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Sample records for auxin-responsive transcriptome downstream

  1. Comprehensive Transcriptome Analysis of Auxin Responses in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Ivan A.Paponov; Martina Paponov; William Teale; Margit Menges; Sohini Chakrabortee; James A.H.Murray; Klaus Palme

    2008-01-01

    In plants,the hormone auxin shapes gene expression to regulate growth and development.Despite the detailed characterization of auxin-inducible genes,a comprehensive overview of the temporal and spatial dynamics of auxinregulated gene expression is lacking.Here,we analyze transcriptome data from many publicly available Arabidopsis profiling experiments and assess tissue-specific gene expression both in response to auxin concentration and exposure time and in relation to other plant growth regulators.Our analysis shows that the primary response to auxin over a wide range of auxin application conditions and in specific tissues comprises almost exclusively the up-regulation of genes and identifies the most robust auxin marker genes.Tissue-specific auxin responses correlate with differential expression of Aux/IAA genes and the subsequent regulation of context- and sequence-specific patterns of gene expression.Changes in transcript levels were consistent with a distinct sequence of conjugation,increased transport capacity and down-regulation of biosynthesis in the temperance of high cellular auxin concentrations.Our data show that auxin regulates genes associated with the biosynthesis,catabolism and signaling pathways of other phytohormones.We present a transcriptional overview of the auxin response.Specific interactions between auxin and other phytohormones are highlighted,particularly the regulation of their metabolism.Our analysis provides a roadmap for auxin-dependent processes that underpins the concept of an 'auxin code'-a tissue-specific fingerprint of gene expression that initiates specific developmental processes.

  2. Transcriptome analysis of the rhizosphere bacterium Azospirillum brasilense reveals an extensive auxin response.

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    Van Puyvelde, Sandra; Cloots, Lore; Engelen, Kristof; Das, Frederik; Marchal, Kathleen; Vanderleyden, Jos; Spaepen, Stijn

    2011-05-01

    The rhizosphere bacterium Azospirillum brasilense produces the auxin indole-3-acetic acid (IAA) through the indole-3-pyruvate pathway. As we previously demonstrated that transcription of the indole-3-pyruvate decarboxylase (ipdC) gene is positively regulated by IAA, produced by A. brasilense itself or added exogenously, we performed a microarray analysis to study the overall effects of IAA on the transcriptome of A. brasilense. The transcriptomes of A. brasilense wild-type and the ipdC knockout mutant, both cultured in the absence and presence of exogenously added IAA, were compared.Interfering with the IAA biosynthesis/homeostasis in A. brasilense through inactivation of the ipdC gene or IAA addition results in much broader transcriptional changes than anticipated. Based on the multitude of changes observed by comparing the different transcriptomes, we can conclude that IAA is a signaling molecule in A. brasilense. It appears that the bacterium, when exposed to IAA, adapts itself to the plant rhizosphere, by changing its arsenal of transport proteins and cell surface proteins. A striking example of adaptation to IAA exposure, as happens in the rhizosphere, is the upregulation of a type VI secretion system (T6SS) in the presence of IAA. The T6SS is described as specifically involved in bacterium-eukaryotic host interactions. Additionally, many transcription factors show an altered regulation as well, indicating that the regulatory machinery of the bacterium is changing.

  3. Auxin response factors.

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    Chandler, John William

    2016-05-01

    Auxin signalling involves the activation or repression of gene expression by a class of auxin response factor (ARF) proteins that bind to auxin response elements in auxin-responsive gene promoters. The release of ARF repression in the presence of auxin by the degradation of their cognate auxin/indole-3-acetic acid repressors forms a paradigm of transcriptional response to auxin. However, this mechanism only applies to activating ARFs, and further layers of complexity of ARF function and regulation are being revealed, which partly reflect their highly modular domain structure. This review summarizes our knowledge concerning ARF binding site specificity, homodimer and heterodimer multimeric ARF association and cooperative function and how activator ARFs activate target genes via chromatin remodelling and evolutionary information derived from phylogenetic comparisons from ARFs from diverse species. ARFs are regulated in diverse ways, and their importance in non-auxin-regulated pathways is becoming evident. They are also embedded within higher-order transcription factor complexes that integrate signalling pathways from other hormones and in response to the environment. The ways in which new information concerning ARFs on many levels is causing a revision of existing paradigms of auxin response are discussed.

  4. Auxin response under osmotic stress.

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    Naser, Victoria; Shani, Eilon

    2016-08-01

    The phytohormone auxin (indole-3-acetic acid, IAA) is a small organic molecule that coordinates many of the key processes in plant development and adaptive growth. Plants regulate the auxin response pathways at multiple levels including biosynthesis, metabolism, transport and perception. One of the most striking aspects of plant plasticity is the modulation of development in response to changing growth environments. In this review, we explore recent findings correlating auxin response-dependent growth and development with osmotic stresses. Studies of water deficit, dehydration, salt, and other osmotic stresses point towards direct and indirect molecular perturbations in the auxin pathway. Osmotic stress stimuli modulate auxin responses by affecting auxin biosynthesis (YUC, TAA1), transport (PIN), perception (TIR/AFB, Aux/IAA), and inactivation/conjugation (GH3, miR167, IAR3) to coordinate growth and patterning. In turn, stress-modulated auxin gradients drive physiological and developmental mechanisms such as stomata aperture, aquaporin and lateral root positioning. We conclude by arguing that auxin-mediated growth inhibition under abiotic stress conditions is one of the developmental and physiological strategies to acclimate to the changing environment.

  5. Research Progresses on Auxin Response Factors

    Institute of Scientific and Technical Information of China (English)

    Hai-Bin Wei; Bai-Ming Cui; Yan-Li Ren; Juan-Hua Li; Wei-Bin Liao; Nan-Fei Xu; Ming Peng

    2006-01-01

    Auxin response factors (ARFs), a family of transcription factors, have been discovered recently. The ARFs bind specifically to the auxin response elements (AuxREs) within promoters of primary auxin responsive genes and function as activators or repressors. The ARFs contain three domains, namely a conserved Nterminal DNA-binding domain, a non-conserved middle region, and a conserved C-terminal dirnerization domain. The ARFs can form a protein complex with auxin/indoleacetic acid through homodimerization or heterodimerization. The particular protein-protein interaction may play a key role in modulating the expression of early auxin responsive genes. The identification of ARF mutations in Arabidopsis helps to demonstrate/dissect the function of ARFs in the normal growth and development of plants. Phylogenetic analysis also reveals some interesting protein evolution points in the ARF family.

