal new Poly(A) RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restrictions sites of cDNAs. New transcripts are then tentatively defined by the two SAGE tags in tandem and by the spanning sequence read on the genome between these tagged sites. Having developed a new algorithm to locate these tag-delimited genomic sequences (TDGS), we first validated its capacity to recognize known genes and its ability to reveal new transcripts with two SAGE libraries built in parallel from a single RNA sample. Our algorithm proves fast enough to experiment this strategy at a large scale. We then collected and processed the complete sets of human SAGE tags to predict yet unknown transcripts. A cross-validation with tiling arrays data shows that 47% of these TDGS overlap transcriptional active regions. Our method provides a new and complementary approach for complex transcriptome annotation. PMID:17709346

  14. De Novo Transcriptome of the Hemimetabolous German Cockroach (Blattella germanica)

    PubMed Central

    Zhou, Xiaojie; Qian, Kun; Tong, Ying; Zhu, Junwei Jerry; Qiu, Xinghui; Zeng, Xiaopeng

    2014-01-01

    Background The German cockroach, Blattella germanica, is an important insect pest that transmits various pathogens mechanically and causes severe allergic diseases. This insect has long served as a model system for studies of insect biology, physiology and ecology. However, the lack of genome or transcriptome information heavily hinder our further understanding about the German cockroach in every aspect at a molecular level and on a genome-wide scale. To explore the transcriptome and identify unique sequences of interest, we subjected the B. germanica transcriptome to massively parallel pyrosequencing and generated the first reference transcriptome for B. germanica. Methodology/Principal Findings A total of 1,365,609 raw reads with an average length of 529 bp were generated via pyrosequencing the mixed cDNA library from different life stages of German cockroach including maturing oothecae, nymphs, adult females and males. The raw reads were de novo assembled to 48,800 contigs and 3,961 singletons with high-quality unique sequences. These sequences were annotated and classified functionally in terms of BLAST, GO and KEGG, and the genes putatively coding detoxification enzyme systems, insecticide targets, key components in systematic RNA interference, immunity and chemoreception pathways were identified. A total of 3,601 SSRs (Simple Sequence Repeats) loci were also predicted. Conclusions/Significance The whole transcriptome pyrosequencing data from this study provides a usable genetic resource for future identification of potential functional genes involved in various biological processes. PMID:25265537

  15. 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

  16. Evolution of Neuronal and Endothelial Transcriptomes in Primates

    PubMed Central

    Giger, Thomas; Khaitovich, Philipp; Somel, Mehmet; Lorenc, Anna; Lizano, Esther; Harris, Laura W.; Ryan, Margaret M.; Lan, Martin; Wayland, Matthew T.; Bahn, Sabine; Pääbo, Svante

    2010-01-01

    The study of gene expression evolution in vertebrates has hitherto focused on the analysis of transcriptomes in tissues of different species. However, because a tissue is made up of different cell types, and cell types differ with respect to their transcriptomes, the analysis of tissues offers a composite picture of transcriptome evolution. The isolation of individual cells from tissue sections opens up the opportunity to study gene expression evolution at the cell type level. We have stained neurons and endothelial cells in human brains by antibodies against cell type-specific marker proteins, isolated the cells using laser capture microdissection, and identified genes preferentially expressed in the two cell types. We analyze these two classes of genes with respect to their expression in 62 different human tissues, with respect to their expression in 44 human “postmortem” brains from different developmental stages and with respect to between-species brain expression differences. We find that genes preferentially expressed in neurons differ less across tissues and developmental stages than genes preferentially expressed in endothelial cells. We also observe less expression differences within primate species for neuronal transcriptomes. In stark contrast, we see more gene expression differences between humans, chimpanzees, and rhesus macaques relative to within-species differences in genes expressed preferentially in neurons than in genes expressed in endothelial cells. This suggests that neuronal and endothelial transcriptomes evolve at different rates within brain tissue. PMID:20624733

  17. RNA-Seq Technology and Its Application in Fish Transcriptomics

    PubMed Central

    Ba, Yi; Zhuang, Qianfeng

    2014-01-01

    Abstract High-throughput sequencing technologies, also known as next-generation sequencing (NGS) technologies, have revolutionized the way that genomic research is advancing. In addition to the static genome, these state-of-art technologies have been recently exploited to analyze the dynamic transcriptome, and the resulting technology is termed RNA sequencing (RNA-seq). RNA-seq is free from many limitations of other transcriptomic approaches, such as microarray and tag-based sequencing method. Although RNA-seq has only been available for a short time, studies using this method have completely changed our perspective of the breadth and depth of eukaryotic transcriptomes. In terms of the transcriptomics of teleost fishes, both model and non-model species have benefited from the RNA-seq approach and have undergone tremendous advances in the past several years. RNA-seq has helped not only in mapping and annotating fish transcriptome but also in our understanding of many biological processes in fish, such as development, adaptive evolution, host immune response, and stress response. In this review, we first provide an overview of each step of RNA-seq from library construction to the bioinformatic analysis of the data. We then summarize and discuss the recent biological insights obtained from the RNA-seq studies in a variety of fish species. PMID:24380445

  18. RNA sequencing of the nephron transcriptome: a technical note

    PubMed Central

    Lee, Jae Wook

    2015-01-01

    To understand the functions of the kidney, the transcriptome of each part of the nephron needs to be profiled using a highly sensitive and unbiased tool. RNA sequencing (RNA-seq) has revolutionized transcriptomic research, enabling researchers to define transcription activity and functions of genomic elements with unprecedented sensitivity and precision. Recently, RNA-seq for polyadenylated messenger RNAs [poly(A)′-mRNAs] and classical microdissection were successfully combined to investigate the transcriptome of glomeruli and 14 different renal tubule segments. A rat kidney is perfused with and incubated in collagenase solution, and the digested kidney was manually dissected under a stereomicroscope. Individual glomeruli and renal tubule segments are identified by their anatomical and morphological characteristics and collected in phosphate-buffered saline. Poly(A)′-tailed mRNAs are released from cell lysate, captured by oligo-dT primers, and made into complementary DNAs (cDNAs) using a highly sensitive reverse transcription method. These cDNAs are sheared by sonication and prepared into adapter-ligated cDNA libraries for Illumina sequencing. Nucleotide sequences reported from the sequencing reaction are mapped to the rat reference genome for gene expression analysis. These RNA-seq transcriptomic data were highly consistent with prior knowledge of gene expression along the nephron. The gene expression data obtained in this work are available as a public Web page (https://helixweb.nih.gov/ESBL/Database/NephronRNAseq/) and can be used to explore the transcriptomic landscape of the nephron. PMID:26779425

  19. Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

    PubMed Central

    2012-01-01

    Background Environmentally induced epigenetic transgenerational inheritance of adult onset disease involves a variety of phenotypic changes, suggesting a general alteration in genome activity. Results Investigation of different tissue transcriptomes in male and female F3 generation vinclozolin versus control lineage rats demonstrated all tissues examined had transgenerational transcriptomes. The microarrays from 11 different tissues were compared with a gene bionetwork analysis. Although each tissue transgenerational transcriptome was unique, common cellular pathways and processes were identified between the tissues. A cluster analysis identified gene modules with coordinated gene expression and each had unique gene networks regulating tissue-specific gene expression and function. A large number of statistically significant over-represented clusters of genes were identified in the genome for both males and females. These gene clusters ranged from 2-5 megabases in size, and a number of them corresponded to the epimutations previously identified in sperm that transmit the epigenetic transgenerational inheritance of disease phenotypes. Conclusions Combined observations demonstrate that all tissues derived from the epigenetically altered germ line develop transgenerational transcriptomes unique to the tissue, but common epigenetic control regions in the genome may coordinately regulate these tissue-specific transcriptomes. This systems biology approach provides insight into the molecular mechanisms involved in the epigenetic transgenerational inheritance of a variety of adult onset disease phenotypes. PMID:23034163

  20. Analysis of the Citrullus colocynthis Transcriptome during Water Deficit Stress

    PubMed Central

    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. PMID:25118696

  1. 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

  2. Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome.