  6. Composite structure of auxin response elements.

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    Ulmasov, T; Liu, Z B; Hagen, G; Guilfoyle, T J

    1995-10-01

    The auxin-responsive soybean GH3 gene promoter is composed of multiple auxin response elements (AuxREs), and each AuxRE contributes incrementally to the strong auxin inducibility to the promoter. Two independent AuxREs of 25 bp (D1) and 32 bp (D4) contain the sequence TGTCTC. Results presented here show that the TGTCTC element in D1 and D4 is required but not sufficient for auxin inducibility in carrot protoplast transient expression assays. Additional nucleotides upstream of TGTCTC are also required for auxin inducibility. These upstream sequences showed constitutive activity and no auxin inducibility when part or all of the TGTCTC element was mutated or deleted. In D1, the constitutive element overlaps the 5' portion of TGTCTC; in D4, the constitutive element is separated from TGTCTC. An 11-bp element in D1, CCTCGTGTCTC, conferred auxin inducibility to a minimal cauliflower mosaic virus 35S promoter in transgenic tobacco seedlings as well as in carrot protoplasts (i.e., transient expression assays). Both constitutive elements bound specifically to plant nuclear proteins, and the constitutive element in D1 bound to a recombinant soybean basic leucine zipper transcription factor with G-box specificity. To demonstrate further the composite nature of AuxREs and the ability of the TGTCTC element to confer auxin inducibility, we created a novel AuxRE by placing a yeast GAL4 DNA binding site adjacent to the TGTCTC element. Expression of a GAL4-c-Rel transactivator in the presence of this novel AuxRE resulted in auxin-inducible expression. Our results indicate that at least some AuxREs have a composite structure consisting of a constitutive element adjacent to a conserved TGTCTC element that confers auxin inducibility.

  7. Solanum lycopersicum AUXIN RESPONSE FACTOR 9 regulates cell division activity during early tomato fruit development

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    de Jong, Maaike; Wolters-Arts, Mieke; Schimmel, Bernardus C. J.; Stultiens, Catharina L. M.; de Groot, Peter F. M.; Powers, Stephen J.; Tikunov, Yury M.; Bovy, Arnoud G.; Mariani, Celestina; Vriezen, Wim H.; Rieu, Ivo

    2015-01-01

    The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early fruit development in tomato is Solanum lycopersicum AUXIN RESPONSE FACTOR 9 (SlARF9). Here, the functional analysis of this ARF is described. SlARF9 expression was found to be auxin-responsive and SlARF9 mRNA levels were high in the ovules, placenta, and pericarp of pollinated ovaries, but also in other plant tissues with high cell division activity, such as the axillary meristems and root meristems. Transgenic plants with increased SlARF9 mRNA levels formed fruits that were smaller than wild-type fruits because of reduced cell division activity, whereas transgenic lines in which SlARF9 mRNA levels were reduced showed the opposite phenotype. The expression analysis, together with the phenotype of the transgenic lines, suggests that, in tomato, ARF9 negatively controls cell division during early fruit development. PMID:25883382

  8. Genome-wide identification and expression analysis of auxin response factor gene family in Medicago truncatula

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    Chenjia eShen

    2015-02-01

    Full Text Available Auxin response factors (ARFs bind specifically to auxin response elements (AuxREs in the promoters of down-stream target genes and play roles in plant responses to diverse environmental factors. Using the latest updated Medicago truncatula reference genome sequence, a comprehensive characterization and analysis of 24 MtARF genes were performed. To uncover the basic information and functions of MtARF genes during symbiosis, we analyze the expression patterns of MtARF genes during the early phase of Sinorhizobium meliloti infection. The systematic analysis indicated that MtARF gene expressions were involved in the symbiosis processes. Furthermore, the roles of MtARF-mediated auxin signaling in symbiosis were tested in the infection resistant mutant (dmi3. The expression responses of MtARFs to S. meliloti infection were attenuated in the mutant compared to wild-type A17. In summary, our results shed that the MtARF gene expressions was involved in responses to S. meliloti infection, which may play an essential role in the regulation of nodule formation.

  9. Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis

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    Daniel Spies

    2015-01-01

    Full Text Available Analysis of gene expression has contributed to a plethora of biological and medical research studies. Microarrays have been intensively used for the profiling of gene expression during diverse developmental processes, treatments and diseases. New massively parallel sequencing methods, often named as RNA-sequencing (RNA-seq are extensively improving our understanding of gene regulation and signaling networks. Computational methods developed originally for microarrays analysis can now be optimized and applied to genome-wide studies in order to have access to a better comprehension of the whole transcriptome. This review addresses current challenges on RNA-seq analysis and specifically focuses on new bioinformatics tools developed for time series experiments. Furthermore, possible improvements in analysis, data integration as well as future applications of differential expression analysis are discussed.

  10. Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis

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    Spies, Daniel; Ciaudo, Constance

    2015-01-01

    Analysis of gene expression has contributed to a plethora of biological and medical research studies. Microarrays have been intensively used for the profiling of gene expression during diverse developmental processes, treatments and diseases. New massively parallel sequencing methods, often named as RNA-sequencing (RNA-seq) are extensively improving our understanding of gene regulation and signaling networks. Computational methods developed originally for microarrays analysis can now be optimized and applied to genome-wide studies in order to have access to a better comprehension of the whole transcriptome. This review addresses current challenges on RNA-seq analysis and specifically focuses on new bioinformatics tools developed for time series experiments. Furthermore, possible improvements in analysis, data integration as well as future applications of differential expression analysis are discussed. PMID:26430493

  11. The role of SEUSS in auxin response and floral organ patterning.

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    Pfluger, Jennifer; Zambryski, Patricia

    2004-10-01

    Genetic and physiological analyses implicate auxin flux in patterning, initiation and growth of floral organs. Within the Arabidopsis flower, the ETTIN/ARF3 transcription factor responds to auxin to effect perianth organ number and reproductive organ differentiation. This work describes a modifier of ettin that causes filamentous, mispositioned outer whorl organs and reduced numbers of malformed stamens in the double mutant. The modifier was discovered to be a new allele of the seuss (seu) mutant. SEU encodes a novel protein that is predicted to transcriptionally co-repress the AGAMOUS floral organ identity gene. The effects of seu on ett are shown to be independent of the SEU-AG pathway. Furthermore, morphological, physiological and genetic evidence implicate SEU in auxin-regulated growth and development. seu has a pleiotropic phenotype that includes reductions in several classic auxin responses such as apical dominance, lateral root initiation, sensitivity to exogenous auxin and activation of the DR5 auxin response reporter. seu displays a synergistic interaction with the auxin response mutant pinoid, producing flowers with few outer whorl organs. Collectively, these data suggest that SEU is a novel factor affecting auxin response. A model is proposed in which SEU functions jointly with ETT in auxin response to promote floral organ patterning and growth.

  12. Isolation of transcription factors binding auxin response elements using a yeast one-hybrid system

    Institute of Scientific and Technical Information of China (English)

    齐眉; 黄美娟; 陈凡

    2002-01-01

    Plant hormones play an important role during higher plant embryogenesis. Auxin is central to the development of vascular tissues, formation of lateral and adventitious roots, control of apical dominance, and tropic responses. Auxin response element (AuxRE), present in the promoters of many auxin-induced genes, can confer auxin responsiveness. Using carrot somatic embryo under specific developmental phase, a cDNA expression library was constructed. Several plasmids were recombined containing the tetramer of AuxRE as a bait. After screening by a yeast one-hy- brid system, one positive clone was confirmed and characterized. Electrophoretic mobility shift assay showed that AxRF1 protein expressed in yeast cell could bind AuxRE in vitro. It suggests that AxRF1 participates in regulation of the expression of auxin responsive gene during carrot somatic embryogenesis.