    PubMed

    Shanku, Alexander G; McPeek, Mark A; Kern, Andrew D

    2013-03-11

    In this paper we present a de novo assembly of the transcriptome of the damselfly, Enallagma hageni, through the use of 454 pyrosequencing. E. hageni is a member of the suborder Zygoptera within the order Odonata, and the Odonata are the basal lineage of the winged insects (Pterygota). To date, sequence data used in phylogenetic analysis of Enallagma species have been derived from either mtDNA or ribosomal nuclear DNA. This transcriptome contained 31,661 contigs that were assembled and translated into 14,813 individual open reading frames. Using these data, we constructed an extensive dataset of 634 orthologous nuclear protein-coding genes across 11 species of Arthropoda, and used Bayesian techniques to elucidate Enallagma's place in the Arthropod phylogenetic tree. Additionally, we demonstrate that the Enallagma transcriptome contains 169 genes that are evolving at rates that differ relative to the rest of the transcriptome (29 accelerated and 140 decreased), and through multiple Gene Ontology searches and clustering methods, we present the first functional-annotation of any palaeopteran's transcriptome in the literature. PMID:23550132

  3. The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling

    PubMed Central

    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. PMID:26694548

  4. 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...

  5. The transcriptome of mouse central nervous system myelin

    PubMed Central

    Thakurela, Sudhir; Garding, Angela; Jung, Ramona B.; Müller, Christina; Goebbels, Sandra; White, Robin; Werner, Hauke B.; Tiwari, Vijay K.

    2016-01-01

    Rapid nerve conduction in the CNS is facilitated by insulation of axons with myelin, a specialized oligodendroglial compartment distant from the cell body. Myelin is turned over and adapted throughout life; however, the molecular and cellular basis of myelin dynamics remains elusive. Here we performed a comprehensive transcriptome analysis (RNA-seq) of myelin biochemically purified from mouse brains at various ages and find a surprisingly large pool of transcripts enriched in myelin. Further computational analysis showed that the myelin transcriptome is closely related to the myelin proteome but clearly distinct from the transcriptomes of oligodendrocytes and brain tissues, suggesting a highly selective incorporation of mRNAs into the myelin compartment. The mRNA-pool in myelin displays maturation-dependent dynamic changes of composition, abundance, and functional associations; however ageing-dependent changes after 6 months were minor. We suggest that this transcript pool enables myelin turnover and the local adaptation of individual pre-existing myelin sheaths. PMID:27173133

  6. The transcriptome of mouse central nervous system myelin.

    PubMed

    Thakurela, Sudhir; Garding, Angela; Jung, Ramona B; Müller, Christina; Goebbels, Sandra; White, Robin; Werner, Hauke B; Tiwari, Vijay K

    2016-01-01

    Rapid nerve conduction in the CNS is facilitated by insulation of axons with myelin, a specialized oligodendroglial compartment distant from the cell body. Myelin is turned over and adapted throughout life; however, the molecular and cellular basis of myelin dynamics remains elusive. Here we performed a comprehensive transcriptome analysis (RNA-seq) of myelin biochemically purified from mouse brains at various ages and find a surprisingly large pool of transcripts enriched in myelin. Further computational analysis showed that the myelin transcriptome is closely related to the myelin proteome but clearly distinct from the transcriptomes of oligodendrocytes and brain tissues, suggesting a highly selective incorporation of mRNAs into the myelin compartment. The mRNA-pool in myelin displays maturation-dependent dynamic changes of composition, abundance, and functional associations; however ageing-dependent changes after 6 months were minor. We suggest that this transcript pool enables myelin turnover and the local adaptation of individual pre-existing myelin sheaths. PMID:27173133

  7. 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

  8. Transcriptome research on spermatogenic molecular drive in mammals

    PubMed Central

    Zhu, Zi-Jue; Yang, Shi; Li, Zheng

    2015-01-01

    It is known that spermatogenic disorders are associated with genetic deficiency, although the primary mechanism is still unclear. It is difficult to demonstrate the molecular events occurring in testis, which contains germ cells at different developmental stages. However, transcriptomic methods can help us reveal the molecular drive of male gamete generation. Many transcriptomic studies have been performed on rodents by utilizing the timing of the first wave of spermatogenesis, which is not a suitable strategy for research in fertile men. With the development of separation methods for male germ cells, transcriptome research on the molecular drive of spermatogenesis in fertile men has seen great progress, and the results could be ultimately applied to improve the diagnosis and treatment for male infertility. PMID:26306849

  9. Transcriptomic analyses of Onecut1 and Onecut2 deficient retinas.

    PubMed

    Goetz, Jillian J; Trimarchi, Jeffrey M

    2015-06-01

    In this article, we further explore the data generated for the research article "Onecut1 and Onecut2 play critical roles in the development of the mouse retina". To better understand the functionality of the Onecut family of transcription factors in retinogenesis, we investigated the retinal transcriptomes of developing and mature mice to identify genes with differential expression. This data article reports the full transcriptomes resulting from these experiments and provides tables detailing the differentially expressed genes between wildtype and Onecut1 or 2 deficient retinas. The raw array data of our transcriptomes as generated using Affymetrix microarrays are available on the NCBI Gene Expression Omnibus (GEO) browser (Reference number GSE57917 and GSE57918GSE57917GSE57918). PMID:26484186

  10. 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

  11. Analysis of the Thinopyrum elongatum Transcriptome under Water Deficit Stress

    PubMed Central

    Shu, Yongjun; Zhang, Jun; Ao, You; Song, Lili; Guo, Changhong

    2015-01-01

    The transcriptome of Thinopyrum elongatum under water deficit stress was analyzed using RNA-Seq technology. The results showed that genes involved in processes of amplification of stress signaling, reductions in oxidative damage, creation of protectants, and roots development were expressed differently, which played an important role in the response to water deficit. The Th. elongatum transcriptome research highlights the activation of a large set of water deficit-related genes in this species and provides a valuable resource for future functional analysis of candidate genes in the water deficit stress response. PMID:25722968

  12. Transcriptomic Signatures of Ash (Fraxinus spp.) Phloem

    PubMed Central

    Mamidala, Praveen; Bonello, Pierluigi; Herms, Daniel A.; Mittapalli, Omprakash

    2011-01-01

    Background Ash (Fraxinus spp.) is a dominant tree species throughout urban and forested landscapes of North America (NA). The rapid invasion of NA by emerald ash borer (Agrilus planipennis), a wood-boring beetle endemic to Eastern Asia, has resulted in the death of millions of ash trees and threatens billions more. Larvae feed primarily on phloem tissue, which girdles and kills the tree. While NA ash species including black (F. nigra), green (F. pennsylvannica) and white (F. americana) are highly susceptible, the Asian species Manchurian ash (F. mandshurica) is resistant to A. planipennis perhaps due to their co-evolutionary history. Little is known about the molecular genetics of ash. Hence, we undertook a functional genomics approach to identify the repertoire of genes expressed in ash phloem. Methodology and Principal Findings Using 454 pyrosequencing we obtained 58,673 high quality ash sequences from pooled phloem samples of green, white, black, blue and Manchurian ash. Intriguingly, 45% of the deduced proteins were not significantly similar to any sequences in the GenBank non-redundant database. KEGG analysis of the ash sequences revealed a high occurrence of defense related genes. Expression analysis of early regulators potentially involved in plant defense (i.e. transcription factors, calcium dependent protein kinases and a lipoxygenase 3) revealed higher mRNA levels in resistant ash compared to susceptible ash species. Lastly, we predicted a total of 1,272 single nucleotide polymorphisms and 980 microsatellite loci, among which seven microsatellite loci showed polymorphism between different ash species. Conclusions and Significance The current transcriptomic data provide an invaluable resource for understanding the genetic make-up of ash phloem, the target tissue of A. planipennis. These data along with future functional studies could lead to the identification/characterization of defense genes involved in resistance of ash to A. planipennis, and in future

  13. Transcriptome analysis of aging mouse meibomian glands

    PubMed Central

    Parfitt, Geraint J.; Brown, Donald J.