  13. Transcriptomic-based effects monitoring for endocrine active chemicals: Assessing relative contribution of treated wastewater to downstream pollution

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    The present study investigated whether combining of targeted analytical chemistry methods with unsupervised, data-rich methodologies (i.e. transcriptomics) can be utilized to evaluate relative contributions of wastewater treatment plant (WWTP) effluents to biological effects. The...

  14. ARF-Aux/IAA interactions through domain III/IV are not strictly required for auxin-responsive gene expression

    OpenAIRE

    2013-01-01

    Auxin response factors (ARFs), together with auxin/indole acetic acid proteins (Aux/IAAs), are transcription factors that play key roles in regulating auxin-responsive transcription in plants. Current models for auxin signaling predict that auxin response is dependent on ARF-Aux/IAA interactions mediated by the related protein-protein interaction domain (i.e., referred to as the CTD) found in the ARF and Aux/IAA C-terminal regions. When auxin concentrations in a cell are low, ARF activators r...

  15. Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato.

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    Hao, Yanwei; Hu, Guojian; Breitel, Dario; Liu, Mingchun; Mila, Isabelle; Frasse, Pierre; Fu, Yongyao; Aharoni, Asaph; Bouzayen, Mondher; Zouine, Mohamed

    2015-12-01

    Ethylene is the main regulator of climacteric fruit ripening, by contrast the putative role of other phytohormones in this process remains poorly understood. The present study brings auxin signaling components into the mechanism regulating tomato fruit ripening through the functional characterization of Auxin Response Factor2 (SlARF2) which encodes a downstream component of auxin signaling. Two paralogs, SlARF2A and SlARF2B, are found in the tomato genome, both displaying a marked ripening-associated expression but distinct responsiveness to ethylene and auxin. Down-regulation of either SlARF2A or SlARF2B resulted in ripening defects while simultaneous silencing of both genes led to severe ripening inhibition suggesting a functional redundancy among the two ARFs. Tomato fruits under-expressing SlARF2 produced less climacteric ethylene and exhibited a dramatic down-regulation of the key ripening regulators RIN, CNR, NOR and TAGL1. Ethylene treatment failed to reverse the non-ripening phenotype and the expression of ethylene signaling and biosynthesis genes was strongly altered in SlARF2 down-regulated fruits. Although both SlARF proteins are transcriptional repressors the data indicate they work as positive regulators of tomato fruit ripening. Altogether, the study defines SlARF2 as a new component of the regulatory network controlling the ripening process in tomato.

  16. Auxin Response Factor SlARF2 Is an Essential Component of the Regulatory Mechanism Controlling Fruit Ripening in Tomato.

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    Yanwei Hao

    2015-12-01

    Full Text Available Ethylene is the main regulator of climacteric fruit ripening, by contrast the putative role of other phytohormones in this process remains poorly understood. The present study brings auxin signaling components into the mechanism regulating tomato fruit ripening through the functional characterization of Auxin Response Factor2 (SlARF2 which encodes a downstream component of auxin signaling. Two paralogs, SlARF2A and SlARF2B, are found in the tomato genome, both displaying a marked ripening-associated expression but distinct responsiveness to ethylene and auxin. Down-regulation of either SlARF2A or SlARF2B resulted in ripening defects while simultaneous silencing of both genes led to severe ripening inhibition suggesting a functional redundancy among the two ARFs. Tomato fruits under-expressing SlARF2 produced less climacteric ethylene and exhibited a dramatic down-regulation of the key ripening regulators RIN, CNR, NOR and TAGL1. Ethylene treatment failed to reverse the non-ripening phenotype and the expression of ethylene signaling and biosynthesis genes was strongly altered in SlARF2 down-regulated fruits. Although both SlARF proteins are transcriptional repressors the data indicate they work as positive regulators of tomato fruit ripening. Altogether, the study defines SlARF2 as a new component of the regulatory network controlling the ripening process in tomato.

  17. De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of 'Pre-miRNAs' of black pepper.

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    Nisha Joy

    Full Text Available Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L., an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs. We used the array of transcripts generated, for the in silico prediction and detection of '43 pre-miRNA candidates bearing different types of SSR motifs'. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted 'pre-miRNA candidates bearing SSRs'. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted 'pre-miRNA candidates'. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of 'tandem repeats' in miRNAs.

  18. Dynamic Regulation of Auxin Response during Rice Development Revealed by Newly Established Hormone Biosensor Markers

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    Yang, Jing; Yuan, Zheng; Meng, Qingcai; Huang, Guoqiang; Périn, Christophe; Bureau, Charlotte; Meunier, Anne-Cécile; Ingouff, Mathieu; Bennett, Malcolm J.; Liang, Wanqi; Zhang, Dabing

    2017-01-01

    The hormone auxin is critical for many plant developmental processes. Unlike the model eudicot plant Arabidopsis (Arabidopsis thaliana), auxin distribution and signaling in rice tissues has not been systematically investigated due to the absence of suitable auxin response reporters. In this study we observed the conservation of auxin signaling components between Arabidopsis and model monocot crop rice (Oryza sativa), and generated complementary types of auxin biosensor constructs, one derived from the Aux/IAA-based biosensor DII-VENUS but constitutively driven by maize ubiquitin-1 promoter, and the other termed DR5-VENUS in which a synthetic auxin-responsive promoter (DR5rev) was used to drive expression of the yellow fluorescent protein (YFP). Using the obtained transgenic lines, we observed that during the vegetative development, accumulation of DR5-VENUS signal was at young and mature leaves, tiller buds and stem base. Notably, abundant DR5-VENUS signals were observed in the cytoplasm of cortex cells surrounding lateral root primordia (LRP) in rice. In addition, auxin maxima and dynamic re-localization were seen at the initiation sites of inflorescence and spikelet primordia including branch meristems (BMs), female and male organs. The comparison of these observations among Arabidopsis, rice and maize suggests the unique role of auxin in regulating rice lateral root emergence and reproduction. Moreover, protein localization of auxin transporters PIN1 homologs and GFP tagged OsAUX1 overlapped with DR5-VENUS during spikelet development, helping validate these auxin response reporters are reliable markers in rice. This work firstly reveals the direct correspondence between auxin distribution and rice reproductive and root development at tissue and cellular level, and provides high-resolution auxin tools to probe fundamental developmental processes in rice and to establish links between auxin, development and agronomical traits like yield or root architecture. PMID

  19. An auxin-responsive endogenous peptide regulates root development in Arabidopsis.

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    Yang, Fengxi; Song, Yu; Yang, Hao; Liu, Zhibin; Zhu, Genfa; Yang, Yi

    2014-07-01

    Auxin plays critical roles in root formation and development. The components involved in this process, however, are not well understood. Here, we newly identified a peptide encoding gene, auxin-responsive endogenous polypeptide 1 (AREP1), which is induced by auxin, and mediates root development in Arabidopsis. Expression of AREP1 was specific to the cotyledon and to root and shoot meristem tissues. Amounts of AREP1 transcripts and AREP1-green fluorescent protein fusion proteins were elevated in response to indoleacetic acid treatment. Suppression of AREP1 through RNAi silencing resulted in reduction of primary root length, increase of lateral root number, and expansion of adventitious roots, compared to the observations in wild-type plants in the presence of auxin. By contrast, transgenic plants overexpressing AREP1 showed enhanced growth of the primary root under auxin treatment. Additionally, root morphology, including lateral root number and adventitious roots, differed greatly between transgenic and wild-type plants. Further analysis indicated that the expression of auxin-responsive genes, such as IAA3, IAA7, IAA17, GH3.2, GH3.3, and SAUR-AC1, was significantly higher in AREP1 RNAi plants, and was slightly lower in AREP1 overexpressing plants than in wild-type plants. These results suggest that the novel endogenous peptide AREP1 plays an important role in the process of auxin-mediated root development.

  20. Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas

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    Sun, Yanwei; Wang, Chunming; Wang, Ning; Jiang, Xiyuan; Mao, Huizhu; Zhu, Changxiang; Wen, Fujiang; Wang, Xianghua; Lu, Zhijun; Yue, Genhua; Xu, Zengfu; Ye, Jian

    2017-01-01

    Seed size is a major determinant of seed yield but few is known about the genetics controlling of seed size in plants. Phytohormones cytokinin and brassinosteroid were known to be involved in the regulation of herbaceous plant seed development. Here we identified a homolog of Auxin Response Factor 19 (JcARF19) from a woody plant Jatropha curcas and genetically demonstrated its functions in controlling seed size and seed yield. Through Virus Induced Gene Silencing (VIGS), we found that JcARF19 was a positive upstream modulator in auxin signaling and may control plant organ size in J. curcas. Importantly, transgenic overexpression of JcARF19 significantly increased seed size and seed yield in plants Arabidopsis thaliana and J. curcas, indicating the importance of auxin pathway in seed yield controlling in dicot plants. Transcripts analysis indicated that ectopic expression of JcARF19 in J. curcas upregulated auxin responsive genes encoding essential regulators in cell differentiation and cytoskeletal dynamics of seed development. Our data suggested the potential of improving seed traits by precisely engineering auxin signaling in woody perennial plants. PMID:28102350

  1. An auxin-responsive endogenous peptide regulates root development in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    Fengxi Yang; Yu Song; Hao Yang; Zhibin Liu; Genfa Zhu; Yi Yang

    2014-01-01

    Auxin plays critical roles in root formation and development. The components involved in this process, however, are not well understood. Here, we newly identified a peptide encoding gene, auxin-responsive endogenous polypeptide 1 (AREP1), which is induced by auxin, and mediates root development in Arabidopsis. Expression of AREP1 was specific to the cotyledon and to root and shoot meristem tissues. Amounts of AREP1 transcripts and AREP1-green fluorescent protein fusion proteins were elevated in response to indoleacetic acid treatment. Suppression of AREP1 through RNAi silencing resulted in reduction of primary root length, increase of lateral root number, and expansion of adventitious roots, compared to the observations in wild-type plants in the presence of auxin. By contrast, transgenic plants overexpressing AREP1 showed enhanced growth of the primary root under auxin treatment. Additionally, rootmorphology, including lateral root number and adventitious roots, differed greatly between transgenic and wildtype plants. Further analysis indicated that the expression of auxin-responsive genes, such as IAA3, IAA7, IAA17, GH3.2, GH3.3, and SAUR-AC1, was significantly higher in AREP1 RNAi plants, and was slightly lower in AREP1 overexpressing plants than in wildtype plants. These results suggest that the novel endogenous peptide AREP1 plays an important role in the process of auxinmediated root development.

  2. Misregulation of AUXIN RESPONSE FACTOR 8 underlies the developmental abnormalities caused by three distinct viral silencing suppressors in Arabidopsis.

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    Florence Jay

    2011-05-01

    Full Text Available In Arabidopsis, micro (miRNAs and trans-acting (ta-siRNAs synthesized directly or indirectly through the DICER-LIKE-1 (DCL1 ribonuclease have roles in patterning and hormonal responses, while DCL2,3,4-dependent small-interfering (siRNAs are mainly involved in silencing of transposable elements and antiviral defense. Viral suppressors of RNA silencing (VSRs produced by phytoviruses to counter plant defense may perturb plant developmental programs because of the collision of their inhibitory effects with the regulatory action of endogenous miRNAs and ta-siRNAs. This could explain the similar developmental aberrations displayed by Arabidopsis miRNA/ta-siRNA pathway mutants, including dcl1, and by some VSR-expressing plants. Nonetheless, the molecular bases for these morphological aberrations have remained mysterious, and their contribution to viral disease symptoms/virulence unexplored. The extent of VSR inhibitory actions to other types of endogenous small RNAs remains also unclear. Here, we present an in-depth analysis of transgenic Arabidopsis expressing constitutively HcPro, P19 and P15, three unrelated VSRs. We show that VSR expression has comparable, yet modest effects on known miRNA and ta-siRNA target RNA levels, similar to those observed using an hypomorphic dcl1 mutation. However, by combining results of transcriptome studies with deep-sequencing data from immuno-precipitated small RNAs, additional, novel endogenous targets of miRNA and ta-siRNA were identified, unraveling an unsuspected complexity in the origin and scope-of-action of these molecules. Other stringent analyses pinpointed misregulation of the miR167 target AUXIN RESPONSE FACTOR 8 (ARF8 as a major cause for the developmental aberrations exhibited by VSR transgenic plants, but also for the phenotypes induced during normal viral infection caused by the HcPro-encoding Turnip mosaic virus (TuMV. Neither RNA silencing, its suppression by VSRs, nor the virulence/accumulation of Tu

  3. Oligogalacturonide-auxin antagonism does not require posttranscriptional gene silencing or stabilization of auxin response repressors in Arabidopsis.

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    Savatin, Daniel V; Ferrari, Simone; Sicilia, Francesca; De Lorenzo, Giulia

    2011-11-01

    α-1-4-Linked oligogalacturonides (OGs) derived from plant cell walls are a class of damage-associated molecular patterns and well-known elicitors of the plant immune response. Early transcript changes induced by OGs largely overlap those induced by flg22, a peptide derived from bacterial flagellin, a well-characterized microbe-associated molecular pattern, although responses diverge over time. OGs also regulate growth and development of plant cells and organs, due to an auxin-antagonistic activity. The molecular basis of this antagonism is still unknown. Here we show that, in Arabidopsis (Arabidopsis thaliana), OGs inhibit adventitious root formation induced by auxin in leaf explants as well as the expression of several auxin-responsive genes. Genetic, biochemical, and pharmacological experiments indicate that inhibition of auxin responses by OGs does not require ethylene, jasmonic acid, and salicylic acid signaling and is independent of RESPIRATORY BURST OXIDASE HOMOLOGUE D-mediated reactive oxygen species production. Free indole-3-acetic acid levels are not noticeably altered by OGs. Notably, OG- as well as flg22-auxin antagonism does not involve any of the following mechanisms: (1) stabilization of auxin-response repressors; (2) decreased levels of auxin receptor transcripts through the action of microRNAs. Our results suggest that OGs and flg22 antagonize auxin responses independently of Aux/Indole-3-Acetic Acid repressor stabilization and of posttranscriptional gene silencing.