    2016-01-01

    Purpose Dry eye disease is a common condition associated with age-related meibomian gland dysfunction (ARMGD). We have previously shown that ARMGD occurs in old mice, similar to that observed in human patients with MGD. To begin to understand the mechanism underlying ARMGD, we generated transcriptome profiles of eyelids excised from young and old mice of both sexes. Methods Male and female C57BL/6 mice were euthanized at ages of 3 months or 2 years and their lower eyelids removed, the conjunctival epithelium scrapped off, and the tarsal plate, containing the meibomian glands, dissected from the overlying muscle and lid epidermis. RNA was isolated, enriched, and transcribed into cDNA and processed to generate four non-stranded libraries with distinct bar codes on each adaptor. The libraries were then sequenced and mapped to the mm10 reference genome, and expression results were gathered as reads per length of transcript in kilobases per million mapped reads (RPKM) values. Differential gene expression analyses were performed using CyberT. Results Approximately 55 million reads were generated from each library. Expression data indicated that about 15,000 genes were expressed in these tissues. Of the genes that showed more than twofold significant differences in either young or old tissue, 698 were identified as differentially expressed. According to the Gene Ontology (GO) analysis, the cellular, developmental, and metabolic processes were found to be highly represented with Wnt function noted to be altered in the aging mouse. Conclusions The RNA sequencing data identified several signaling pathways, including fibroblast growth factor (FGF) and Wnt that were altered in the meibomian glands of aging mice. PMID:27279727

  14. 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

  15. Response of Sunflower (Helianthus annuus L.) Leaf Surface Defenses to Exogenous Methyl Jasmonate

    PubMed Central

    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. PMID:22623991

  16. A transcriptome resource for the Antarctic pteropod Limacina helicina antarctica.

    PubMed

    Johnson, Kevin M; Hofmann, Gretchen E

    2016-08-01

    The pteropod Limacina helicina antarctica is a dominant member of the zooplankton assemblage in the Antarctic marine ecosystem, and is part of a relatively simple food web in nearshore marine Antarctic waters. As a shelled pteropod, Limacina has been suggested as a candidate sentinel organism for the impacts of ocean acidification, due to the potential for shell dissolution in undersaturated waters. In this study, our goal was to develop a transcriptomic resource for Limacina that would support mechanistic studies to explore the physiological response of Limacina to abiotic stressors such as ocean acidification and ocean warming. To this end, RNA sequencing libraries were prepared from Limacina that had been exposed to a range of pH levels and an elevated temperature to maximize the diversity of expressed genes. RNA sequencing (RNA-seq) was conducted on an Illumina NextSeq500 which produced 339,000,000 150bp paired-end reads. The de novo transcriptome was produced using Trinity and annotation of the assembled transcriptome resulted in the identification of 81,229 transcripts in 137 KEGG pathways. This RNA-seq effort resulted in a transcriptome for the Antarctic pteropod, Limacina helicina antarctica, that is a major resource for an international marine science research community studying these pelagic molluscs in a global change context. PMID:27157132

  17. 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...

  18. Global transcriptome analyses of human and murine terminal erythroid differentiation

    PubMed Central

    An, Xiuli; Schulz, Vincent P.; Li, Jie; Wu, Kunlu; Liu, Jing; Xue, Fumin; Hu, Jingping; Mohandas, Narla

    2014-01-01

    We recently developed fluorescence-activated cell sorting (FACS)-based methods to purify morphologically and functionally discrete populations of cells, each representing specific stages of terminal erythroid differentiation. We used these techniques to obtain pure populations of both human and murine erythroblasts at distinct developmental stages. RNA was prepared from these cells and subjected to RNA sequencing analyses, creating unbiased, stage-specific transcriptomes. Tight clustering of transcriptomes from differing stages, even between biologically different replicates, validated the utility of the FACS-based assays. Bioinformatic analyses revealed that there were marked differences between differentiation stages, with both shared and dissimilar gene expression profiles defining each stage within transcriptional space. There were vast temporal changes in gene expression across the differentiation stages, with each stage exhibiting unique transcriptomes. Clustering and network analyses revealed that varying stage-specific patterns of expression observed across differentiation were enriched for genes of differing function. Numerous differences were present between human and murine transcriptomes, with significant variation in the global patterns of gene expression. These data provide a significant resource for studies of normal and perturbed erythropoiesis, allowing a deeper understanding of mechanisms of erythroid development in various inherited and acquired erythroid disorders. PMID:24637361

  19. Translating cancer genomes and transcriptomes for precision oncology.

    PubMed

    Roychowdhury, Sameek; Chinnaiyan, Arul M

    2016-01-01

    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 like 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 that is beginning to impact real-time clinical decision-making. The authors 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, key applications and new directions are outlined for translating the cancer genome and transcriptome into patient care in the clinic. PMID:26528881

  20. The transcriptomics of an experimentally evolved plant-virus interaction.

    PubMed

    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

  1. 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...

  2. Characterization of the rainbow trout oocyte microRNA transcriptome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    MicroRNAs (miRNAs) are a class of endogenous small non-coding RNA molecules that regulate post-transcriptional expression of target genes and play important roles in animal development. The objectives of this study were to characterize the egg miRNA transcriptome and identify novel egg-specific miRN...

  3. 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 ...

  4. 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

  5. Dynamic transcriptome landscape of maize embryo and endosperm development.

    PubMed

    Chen, Jian; Zeng, Biao; Zhang, Mei; Xie, Shaojun; Wang, Gaokui; Hauck, Andrew; Lai, Jinsheng

    2014-09-01

    Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues. A total of 26,105 genes were found to be involved in programming seed development, including 1,614 transcription factors. Global comparisons of gene expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with the published nonseed high-throughput RNA sequencing data, we identified 91 transcription factors and 1,167 other seed-specific genes, which should help elucidate key mechanisms and regulatory networks that underlie seed development. In addition, correlation of gene expression with the pattern of DNA methylation revealed that hypomethylation of the gene body region should be an important factor for the expressional activation of seed-specific genes, especially for extremely highly expressed genes such as zeins. This study provides a valuable resource for understanding the genetic control of seed development of monocotyledon plants. PMID:25037214

  6. 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...

  7. Aging-like Changes in the Transcriptome of Irradiated Microglia

    PubMed Central

    Li, Matthew D.; Burns, Terry C.; Kumar, Sunny; Morgan, Alexander A.; Sloan, Steven A.; Palmer, Theo D.

    2014-01-01

    Whole brain irradiation remains important in the management of brain tumors. Although necessary for improving survival outcomes, cranial irradiation also results in cognitive decline in long-term survivors. A chronic inflammatory state characterized by microglial activation has been implicated in radiation-induced brain injury. We here provide the first comprehensive transcriptional profile of irradiated microglia. Fluorescence-activated cell sorting (FACS) was used to isolate CD11b+ microglia from the hippocampi of C57BL/6 and Balb/c mice 1 month after 10Gy cranial irradiation. Affymetrix gene expression profiles were evaluated using linear modeling, rank product analyses. One month after irradiation, a conserved irradiation signature across strains was identified, comprising 448 and 85 differentially up- and down-regulated genes, respectively. Gene set enrichment analysis (GSEA) demonstrated enrichment for inflammation, including M1 macrophage-associated genes, but also an unexpected enrichment for extracellular matrix and blood coagulation-related gene sets, in contrast previously described microglial states. Weighted gene co-expression network analysis (WGCNA) confirmed these findings and further revealed alterations in mitochondrial function. The RNA-seq transcriptome of microglia 24h post-radiation proved similar to the 1-month transcriptome, but additionally featured alterations in apoptotic and lysosomal gene expression. Re-analysis of published aging mouse microglia transcriptome data demonstrated striking similarity to the 1 month irradiated microglia transcriptome, suggesting that shared mechanisms may underlie aging and chronic irradiation-induced cognitive decline. PMID:25690519

  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. Shooting through time: new insights from transcriptomic data

    PubMed Central

    Harrison, C. Jill

    2015-01-01

    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. PMID:26120036

  10. Ameloblast transcriptome changes from secretory to maturation stages

    PubMed Central

    Simmer, James P.; Richardson, Amelia S.; Wang, Shih-Kai; Reid, Bryan M.; Bai, Yongsheng; Hu, Yuanyuan; Hu, Jan C.-C.