  4. Identification of auxin responsive genes in Arabidopsis by cDNA array

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The plant hormone auxin influences a variety of developmental and physiological processes. But the mechanism of its action is quite unclear. In order to identify and analyze the expression of auxin responsive genes, a cDNA array approach was used to screen for genes with altered expression from Arabidopsis suspension culture after IAA treatment and was identified 50 differentially expressed genes from 13824 cDNA clones. These genes were related to signal transduction, stress responses, senescence, photosynthesis, protein biosynthesis and transportation. The results provide the molecular evidence that auxin influences a variety of physiological processes and pave a way for further investigation of the mechanism of auxin action. Furthermore,we found that the expression of a ClpC (regulation subunit of Clp protease) was repressed by exogenous auxin, but increased in dark-induced senescing leaves. This suggests that ClpC may be a senescence-associated gene and can be regulated by auxin.

  5. An auxin responsive CLE gene regulates shoot apical meristem development in Arabidopsis

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    Hongyan eGuo

    2015-05-01

    Full Text Available Plant hormone auxin regulates most, if not all aspects of plant growth and development, including lateral root formation, organ pattering, apical dominance and tropisms. Peptide hormones are peptides with hormone activities. Some of the functions of peptide hormones in regulating plant growth and development are similar to that of auxin, however, the relationship between auxin and peptide hormones remains largely unknown. Here we report the identification of OsCLE48, a rice (Oryza sativa CLE (CLAVATA3/ENDOSPERM SURROUNDING REGION gene, as an auxin response gene, and the functional characterization of OsCLE48 in Arabidopsis and rice. OsCLE48 encodes a CLE peptide hormone that is similar to Arabidopsis CLEs. RT-PCR analysis showed that OsCLE48 was induced by exogenously application of IAA (indole-3-acetic acid, a naturally occurred auxin. Expression of integrated OsCLE48p:GUS reporter gene in transgenic Arabidopsis plants was also induced by exogenously IAA treatment. These results indicate that OsCLE48 is an auxin responsive gene. Histochemical staining showed that GUS activity was detected in all the tissue and organs of the OsCLE48p:GUS transgenic Arabidopsis plants. Expression of OsCLE48 under the control of the 35S promoter in Arabidopsis inhibited shoot apical meristem development. Expression of OsCLE48 under the control of the CLV3 native regulatory elements almost completely complemented clv3-2 mutant phenotypes, suggesting that OsCLE48 is functionally similar to CLV3. On the other hand, expression of OsCLE48 under the control of the 35S promoter in Arabidopsis has little, if any effects on root apical meristem development, and transgenic rice plants overexpressing OsCLE48 are morphologically indistinguishable from wild type plants, suggesting that the functions of some CLE peptides may not be fully conserved in Arabidopsis and rice.

  6. AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening.

    Science.gov (United States)

    Breitel, Dario A; Chappell-Maor, Louise; Meir, Sagit; Panizel, Irina; Puig, Clara Pons; Hao, Yanwei; Yifhar, Tamar; Yasuor, Hagai; Zouine, Mohamed; Bouzayen, Mondher; Granell Richart, Antonio; Rogachev, Ilana; Aharoni, Asaph

    2016-03-01

    The involvement of ethylene in fruit ripening is well documented, though knowledge regarding the crosstalk between ethylene and other hormones in ripening is lacking. We discovered that AUXIN RESPONSE FACTOR 2A (ARF2A), a recognized auxin signaling component, functions in the control of ripening. ARF2A expression is ripening regulated and reduced in the rin, nor and nr ripening mutants. It is also responsive to exogenous application of ethylene, auxin and abscisic acid (ABA). Over-expressing ARF2A in tomato resulted in blotchy ripening in which certain fruit regions turn red and possess accelerated ripening. ARF2A over-expressing fruit displayed early ethylene emission and ethylene signaling inhibition delayed their ripening phenotype, suggesting ethylene dependency. Both green and red fruit regions showed the induction of ethylene signaling components and master regulators of ripening. Comprehensive hormone profiling revealed that altered ARF2A expression in fruit significantly modified abscisates, cytokinins and salicylic acid while gibberellic acid and auxin metabolites were unaffected. Silencing of ARF2A further validated these observations as reducing ARF2A expression let to retarded fruit ripening, parthenocarpy and a disturbed hormonal profile. Finally, we show that ARF2A both homodimerizes and interacts with the ABA STRESS RIPENING (ASR1) protein, suggesting that ASR1 might be linking ABA and ethylene-dependent ripening. These results revealed that ARF2A interconnects signals of ethylene and additional hormones to co-ordinate the capacity of fruit tissue to initiate the complex ripening process.

  7. Genome-wide analysis of auxin response factor gene family members in medicinal model plant Salvia miltiorrhiza

    Directory of Open Access Journals (Sweden)

    Zhichao Xu

    2016-06-01

    Full Text Available Auxin response factors (ARFs can function as transcriptional activators or repressors to regulate the expression of auxin response genes by specifically binding to auxin response elements (AuxREs during plant development. Based on a genome-wide strategy using the medicinal model plant Salvia miltiorrhiza, 25 S. miltiorrhiza ARF (SmARF gene family members in four classes (class Ia, IIa, IIb and III were comprehensively analyzed to identify characteristics including gene structures, conserved domains, phylogenetic relationships and expression patterns. In a hybrid analysis of the phylogenetic tree, microRNA targets, and expression patterns of SmARFs in different organs, root tissues, and methyl jasmonate or indole-3-acetic acid treatment conditions, we screened for candidate SmARFs involved in various developmental processes of S. miltiorrhiza. Based on this analysis, we predicted that SmARF25, SmARF7, SmARF16 and SmARF20 are involved in flower, leaf, stem and root development, respectively. With the further insight into the targets of miR160 and miR167, specific SmARF genes in S. miltiorrhiza might encode products that participate in biological processes as described for ARF genes in Arabidopsis. Our results provide a foundation for understanding the molecular basis and regulatory mechanisms of SmARFs in S. miltiorrhiza.

  8. WOX5-1AA17 Feedback Circuit-Mediated CellularAuxin Response Is Crucial for the Patterning ofRoot Stem Cell Niches in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    2014-01-01

    In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum thatemerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxinresponse machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell mainte-nance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5)transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thusprovides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is bal-anced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biol-ogy, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediatedauxin production to IAA17-dependent repression of auxin responses. This WOX5-1AA17 feedback circuit further assuresthe maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stemcell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-iAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSCdifferentiation.

  9. Repression of the Auxin Response Pathway Increases Arabidopsis Susceptibility to Necrotrophic Fungi

    Institute of Scientific and Technical Information of China (English)

    Francisco Llorente; Paul Muskett; Andrea Sánchez-Vallet; Gemma López; Brisa Ramos; Clara Sánchez-Rodríguez; Lucia Jordá; Jane Parker; Antonio Molina

    2008-01-01

    In plants, resistance to necrotrophic pathogens depends on the interplay between different hormone systems, such as those regulated by salicylic acid (SA), jasmonic acid (JA), ethylene, and abscisic acid. Repression of auxin signaling by the SA pathway was recently shown to contribute to antibacterial resistance. Here, we demonstrate that Arabidopsis auxin signaling mutants axrl, axr2, and axr6 that have defects in the auxin-stimulated SCF (Skpl-Cullin-F-box) ubiquitination pathway exhibit increased susceptibility to the necrotrophic fungi Plectosphaerella cucumerina and Botrytis cinerea. Also, stabilization of the auxin transcriptional repressor AXR3 that is normally targeted for removal by the SCF-ubiquitin/proteasome machinery occurs upon P. cucumerina infection. Pharmacological inhibition of auxin transport or proteasome function each compromise necrotroph resistance of wild-type plants to a similar extent as in non-treated auxin response mutants. These results suggest that auxin signaling is important for resistance to the necrotrophic fungi P. cucumerina and B. cinerea. SGTlb (one of two Arabidopsis SGT1 genes encoding HSP90/HSC70 co-chaperones) promotes the functions of SCF E3-ubiquitin ligase complexes in auxin and JA responses and resistance conditioned by certain Resistance (R) genes to biotrophic pathogens. We find that sgtlb mutants are as resistant to P. cucumerina as wild-type plants. Conversely, auxin/SCF signaling mutants are uncompromised in RPP4-triggered resistance to the obligate biotrophic oomycete, Hyaloperonospora parasitica. Thus, the predominant action of SGTlb in R gene-conditioned resistance to oomycetes appears to be at a site other than assisting SCF E3-ubiquitin ligases. However, genetic additivity of sgtlb axr1 double mutants in susceptibility to H. parasitica suggests that SCF-mediated ubiquitination contributes to limiting biotrophic pathogen colonization once plant-pathogen compatibility is established.

  10. AUXIN RESPONSE FACTOR 2 Intersects Hormonal Signals in the Regulation of Tomato Fruit Ripening.

    Directory of Open Access Journals (Sweden)

    Dario A Breitel

    2016-03-01

    Full Text Available The involvement of ethylene in fruit ripening is well documented, though knowledge regarding the crosstalk between ethylene and other hormones in ripening is lacking. We discovered that AUXIN RESPONSE FACTOR 2A (ARF2A, a recognized auxin signaling component, functions in the control of ripening. ARF2A expression is ripening regulated and reduced in the rin, nor and nr ripening mutants. It is also responsive to exogenous application of ethylene, auxin and abscisic acid (ABA. Over-expressing ARF2A in tomato resulted in blotchy ripening in which certain fruit regions turn red and possess accelerated ripening. ARF2A over-expressing fruit displayed early ethylene emission and ethylene signaling inhibition delayed their ripening phenotype, suggesting ethylene dependency. Both green and red fruit regions showed the induction of ethylene signaling components and master regulators of ripening. Comprehensive hormone profiling revealed that altered ARF2A expression in fruit significantly modified abscisates, cytokinins and salicylic acid while gibberellic acid and auxin metabolites were unaffected. Silencing of ARF2A further validated these observations as reducing ARF2A expression let to retarded fruit ripening, parthenocarpy and a disturbed hormonal profile. Finally, we show that ARF2A both homodimerizes and interacts with the ABA STRESS RIPENING (ASR1 protein, suggesting that ASR1 might be linking ABA and ethylene-dependent ripening. These results revealed that ARF2A interconnects signals of ethylene and additional hormones to co-ordinate the capacity of fruit tissue to initiate the complex ripening process.

  11. Arabidopsis NAC1 transduces auxin signal downstream of TIR1 to promote lateral root development.

    Science.gov (United States)

    Xie, Q; Frugis, G; Colgan, D; Chua, N H

    2000-12-01

    Auxin plays a key role in lateral root formation, but the signaling pathway for this process is poorly understood. We show here that NAC1, a new member of the NAC family, is induced by auxin and mediates auxin signaling to promote lateral root development. NAC1 is a transcription activator consisting of an N-terminal conserved NAC-domain that binds to DNA and a C-terminal activation domain. This factor activates the expression of two downstream auxin-responsive genes, DBP and AIR3. Transgenic plants expressing sense or antisense NAC1 cDNA show an increase or reduction of lateral roots, respectively. Finally, TIR1-induced lateral root development is blocked by expression of antisense NAC1 cDNA, and NAC1 overexpression can restore lateral root formation in the auxin-response mutant tir1, indicating that NAC1 acts downstream of TIR1.

  12. Genome-wide identification, isolation and expression analysis of auxin response factor (ARF) gene family in sweet orange (Citrus sinensis).

    Science.gov (United States)

    Li, Si-Bei; OuYang, Wei-Zhi; Hou, Xiao-Jin; Xie, Liang-Liang; Hu, Chun-Gen; Zhang, Jin-Zhi

    2015-01-01

    Auxin response factors (ARFs) are an important family of proteins in auxin-mediated response, with key roles in various physiological and biochemical processes. To date, a genome-wide overview of the ARF gene family in citrus was not available. A systematic analysis of this gene family in citrus was begun by carrying out a genome-wide search for the homologs of ARFs. A total of 19 nonredundant ARF genes (CiARF) were found and validated from the sweet orange. A comprehensive overview of the CiARFs was undertaken, including the gene structures, phylogenetic analysis, chromosome locations, conserved motifs of proteins, and cis-elements in promoters of CiARF. Furthermore, expression profiling using real-time PCR revealed many CiARF genes, albeit with different patterns depending on types of tissues and/or developmental stages. Comprehensive expression analysis of these genes was also performed under two hormone treatments using real-time PCR. Indole-3-acetic acid (IAA) and N-1-napthylphthalamic acid (NPA) treatment experiments revealed differential up-regulation and down-regulation, respectively, of the 19 citrus ARF genes in the callus of sweet orange. Our comprehensive analysis of ARF genes further elucidates the roles of CiARF family members during citrus growth and development process.

  13. Auxin-responsive DR5 promoter coupled with transport assays suggest separate but linked routes of auxin transport during woody stem development in Populus.