    2014-01-01

    The purpose of this study was to identify the major molecular components in the secretory and maturation stages of amelogenesis through transcriptome analyses. Ameloblasts (40 sections per age group) were laser micro-dissected from Day 5 (secretory stage) and Days 11–12 (maturation stage) first molars. PolyA+ RNA was isolated from the lysed cells, converted to cDNA, and amplified to generate a cDNA library. DNA sequences were obtained using next generation sequencing and analyzed to identify genes whose expression had increased or decreased at least 1.5-fold in maturation stage relative to secretory stage ameloblasts. Among the 9198 genes that surpassed the quality threshold, 373 showed higher expression in secretory stage, while 614 genes increased in maturation stage ameloblasts. The results were crosschecked against a previously published transcriptome generated from tissues overlying secretory and maturation stage mouse incisor enamel and 34 increasing and 26 decreasing expressers common to the two studies were identified. Expression of F2r, which encodes protease activated receptor 1 (PAR1) that showed 10-fold higher expression during the secretory stage in our transcriptome analysis, was characterized in mouse incisors by immunohistochemistry. PAR1 was detected in secretory, but not maturation stage ameloblasts. We conclude that transcriptome analyses are a good starting point for identifying genes/proteins that are critical for proper dental enamel formation and that PAR1 is specifically expressed by secretory stage ameloblasts. PMID:25158176

  11. Transcriptome dynamics-based operon prediction in prokaryotes

    PubMed Central

    2014-01-01

    Background Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. Results In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. Conclusion We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available. PMID:24884724

  12. Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

    PubMed Central

    Mercer, Tim R.; Dinger, Marcel E.; Bracken, Cameron P.; Kolle, Gabriel; Szubert, Jan M.; Korbie, Darren J.; Askarian-Amiri, Marjan E.; Gardiner, Brooke B.; Goodall, Gregory J.; Grimmond, Sean M.; Mattick, John S.

    2010-01-01

    The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 5′ capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genome-wide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage- and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome. PMID:21045082

  13. Embryonic transcriptome analysis of the Caribbean fruit fly, Anastrepha suspensa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The embryonic transcriptome of the Caribbean fruit fly, Anastrepha suspensa, was sequenced by 454 pyrosequencing in an effort to isolate embryonic promoters and genes involved in programmed cell death. A cDNA library was constructed from total RNA pooled from various time points in embryogenesis usi...

  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. Assessing De Novo transcriptome assembly metrics for consistency and utility

    PubMed Central

    2013-01-01

    Background Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality. Results We simulated sequencing transcripts of Drosophila melanogaster. By assembling these simulated reads using both a “perfect” and a modern transcriptome assembler while varying read length and sequencing depth, we evaluated quality metrics to determine whether they 1) revealed perfect assemblies to be of higher quality, and 2) revealed perfect assemblies to be more complete as data quantity increased. Several commonly used metrics were not consistent with these expectations, including average contig coverage and length, though they became consistent when singletons were included in the analysis. We found several annotation-based metrics to be consistent and informative, including contig reciprocal best hit count and contig unique annotation count. Finally, we evaluated a number of novel metrics such as reverse annotation count, contig collapse factor, and the ortholog hit ratio, discovering that each assess assembly quality in unique ways. Conclusions Although much attention has been given to transcriptome assembly, little research has focused on determining how best to evaluate assemblies, particularly in light of the variety of options available for read length and sequencing depth. Our results provide an important review of these metrics and give researchers tools to produce the highest quality transcriptome assemblies. PMID:23837739

  16. 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

  17. Transcriptomine, a web resource for nuclear receptor signaling transcriptomes.

    PubMed

    Ochsner, Scott A; Watkins, Christopher M; McOwiti, Apollo; Xu, Xueping; Darlington, Yolanda F; Dehart, Michael D; Cooney, Austin J; Steffen, David L; Becnel, Lauren B; McKenna, Neil J

    2012-09-01

    The nuclear receptor (NR) superfamily of ligand-regulated transcription factors directs ligand- and tissue-specific transcriptomes in myriad developmental, metabolic, immunological, and reproductive processes. The NR signaling field has generated a wealth of genome-wide expression data points, but due to deficits in their accessibility, annotation, and integration, the full potential of these studies has not yet been realized. We searched public gene expression databases and MEDLINE for global transcriptomic datasets relevant to NRs, their ligands, and coregulators. We carried out extensive, deep reannotation of the datasets using controlled vocabularies for RNA Source and regulating molecule and resolved disparate gene identifiers to official gene symbols to facilitate comparison of fold changes and their significance across multiple datasets. We assembled these data points into a database, Transcriptomine (http://www.nursa.org/transcriptomine), that allows for multiple, menu-driven querying strategies of this transcriptomic "superdataset," including single and multiple genes, Gene Ontology terms, disease terms, and uploaded custom gene lists. Experimental variables such as regulating molecule, RNA Source, as well as fold-change and P value cutoff values can be modified, and full data records can be either browsed or downloaded for downstream analysis. We demonstrate the utility of Transcriptomine as a hypothesis generation and validation tool using in silico and experimental use cases. Our resource empowers users to instantly and routinely mine the collective biology of millions of previously disparate transcriptomic data points. By incorporating future transcriptome-wide datasets in the NR signaling field, we anticipate Transcriptomine developing into a powerful resource for the NR- and other signal transduction research communities. PMID:22786849

  18. CarrotDB: a genomic and transcriptomic database for carrot.

    PubMed

    Xu, Zhi-Sheng; Tan, Hua-Wei; Wang, Feng; Hou, Xi-Lin; Xiong, Ai-Sheng

    2014-01-01

    Carrot (Daucus carota L.) is an economically important vegetable worldwide and is the largest source of carotenoids and provitamin A in the human diet. Given the importance of this vegetable to humans, research and breeding communities on carrot should obtain useful genomic and transcriptomic information. The first whole-genome sequences of 'DC-27' carrot were de novo assembled and analyzed. Transcriptomic sequences of 14 carrot genotypes were downloaded from the Sequence Read Archive (SRA) database of National Center for Biotechnology Information (NCBI) and mapped to the whole-genome sequence before assembly. Based on these data sets, the first Web-based genomic and transcriptomic database for D. carota (CarrotDB) was developed (database homepage: http://apiaceae.njau.edu.cn/car rotdb). CarrotDB offers the tools of Genome Map and Basic Local Alignment Search Tool. Using these tools, users can search certain target genes and simple sequence repeats along with designed primers of 'DC-27'. Assembled transcriptomic sequences along with fragments per kilobase of transcript sequence per millions base pairs sequenced information (FPKM) information of 14 carrot genotypes are also provided. Users can download de novo assembled whole-genome sequences, putative gene sequences and putative protein sequences of 'DC-27'. Users can also download transcriptome sequence assemblies of 14 carrot genotypes along with their FPKM information. A total of 2826 transcription factor (TF) genes classified into 57 families were identified in the entire genome sequences. These TF genes were embedded in CarrotDB as an interface. The 'GERMPLASM' part of CarrotDB also offers taproot photos of 45 carrot genotypes and a table containing accession numbers, names, countries of origin and colors of cortex, phloem and xylem parts of taproots corresponding to each carrot genotype. CarrotDB will be continuously updated with new information. Database URL: http://apiaceae.njau.edu.cn/carrotdb/ PMID

  19. Microfluidic single-cell whole-transcriptome sequencing.

    PubMed

    Streets, Aaron M; Zhang, Xiannian; Cao, Chen; Pang, Yuhong; Wu, Xinglong; Xiong, Liang; Yang, Lu; Fu, Yusi; Zhao, Liang; Tang, Fuchou; Huang, Yanyi

    2014-05-13

    Single-cell whole-transcriptome analysis is a powerful tool for quantifying gene expression heterogeneity in populations of cells. Many techniques have, thus, been recently developed to perform transcriptome sequencing (RNA-Seq) on individual cells. To probe subtle biological variation between samples with limiting amounts of RNA, more precise and sensitive methods are still required. We adapted a previously developed strategy for single-cell RNA-Seq that has shown promise for superior sensitivity and implemented the chemistry in a microfluidic platform for single-cell whole-transcriptome analysis. In this approach, single cells are captured and lysed in a microfluidic device, where mRNAs with poly(A) tails are reverse-transcribed into cDNA. Double-stranded cDNA is then collected and sequenced using a next generation sequencing platform. We prepared 94 libraries consisting of single mouse embryonic cells and technical replicates of extracted RNA and thoroughly characterized the performance of this technology. Microfluidic implementation increased mRNA detection sensitivity as well as improved measurement precision compared with tube-based protocols. With 0.2 M reads per cell, we were able to reconstruct a majority of the bulk transcriptome with 10 single cells. We also quantified variation between and within different types of mouse embryonic cells and found that enhanced measurement precision, detection sensitivity, and experimental throughput aided the distinction between biological variability and technical noise. With this work, we validated the advantages of an early approach to single-cell RNA-Seq and showed that the benefits of combining microfluidic technology with high-throughput sequencing will be valuable for large-scale efforts in single-cell transcriptome analysis. PMID:24782542

  20. Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis.

    PubMed

    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

  1. 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

  2. Dissecting Childhood Asthma with Nasal Transcriptomics Distinguishes Subphenotypes of Disease

    PubMed Central

    Poole, Alex; Urbanek, Cydney; Eng, Celeste; Schageman, Jeoffrey; Jacobson, Sean; O’Connor, Brian P.; Galanter, Joshua M.; Gignoux, Christopher R.; Roth, Lindsey A.; Kumar, Rajesh; Lutz, Sharon; Liu, Andrew H.; Fingerlin, Tasha; Setterquist, Robert A.; Burchard, Esteban G.; Rodriguez-Santana, Jose; Seibold, Max A.

    2014-01-01

    Background Bronchial airway expression profiling has identified inflammatory subphenotypes of asthma, but invasiveness of this technique has limited its application to childhood asthma. Objectives To determine if the nasal transcriptome can proxy expression changes in the lung airway transcriptome in asthma. To determine if the nasal transcriptome can distinguish subphenotypes of asthma. Methods Whole transcriptome RNA-sequencing (RNA-seq) was performed on nasal airway brushings from 10 controls and 10 subjects with asthma, which was compared to established bronchial and small airway transcriptomes. Targeted RNA-seq nasal expression analysis was used to profile 105 genes in 50 subjects with asthma and 50 controls for differential expression and clustering analyses. Results We found 90.2% overlap in expressed genes and strong correlation in gene expression (ρ=0.87) between the nasal and bronchial transcriptomes. Previously observed asthmatic bronchial differential expression was strongly correlated with asthmatic nasal differential expression (ρ=0.77, p=5.6×10−9). Clustering analysis identified Th2-high and Th2-low subjects differentiated by expression of 70 genes including IL-13, IL-5, POSTN, CLCA1, and SERPINB2. Th2-high subjects were more likely to have atopy (O.R.=10.3, p=3.5×10−6), atopic asthma (OR=32.6, p=6.9×10−7), high blood eosinophils (OR=9.1, 2.6×10−6), and rhinitis (OR=8.3, p=4.1×10−6) compared to Th2-low subjects. Nasal IL-13 expression levels were 3.9-fold higher in asthmatic participants who experienced asthma exacerbation in the past year (p=0.01). Several differentially expressed nasal genes were specific to asthma and independent of atopic status. Conclusion Nasal airway gene expression profiles largely recapitulate expression profiles in the lung airways. Nasal expression profiling can be used to identify individuals with IL13-driven asthma and a Th2-skewed systemic immune response. Clinical Implications Nasal airway gene

  3. 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

  4. 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. PMID:26966169

  5. 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

  6. Annual Killifish Transcriptomics and Candidate Genes for Metazoan Diapause.

    PubMed

    Thompson, Andrew W; Ortí, Guillermo

    2016-09-01

    Dormancy has evolved in all major metazoan lineages. It is critical for survival when environmental stresses are not conducive to growth, maturation, or reproduction. Embryonic diapause is a form of dormancy where development is reversibly delayed and metabolism is depressed. We report the diapause transcriptome of the annual killifish Nematolebias whitei, and compare gene expression between diapause embryos and free-living larvae to identify a candidate set of 945 differentially expressed "diapause" genes for this species. Similarity of transcriptional patterns among N. whitei and other diapausing animals is striking for a small set of genes associated with stress resistance, circadian rhythm, and metabolism, while other genes show discordant patterns. Although convergent evolution of diapause may require shared molecular mechanisms for fundamental processes, similar physiological phenotypes also may arise through modification of alternative pathways. Annual killifishes are a tractable model system for comparative transcriptomic studies on the evolution of diapause. PMID:27297470

  7. 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

    2016-01-01

    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

  8. 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

  9. Single-cell transcriptome sequencing: recent advances and remaining challenges

    PubMed Central

    Liu, Serena; Trapnell, Cole

    2016-01-01

    Single-cell RNA-sequencing methods are now robust and economically practical and are becoming a powerful tool for high-throughput, high-resolution transcriptomic analysis of cell states and dynamics. Single-cell approaches circumvent the averaging artifacts associated with traditional bulk population data, yielding new insights into the cellular diversity underlying superficially homogeneous populations. Thus far, single-cell RNA-sequencing has already shown great effectiveness in unraveling complex cell populations, reconstructing developmental trajectories, and modeling transcriptional dynamics. Ongoing technical improvements to single-cell RNA-sequencing throughput and sensitivity, the development of more sophisticated analytical frameworks for single-cell data, and an increasing array of complementary single-cell assays all promise to expand the usefulness and potential applications of single-cell transcriptomic profiling. PMID:26949524

  10. Granular gland transcriptomes in stimulated amphibian skin secretions.

    PubMed Central

    Chen, Tianbao; Farragher, Susan; Bjourson, Anthony J; Orr, David F; Rao, Pingfan; Shaw, Chris

    2003-01-01

    Amphibian defensive skin secretions are complex, species-specific cocktails of biologically active molecules, including many uncharacterized peptides. The study of such secretions for novel peptide discovery is time-limited, as amphibians are in rapid global decline. While secretion proteome analysis is non-lethal, transcriptome analysis has until now required killing of specimens prior to skin dissection for cDNA library construction. Here we present the discovery that polyadenylated mRNAs encoding dermal granular gland peptides are present in defensive skin secretions, stabilized by endogenous nucleic acid-binding amphipathic peptides. Thus parallel secretory proteome and transcriptome analyses can be performed without killing the specimen in this model amphibian system--a finding that has important implications in conservation of biodiversity within this threatened vertebrate taxon and whose mechanistics may have broader implications in biomolecular science. PMID:12413397

  11. The Anadara trapezia transcriptome: a resource for molluscan physiological genomics.

    PubMed

    Prentis, Peter J; Pavasovic, Ana

    2014-12-01

    In this study we undertook deep sequencing of the blood cockle, Anadara trapezia, transcriptome to generate genomic resources for future functional genomics analyses. Over 27 million high quality paired end reads were assembled into 75024 contigs. Of these contigs, 29013 (38.7%) received significant BLASTx hits and gene ontology (GO) terms were assigned to 13718 of these sequences. This resource will facilitate physiological genomic studies to test the gene expression response of A. trapezia to various environmental stresses. PMID:25151889