    Science.gov (United States)

    Spicer, Rachel; Tisdale-Orr, Tracy; Talavera, Christian

    2013-01-01

    Polar auxin transport (PAT) is a major determinant of plant morphology and internal anatomy with important roles in vascular patterning, tropic growth responses, apical dominance and phyllotactic arrangement. Woody plants present a highly complex system of vascular development in which isolated bundles of xylem and phloem gradually unite to form concentric rings of conductive tissue. We generated several transgenic lines of hybrid poplar (Populus tremula x alba) with the auxin-responsive DR5 promoter driving GUS expression in order to visualize an auxin response during the establishment of secondary growth. Distinct GUS expression in the cambial zone and developing xylem-side derivatives supports the current view of this tissue as a major stream of basipetal PAT. However, we also found novel sites of GUS expression in the primary xylem parenchyma lining the outer perimeter of the pith. Strands of primary xylem parenchyma depart the stem as a leaf trace, and showed GUS expression as long as the leaves to which they were connected remained attached (i.e., until just prior to leaf abscission). Tissue composed of primary xylem parenchyma strands contained measurable levels of free indole-3-acetic acid (IAA) and showed basipetal transport of radiolabeled auxin ((3)H-IAA) that was both significantly faster than diffusion and highly sensitive to the PAT inhibitor NPA. Radiolabeled auxin was also able to move between the primary xylem parenchyma in the interior of the stem and the basipetal stream in the cambial zone, an exchange that was likely mediated by ray parenchyma cells. Our results suggest that (a) channeling of leaf-derived IAA first delineates isolated strands of pre-procambial tissue but then later shifts to include basipetal transport through the rapidly expanding xylem elements, and (b) the transition from primary to secondary vascular development is gradual, with an auxin response preceding the appearance of a unified and radially-organized vascular cambium.

  14. Constitutive expression of pathogen-inducible OsWRKY31 enhances disease resistance and affects root growth and auxin response in transgenic rice plants

    Institute of Scientific and Technical Information of China (English)

    Juan Zhang; Youliang Peng; Zejian Guo

    2008-01-01

    WRKY transcription factors have many regulatory roles in response to biotic and abiotic stresses. In this study, we isolated a rice WRKY gene (OsWRKY31) that is induced by the rice blast fungus Magnaporthe grisea and auxin. This gene encodes a polypeptide of 211 amino-acid residues and belongs to a subgroup of the rice WRKY gene family that probably originated after the divergence of monocot and dicot plants. OsWRKY31 was found to be localized to the nucleus of onion epidermis cells to transiently express OsWRKY31-eGFP fusion protein. Analysis of 0sWRKY31 and its mutants fused with a Cal4 DNA-binding domain indicated that OsWRKY31 has transactivation activity in yeast. Overexpression of the OsWRKY31 gene was found to enhance resistance against infection with M. grisea, and the transgenic lines exhibited reduced lateral root formation and elongation compared with wild-type and RNAi plants. The lines with overexpression showed constitutive expression of many defense-related genes, such as PBZ1 and OsSci2, as well as early auxin-response genes, such as OsIAA4 and OsCrll genes. Furthermore, the plants with overexpression were less sensitive to exogenously supplied IBA, NAA and 2,4-D at high concentrations, suggesting that overexpression of the OsWRKY31 gene might alter the auxin response or transport. These results also suggest that OsWRKY31 might be a common component in the signal transduction pathways of the auxin response and the defense response in rice.

  15. Genome-wide identification, isolation and expression analysis of auxin response factor(ARF gene family in sweet orange (Citrus sinensis

    Directory of Open Access Journals (Sweden)

    si-bei eli

    2015-03-01

    Full Text Available Auxin response factors (ARFs are an important family of proteins in auxin-mediated response, with key roles in various physiological and biochemical processes. To date, a genome-wide overview of the ARF gene family in citrus was not available. A systematic analysis of this gene family in citrus was begun by carrying out a genome-wide search for the homologues of auxin response genes. A total of 19 non-redundant ARF genes (CiARF were identified and validated from the sweet orange genome. A comprehensive overview of the CiARF gene family was undertaken, including the gene structures, phylogeny, chromosome locations, conserved motifs, and cis-elements in promoter sequences. Furthermore, expression profiling using real-time PCR revealed many CiARF genes, albeit with different patterns depending on types of tissues and/or developmental stages. Comprehensive expression analysis of these genes was also performed under two hormone treatments using real-time PCR. Indole-3-acetic acid and N-1-napthylphthalamic acid treatment experiments revealed differential up-regulation and down-regulation, respectively, of the 19 citrus ARF genes in the callus of sweet orange. Our comprehensive analysis of ARF genes further elucidates the roles of CiARF family members in citrus growth and development.

  16. Genome-wide identification, expression analysis of auxin-responsive GH3 family genes in maize (Zea mays L.) under abiotic stresses.

    Science.gov (United States)

    Feng, Shangguo; Yue, Runqing; Tao, Sun; Yang, Yanjun; Zhang, Lei; Xu, Mingfeng; Wang, Huizhong; Shen, Chenjia

    2015-09-01

    Auxin is involved in different aspects of plant growth and development by regulating the expression of auxin-responsive family genes. As one of the three major auxin-responsive families, GH3 (Gretchen Hagen3) genes participate in auxin homeostasis by catalyzing auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids. However, how GH3 genes function in responses to abiotic stresses and various hormones in maize is largely unknown. Here, the latest updated maize (Zea mays L.) reference genome sequence was used to characterize and analyze the ZmGH3 family genes from maize. The results showed that 13 ZmGH3 genes were mapped on five maize chromosomes (total 10 chromosomes). Highly diversified gene structures and tissue-specific expression patterns suggested the possibility of function diversification for these genes in response to environmental stresses and hormone stimuli. The expression patterns of ZmGH3 genes are responsive to several abiotic stresses (salt, drought and cadmium) and major stress-related hormones (abscisic acid, salicylic acid and jasmonic acid). Various environmental factors suppress auxin free IAA contents in maize roots suggesting that these abiotic stresses and hormones might alter GH3-mediated auxin levels. The responsiveness of ZmGH3 genes to a wide range of abiotic stresses and stress-related hormones suggested that ZmGH3s are involved in maize tolerance to environmental stresses.

  17. Genome-wide identification, expression analysis of auxin-responsive GH3 family genes in maize (Zea mays L.) under abiotic stresses

    Institute of Scientific and Technical Information of China (English)

    Shangguo Feng; Runqing Yue; Sun Tao Yanjun Yang; Lei Zhang; Mingfeng Xu; Huizhong Wang; Chenjia Shen

    2015-01-01

    Auxin is involved in different aspects of plant growth and development by regulating the expression of auxin-responsive family genes. As one of the three major auxin-responsive families, GH3 (Gretchen Hagen3) genes participate in auxin homeostasis by catalyzing auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids. However, how GH3 genes function in responses to abiotic stresses and various hormones in maize is largely unknown. Here, the latest updated maize (Zea mays L.) reference genome sequence was used to characterize and analyze the ZmGH3 family genes from maize. The results showed that 13 ZmGH3 genes were mapped on five maize chromosomes (total 10 chromosomes). Highly diversified gene structures and tissue-specific expression patterns suggested the possibility of function diversification for these genes in response to environmental stresses and hormone stimuli. The expression patterns of ZmGH3 genes are responsive to several abiotic stresses (salt, drought and cadmium) and major stress-related hormones (abscisic acid, salicylic acid and jasmonic acid). Various environmental factors suppress auxin free IAA contents in maize roots suggesting that these abiotic stresses and hormones might alter GH3-mediated auxin levels. The respon-siveness of ZmGH3 genes to a wide range of abiotic stresses and stress-related hormones suggested that ZmGH3s are involved in maize tolerance to environmental stresses.