  12. NGS-Trex: Next Generation Sequencing Transcriptome profile explorer

    PubMed Central

    2013-01-01

    Background Next-Generation Sequencing (NGS) technology has exceptionally increased the ability to sequence DNA in a massively parallel and cost-effective manner. Nevertheless, NGS data analysis requires bioinformatics skills and computational resources well beyond the possibilities of many "wet biology" laboratories. Moreover, most of projects only require few sequencing cycles and standard tools or workflows to carry out suitable analyses for the identification and annotation of genes, transcripts and splice variants found in the biological samples under investigation. These projects can take benefits from the availability of easy to use systems to automatically analyse sequences and to mine data without the preventive need of strong bioinformatics background and hardware infrastructure. Results To address this issue we developed an automatic system targeted to the analysis of NGS data obtained from large-scale transcriptome studies. This system, we named NGS-Trex (NGS Transcriptome profile explorer) is available through a simple web interface http://www.ngs-trex.org and allows the user to upload raw sequences and easily obtain an accurate characterization of the transcriptome profile after the setting of few parameters required to tune the analysis procedure. The system is also able to assess differential expression at both gene and transcript level (i.e. splicing isoforms) by comparing the expression profile of different samples. By using simple query forms the user can obtain list of genes, transcripts, splice sites ranked and filtered according to several criteria. Data can be viewed as tables, text files or through a simple genome browser which helps the visual inspection of the data. Conclusions NGS-Trex is a simple tool for RNA-Seq data analysis mainly targeted to "wet biology" researchers with limited bioinformatics skills. It offers simple data mining tools to explore transcriptome profiles of samples investigated taking advantage of NGS technologies

  13. Deep sequencing of the murine olfactory receptor neuron transcriptome.

    PubMed

    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

  14. Separating homeologs by phasing in the tetraploid wheat transcriptome

    PubMed Central

    2013-01-01

    Background The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. Results A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Conclusions Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies. PMID:23800085

  15. Comparing de novo assemblers for 454 transcriptome data

    PubMed Central

    2010-01-01

    Background Roche 454 pyrosequencing has become a method of choice for generating transcriptome data from non-model organisms. Once the tens to hundreds of thousands of short (250-450 base) reads have been produced, it is important to correctly assemble these to estimate the sequence of all the transcripts. Most transcriptome assembly projects use only one program for assembling 454 pyrosequencing reads, but there is no evidence that the programs used to date are optimal. We have carried out a systematic comparison of five assemblers (CAP3, MIRA, Newbler, SeqMan and CLC) to establish best practices for transcriptome assemblies, using a new dataset from the parasitic nematode Litomosoides sigmodontis. Results Although no single assembler performed best on all our criteria, Newbler 2.5 gave longer contigs, better alignments to some reference sequences, and was fast and easy to use. SeqMan assemblies performed best on the criterion of recapitulating known transcripts, and had more novel sequence than the other assemblers, but generated an excess of small, redundant contigs. The remaining assemblers all performed almost as well, with the exception of Newbler 2.3 (the version currently used by most assembly projects), which generated assemblies that had significantly lower total length. As different assemblers use different underlying algorithms to generate contigs, we also explored merging of assemblies and found that the merged datasets not only aligned better to reference sequences than individual assemblies, but were also more consistent in the number and size of contigs. Conclusions Transcriptome assemblies are smaller than genome assemblies and thus should be more computationally tractable, but are often harder because individual contigs can have highly variable read coverage. Comparing single assemblers, Newbler 2.5 performed best on our trial data set, but other assemblers were closely comparable. Combining differently optimal assemblies from different programs

  16. Transcriptome Analysis of the Asian Honey Bee Apis cerana cerana

    PubMed Central

    Huang, Zachary Y.; Wu, Xiao Bo; Yan, Wei Yu; Zeng, Zhi Jiang

    2012-01-01

    Background The Eastern hive honey bee, Apis cerana cerana is a native and widely bred honey bee species in China. Molecular biology research about this honey bee species is scarce, and genomic information for A. c. cerana is not currently available. Transcriptome and expression profiling data for this species are therefore important resources needed to better understand the biological mechanisms of A. c. cerana. In this study, we obtained the transcriptome information of A. c. cerana by RNA-sequencing and compared gene expression differences between queens and workers of A. c. cerana by digital gene expression (DGE) analysis. Results Using high-throughput Illumina RNA sequencing we obtained 51,581,510 clean reads corresponding to 4.64 Gb total nucleotides from a single run. These reads were assembled into 46,999 unigenes with a mean length of 676 bp. Based on a sequence similarity search against the five public databases (NR, Swissport, GO, COG, KEGG) with a cut-off E-value of 10−5 using BLASTX, a total of 24,630 unigenes were annotated with gene descriptions, gene ontology terms, or metabolic pathways. Using these transcriptome data as references we analyzed the gene expression differences between the queens and workers of A. c. cerana using a tag-based digital gene expression method. We obtained 5.96 and 5.66 million clean tags from the queen and worker samples, respectively. A total of 414 genes were differentially expressed between them, with 189 up-regulated and 225 down-regulated in queens. Conclusions Our transcriptome data provide a comprehensive sequence resource for future A. c. cerana study, establishing an important public information platform for functional genomic studies in A. c. cerana. Furthermore, the DGE data provide comprehensive gene expression information for the queens and workers, which will facilitate our understanding of the molecular mechanisms of the different physiological aspects of the two castes. PMID:23112877

  17. 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

  18. Analysis of the salivary gland transcriptome of Frankliniella occidentalis.

    PubMed

    Stafford-Banks, Candice A; Rotenberg, Dorith; Johnson, Brian R; Whitfield, Anna E; Ullman, Diane E

    2014-01-01

    Saliva is known to play a crucial role in insect feeding behavior and virus transmission. Currently, little is known about the salivary glands and saliva of thrips, despite the fact that Frankliniella occidentalis (Pergande) (the western flower thrips) is a serious pest due to its destructive feeding, wide host range, and transmission of tospoviruses. As a first step towards characterizing thrips salivary gland functions, we sequenced the transcriptome of the primary salivary glands of F. occidentalis using short read sequencing (Illumina) technology. A de novo-assembled transcriptome revealed 31,392 high quality contigs with an average size of 605 bp. A total of 12,166 contigs had significant BLASTx or tBLASTx hits (E≤1.0E-6) to known proteins, whereas a high percentage (61.24%) of contigs had no apparent protein or nucleotide hits. Comparison of the F. occidentalis salivary gland transcriptome (sialotranscriptome) against a published F. occidentalis full body transcriptome assembled from Roche-454 reads revealed several contigs with putative annotations associated with salivary gland functions. KEGG pathway analysis of the sialotranscriptome revealed that the majority (18 out of the top 20 predicted KEGG pathways) of the salivary gland contig sequences match proteins involved in metabolism. We identified several genes likely to be involved in detoxification and inhibition of plant defense responses including aldehyde dehydrogenase, metalloprotease, glucose oxidase, glucose dehydrogenase, and regucalcin. We also identified several genes that may play a role in the extra-oral digestion of plant structural tissues including β-glucosidase and pectin lyase; and the extra-oral digestion of sugars, including α-amylase, maltase, sucrase, and α-glucosidase. This is the first analysis of a sialotranscriptome for any Thysanopteran species and it provides a foundational tool to further our understanding of how thrips interact with their plant hosts and the viruses they

  19. Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome

    PubMed Central

    Gunewardena, Sumedha S.; Yoo, Byunggil; Peng, Lai; Lu, Hong; Zhong, Xiaobo; Klaassen, Curtis D.; Cui, Julia Yue

    2015-01-01

    During development, liver undergoes a rapid transition from a hematopoietic organ to a major organ for drug metabolism and nutrient homeostasis. However, little is known on a transcriptome level of the genes and RNA-splicing variants that are differentially regulated with age, and which up-stream regulators orchestrate age-specific biological functions in liver. We used RNA-Seq to interrogate the developmental dynamics of the liver transcriptome in mice at 12 ages from late embryonic stage (2-days before birth) to maturity (60-days after birth). Among 21,889 unique NCBI RefSeq-annotated genes, 9,641 were significantly expressed in at least one age, 7,289 were differently regulated with age, and 859 had multiple (> = 2) RNA splicing-variants. Factor analysis showed that the dynamics of hepatic genes fall into six distinct groups based on their temporal expression. The average expression of cytokines, ion channels, kinases, phosphatases, transcription regulators and translation regulators decreased with age, whereas the average expression of peptidases, enzymes and transmembrane receptors increased with age. The average expression of growth factors peak between Day-3 and Day-10, and decrease thereafter. We identified critical biological functions, upstream regulators, and putative transcription modules that seem to govern age-specific gene expression. We also observed differential ontogenic expression of known splicing variants of certain genes, and 1,455 novel splicing isoform candidates. In conclusion, the hepatic ontogeny of the transcriptome ontogeny has unveiled critical networks and up-stream regulators that orchestrate age-specific biological functions in liver, and suggest that age contributes to the complexity of the alternative splicing landscape of the hepatic transcriptome. PMID:26496202

  20. Analysis of the Salivary Gland Transcriptome of Frankliniella occidentalis

    PubMed Central

    Stafford-Banks, Candice A.; Rotenberg, Dorith; Johnson, Brian R.; Whitfield, Anna E.; Ullman, Diane E.

    2014-01-01

    Saliva is known to play a crucial role in insect feeding behavior and virus transmission. Currently, little is known about the salivary glands and saliva of thrips, despite the fact that Frankliniella occidentalis (Pergande) (the western flower thrips) is a serious pest due to its destructive feeding, wide host range, and transmission of tospoviruses. As a first step towards characterizing thrips salivary gland functions, we sequenced the transcriptome of the primary salivary glands of F. occidentalis using short read sequencing (Illumina) technology. A de novo-assembled transcriptome revealed 31,392 high quality contigs with an average size of 605 bp. A total of 12,166 contigs had significant BLASTx or tBLASTx hits (E≤1.0E−6) to known proteins, whereas a high percentage (61.24%) of contigs had no apparent protein or nucleotide hits. Comparison of the F. occidentalis salivary gland transcriptome (sialotranscriptome) against a published F. occidentalis full body transcriptome assembled from Roche-454 reads revealed several contigs with putative annotations associated with salivary gland functions. KEGG pathway analysis of the sialotranscriptome revealed that the majority (18 out of the top 20 predicted KEGG pathways) of the salivary gland contig sequences match proteins involved in metabolism. We identified several genes likely to be involved in detoxification and inhibition of plant defense responses including aldehyde dehydrogenase, metalloprotease, glucose oxidase, glucose dehydrogenase, and regucalcin. We also identified several genes that may play a role in the extra-oral digestion of plant structural tissues including β-glucosidase and pectin lyase; and the extra-oral digestion of sugars, including α-amylase, maltase, sucrase, and α-glucosidase. This is the first analysis of a sialotranscriptome for any Thysanopteran species and it provides a foundational tool to further our understanding of how thrips interact with their plant hosts and the viruses

  1. Transcriptomic Analysis of the Salivary Glands of an Invasive Whitefly

    PubMed Central

    Su, Yun-Lin; Li, Jun-Min; Li, Meng; Luan, Jun-Bo; Ye, Xiao-Dong; Wang, Xiao-Wei; Liu, Shu-Sheng

    2012-01-01

    Background Some species of the whitefly Bemisia tabaci complex cause tremendous losses to crops worldwide through feeding directly and virus transmission indirectly. The primary salivary glands of whiteflies are critical for their feeding and virus transmission. However, partly due to their tiny size, research on whitefly salivary glands is limited and our knowledge on these glands is scarce. Methodology/Principal Findings We sequenced the transcriptome of the primary salivary glands of the Mediterranean species of B. tabaci complex using an effective cDNA amplification method in combination with short read sequencing (Illumina). In a single run, we obtained 13,615 unigenes. The quantity of the unigenes obtained from the salivary glands of the whitefly is at least four folds of the salivary gland genes from other plant-sucking insects. To reveal the functions of the primary glands, sequence similarity search and comparisons with the whole transcriptome of the whitefly were performed. The results demonstrated that the genes related to metabolism and transport were significantly enriched in the primary salivary glands. Furthermore, we found that a number of highly expressed genes in the salivary glands might be involved in secretory protein processing, secretion and virus transmission. To identify potential proteins of whitefly saliva, the translated unigenes were put into secretory protein prediction. Finally, 295 genes were predicted to encode secretory proteins and some of them might play important roles in whitefly feeding. Conclusions/Significance: The combined method of cDNA amplification, Illumina sequencing and de novo assembly is suitable for transcriptomic analysis of tiny organs in insects. Through analysis of the transcriptome, genomic features of the primary salivary glands were dissected and biologically important proteins, especially secreted proteins, were predicted. Our findings provide substantial sequence information for the primary salivary glands

  2. Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing

    PubMed Central

    Khan, Shahid Y.; Hackett, Sean F.; Lee, Mei-Chong W.; Pourmand, Nader; Talbot, C. Conover; Riazuddin, S. Amer

    2015-01-01

    Purpose Transcriptome is the entire repertoire of transcripts present in a cell at any particular time. We undertook a next-generation whole transcriptome sequencing approach to gain insight into the transcriptional landscape of the developing mouse lens. Methods We ascertained mouse lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). The ocular tissue at each time point was maintained as two distinct pools serving as biological replicates for each developmental stage. The mRNA and small RNA libraries were paired-end sequenced on Illumina HiSeq 2000 and subsequently analyzed using bioinformatics tools. Results Mapping of mRNA and small RNA libraries generated 187.56 and 154.22 million paired-end reads, respectively. We detected a total of 14,465 genes in the mouse ocular lens at the above-mentioned six developmental stages. Of these, 46 genes exhibited a 40-fold differential (higher or lower) expression at one the five developmental stages (E18, P0, P3, P6, and P9) compared with their expression level at E15. Likewise, small RNA profiling identified 379 microRNAs (miRNAs) expressed in mouse lens at six developmental time points. Of these, 49 miRNAs manifested an 8-fold differential (higher or lower) expression at one the five developmental stages, as mentioned above compared with their expression level at E15. Conclusions We report a comprehensive profile of developing murine lens transcriptome including both mRNA and miRNA through next-generation RNA sequencing. A complete repository of the lens transcriptome of six developmental time points will be monumental in elucidating processes essential for the development of the ocular lens and maintenance of its transparency. PMID:26225632

  3. De novo transcriptome assembly of two contrasting pumpkin cultivars.

    PubMed

    Xanthopoulou, Aliki; Psomopoulos, Fotis; Ganopoulos, Ioannis; Manioudaki, Maria; Tsaftaris, Athanasios; Nianiou-Obeidat, Irini; Madesis, Panagiotis

    2016-03-01

    Cucurbita pepo (squash, pumpkin, gourd), a worldwide-cultivated vegetable of American origin, is extremely variable in fruit characteristics. However, the information associated with genes and genetic markers for pumpkin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis (RNA-Seq) of two contrasting pumpkin cultivars. Leaves and female flowers of cultivars, 'Big Moose' with large round fruits and 'Munchkin' with small round fruits, were harvested for total RNA extraction. We obtained a total of 6 GB (Big Moose; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056882) and 5 GB (Munchkin; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056883) sequence data (NCBI SRA database SRX1502732 and SRX1502735, respectively), which correspond to 18,055,786 and 14,824,292 150-base reads. After quality assessment, the clean sequences where 17,995,932 and 14,774,486 respectively. The numbers of total transcripts for 'Big Moose' and 'Munchkin' were 84,727 and 68,051, respectively. TransDecoder identified possible coding regions in assembled transcripts. This study provides transcriptome data for two contrasting pumpkin cultivars, which might be useful for genetic marker development and comparative transcriptome analyses. PMID:26981408

  4. De novo transcriptome assembly of two contrasting pumpkin cultivars

    PubMed Central

    Xanthopoulou, Aliki; Psomopoulos, Fotis; Ganopoulos, Ioannis; Manioudaki, Maria; Tsaftaris, Athanasios; Nianiou-Obeidat, Irini; Madesis, Panagiotis

    2016-01-01

    Cucurbita pepo (squash, pumpkin, gourd), a worldwide-cultivated vegetable of American origin, is extremely variable in fruit characteristics. However, the information associated with genes and genetic markers for pumpkin is very limited. In order to identify new genes and to develop genetic markers, we performed a transcriptome analysis (RNA-Seq) of two contrasting pumpkin cultivars. Leaves and female flowers of cultivars, ‘Big Moose’ with large round fruits and ‘Munchkin’ with small round fruits, were harvested for total RNA extraction. We obtained a total of 6 GB (Big Moose; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056882) and 5 GB (Munchkin; http://www.ncbi.nlm.nih.gov/Traces/sra/?run=SRR3056883) sequence data (NCBI SRA database SRX1502732 and SRX1502735, respectively), which correspond to 18,055,786 and 14,824,292 150-base reads. After quality assessment, the clean sequences where 17,995,932 and 14,774,486 respectively. The numbers of total transcripts for ‘Big Moose’ and ‘Munchkin’ were 84,727 and 68,051, respectively. TransDecoder identified possible coding regions in assembled transcripts. This study provides transcriptome data for two contrasting pumpkin cultivars, which might be useful for genetic marker development and comparative transcriptome analyses. PMID:26981408

  5. Genetic basis of transcriptome diversity in Drosophila melanogaster

    PubMed Central

    Huang, Wen; Carbone, Mary Anna; Magwire, Michael M.; Peiffer, Jason A.; Lyman, Richard F.; Stone, Eric A.; Anholt, Robert R. H.; Mackay, Trudy F. C.

    2015-01-01

    Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive but is essential for predicting adaptive evolution, for selecting agriculturally important animals and crops, and for personalized medicine. Gene expression may provide a link between variation in DNA sequence and organismal phenotypes, and its abundance can be measured efficiently and accurately. Here we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP), increasing the annotated Drosophila transcriptome by 11%, including thousands of novel transcribed regions (NTRs). We found that 42% of the Drosophila transcriptome is genetically variable in males and females, including the NTRs, and is organized into modules of genetically correlated transcripts. We found that NTRs often were negatively correlated with the expression of protein-coding genes, which we exploited to annotate NTRs functionally. We identified regulatory variants for the mean and variance of gene expression, which have largely independent genetic control. Expression quantitative trait loci (eQTLs) for the mean, but not for the variance, of gene expression were concentrated near genes. Notably, the variance eQTLs often interacted epistatically with local variants in these genes to regulate gene expression. This comprehensive characterization of population-scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation. PMID:26483487

  6. Quantitative developmental transcriptomes of the Mediterranean sea urchin Paracentrotus lividus.

    PubMed

    Gildor, Tsvia; Malik, Assaf; Sher, Noa; Avraham, Linor; Ben-Tabou de-Leon, Smadar

    2016-02-01

    Embryonic development progresses through the timely activation of thousands of differentially activated genes. Quantitative developmental transcriptomes provide the means to relate global patterns of differentially expressed genes to the emerging body plans they generate. The sea urchin is one of the classic model systems for embryogenesis and the models of its developmental gene regulatory networks are of the most comprehensive of their kind. Thus, the sea urchin embryo is an excellent system for studies of its global developmental transcriptional profiles. Here we produced quantitative developmental transcriptomes of the sea urchin Paracentrotus lividus (P. lividus) at seven developmental stages from the fertilized egg to prism stage. We generated de-novo reference transcriptome and identified 29,817 genes that are expressed at this time period. We annotated and quantified gene expression at the different developmental stages and confirmed the reliability of the expression profiles by QPCR measurement of a subset of genes. The progression of embryo development is reflected in the observed global expression patterns and in our principle component analysis. Our study illuminates the rich patterns of gene expression that participate in sea urchin embryogenesis and provide an essential resource for further studies of the dynamic expression of P. lividus genes. PMID:26671332

  7. Cold acclimation wholly reorganizes the Drosophila melanogaster transcriptome and metabolome.

    PubMed

    MacMillan, Heath A; Knee, Jose M; Dennis, Alice B; Udaka, Hiroko; Marshall, Katie E; Merritt, Thomas J S; Sinclair, Brent J

    2016-01-01

    Cold tolerance is a key determinant of insect distribution and abundance, and thermal acclimation can strongly influence organismal stress tolerance phenotypes, particularly in small ectotherms like Drosophila. However, there is limited understanding of the molecular and biochemical mechanisms that confer such impressive plasticity. Here, we use high-throughput mRNA sequencing (RNA-seq) and liquid chromatography - mass spectrometry (LC-MS) to compare the transcriptomes and metabolomes of D. melanogaster acclimated as adults to warm (rearing) (21.5 °C) or cold conditions (6 °C). Cold acclimation improved cold tolerance and led to extensive biological reorganization: almost one third of the transcriptome and nearly half of the metabolome were differentially regulated. There was overlap in the metabolic pathways identified via transcriptomics and metabolomics, with proline and glutathione metabolism being the most strongly-supported metabolic pathways associated with increased cold tolerance. We discuss several new targets in the study of insect cold tolerance (e.g. dopamine signaling and Na(+)-driven transport), but many previously identified candidate genes and pathways (e.g. heat shock proteins, Ca(2+) signaling, and ROS detoxification) were also identified in the present study, and our results are thus consistent with and extend the current understanding of the mechanisms of insect chilling tolerance. PMID:27357258

  8. Transcriptome dynamics of the microRNA inhibition response.

    PubMed

    Wen, Jiayu; Leucci, Elenora; Vendramin, Roberto; Kauppinen, Sakari; Lund, Anders H; Krogh, Anders; Parker, Brian J

    2015-07-27

    We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line-the first such dynamic study of the microRNA inhibition response-revealing both general and specific aspects of the physiological response. We show miR-9 inhibition inducing a multiphasic transcriptome response, with a direct target perturbation before 4 h, earlier than previously reported, amplified by a downstream peak at ∼32 h consistent with an indirect response due to secondary coherent regulation. Predictive modelling indicates a major role for miR-9 in post-transcriptional control of RNA processing and RNA binding protein regulation. Cluster analysis identifies multiple co-regulated gene regulatory modules. Functionally, we observe a shift over time from mRNA processing at early time points to translation at later time points. We validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies. PMID:26089393

  9. Spatial organization shapes the turnover of a bacterial transcriptome

    PubMed Central

    Moffitt, Jeffrey R; Pandey, Shristi; Boettiger, Alistair N; Wang, Siyuan; Zhuang, Xiaowei

    2016-01-01

    Spatial organization of the transcriptome has emerged as a powerful means for regulating the post-transcriptional fate of RNA in eukaryotes; however, whether prokaryotes use RNA spatial organization as a mechanism for post-transcriptional regulation remains unclear. Here we used super-resolution microscopy to image the E. coli transcriptome and observed a genome-wide spatial organization of RNA: mRNAs encoding inner-membrane proteins are enriched at the membrane, whereas mRNAs encoding outer-membrane, cytoplasmic and periplasmic proteins are distributed throughout the cytoplasm. Membrane enrichment is caused by co-translational insertion of signal peptides recognized by the signal-recognition particle. Time-resolved RNA-sequencing revealed that degradation rates of inner-membrane-protein mRNAs are on average greater that those of the other mRNAs and that this selective destabilization of inner-membrane-protein mRNAs is abolished by dissociating the RNA degradosome from the membrane. Together, these results demonstrate that the bacterial transcriptome is spatially organized and suggest that this organization shapes the post-transcriptional dynamics of mRNAs. DOI: http://dx.doi.org/10.7554/eLife.13065.001 PMID