  18. The Solanum lycopersicum AUXIN RESPONSE FACTOR 7 (SlARF7) mediates cross-talk between auxin and gibberellin signalling during tomato fruit set and development

    Science.gov (United States)

    de Jong, Maaike; Wolters-Arts, Mieke; García-Martínez, José L.; Mariani, Celestina; Vriezen, Wim H.

    2011-01-01

    Transgenic tomato plants (Solanum lycopersicum L.) with reduced mRNA levels of AUXIN RESPONSE FACTOR 7 (SlARF7) form parthenocarpic fruits with morphological characteristics that seem to be the result of both increased auxin and gibberellin (GA) responses during fruit growth. This paper presents a more detailed analysis of these transgenic lines. Gene expression analysis of auxin-responsive genes show that SlARF7 may regulate only part of the auxin signalling pathway involved in tomato fruit set and development. Also, part of the GA signalling pathway was affected by the reduced levels of SlARF7 mRNA, as morphological and molecular analyses display similarities between GA-induced fruits and fruits formed by the RNAi SlARF7 lines. Nevertheless, the levels of GAs were strongly reduced compared with that in seeded fruits. These findings indicate that SlARF7 acts as a modifier of both auxin and gibberellin responses during tomato fruit set and development. PMID:20937732

  19. ROP3 GTPase contributes to polar auxin transport and auxin responses and is important for embryogenesis and seedling growth in Arabidopsis.

    Science.gov (United States)

    Huang, Jia-bao; Liu, Huili; Chen, Min; Li, Xiaojuan; Wang, Mingyan; Yang, Yali; Wang, Chunling; Huang, Jiaqing; Liu, Guolan; Liu, Yuting; Xu, Jian; Cheung, Alice Y; Tao, Li-zhen

    2014-09-01

    ROP GTPases are crucial for the establishment of cell polarity and for controlling responses to hormones and environmental signals in plants. In this work, we show that ROP3 plays important roles in embryo development and auxin-dependent plant growth. Loss-of-function and dominant-negative (DN) mutations in ROP3 induced a spectrum of similar defects starting with altered cell division patterning during early embryogenesis to postembryonic auxin-regulated growth and developmental responses. These resulted in distorted embryo development, defective organ formation, retarded root gravitropism, and reduced auxin-dependent hypocotyl elongation. Our results showed that the expression of AUXIN RESPONSE FACTOR5/MONOPTEROS and root master regulators PLETHORA1 (PLT1) and PLT2 was reduced in DN-rop3 mutant embryos, accounting for some of the observed patterning defects. ROP3 mutations also altered polar localization of auxin efflux proteins (PINs) at the plasma membrane (PM), thus disrupting auxin maxima in the root. Notably, ROP3 is induced by auxin and prominently detected in root stele cells, an expression pattern similar to those of several stele-enriched PINs. Our results demonstrate that ROP3 is important for maintaining the polarity of PIN proteins at the PM, which in turn ensures polar auxin transport and distribution, thereby controlling plant patterning and auxin-regulated responses.

  20. Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS.

    Science.gov (United States)

    Herud, Ole; Weijers, Dolf; Lau, Steffen; Jürgens, Gerd

    2016-01-01

    Primary root formation in early embryogenesis of Arabidopsis thaliana is initiated with the specification of a single cell called hypophysis. This initial step requires the auxin-dependent release of the transcription factor MONOPTEROS (MP, also known as ARF5) from its inhibition by the Aux/IAA protein BODENLOS (BDL, also known as IAA12). Auxin-insensitive bdl mutant embryos and mp loss-of-function embryos fail to specify the hypophysis, giving rise to rootless seedlings. A suppressor screen of rootless bdl mutant seedlings yielded a mutation in the nuclear import receptor IMPORTIN-ALPHA 6 (IMPα6) that promoted primary root formation through rescue of the embryonic hypophysis defects, without causing additional phenotypic changes. Aux/IAA proteins are continually synthesized and degraded, which is essential for rapid transcriptional responses to changing auxin concentrations. Nuclear translocation of bdl:3×GFP was slowed down in impα6 mutants as measured by fluorescence recovery after photobleaching (FRAP) analysis, which correlated with the reduced inhibition of MP by bdl in transient expression assays in impα6 knock-down protoplasts. The MP-BDL module acts like an auxin-triggered genetic switch because MP activates its own expression as well as the expression of its inhibitor BDL. Using an established simulation model, we determined that the reduced nuclear translocation rate of BDL in impα6 mutant embryos rendered the auxin-triggered switch unstable, impairing the fast response to changes in auxin concentration. Our results suggest that the instability of the inhibitor BDL necessitates a fast nuclear uptake in order to reach the critical threshold level required for auxin responsiveness of the MP-BDL module in primary root initiation.

  1. 小麦生长素响应因子 TaARF6转基因烟草植株分子鉴定%Regulation effects of an auxin response gene in wheat (TaARF6) in mediating plant growth under conditions of normal growth and Pi deprivation

    Institute of Scientific and Technical Information of China (English)

    智一鸣; 陈芳; 刘晓曼; 肖凯

    2016-01-01

    系数量增多、主侧根长度、根体积、叶面积和根冠比增加。【结论】TaARF6编码典型的生长素响应因子,其编码蛋白具有生长素响应因子特有结构域。 TaARF6对环境中的低磷胁迫逆境能产生明显应答。上调表达 TaARF6基因,具有增加植株根、叶鲜、干重和改善根叶及植株形态的生物学功能。本研究表明,通过对植株体内生长素响应基因的转录调控,TaARF6在介导植株不同供磷水平下的根叶形态建成和干物质累积过程中发挥着重要作用。%[Objectives] Auxin response factors (ARFs) play a critical role in mediating transduction of auxin signaling and regulating expression of downstream auxin-responsive genes. In this study, an ARF type transcription factor gene referred to TaARF6 identified in a root suppression subtractive cDNA library that enriches the differentially expressed genes under Pi sufficiency as the basis was used to investigate molecular characterization of TaARF6 and its expression patterns under various Pi-supply conditions, as well as its functions in regulating plant phenotypes. The objective of this study was aimed to elucidate biological roles of TaARF6 in mediating plant growth features under the conditions of Pi sufficiency and Pi deficiency. [ Methods] The protein characterization of TaARF6 was predicted by the bioinformatics’ tools. The seedlings of wheat (cv. Shixin 828) were cultured under the sufficient-and deficient-Pi conditions by a hydroponic approach and used to investigate the expression patterns of TaARF6 based on semi-quantitative RT-PCR. A DNA recombinant technique was adopted to construct the expression cassette integrating the TaARF6 open reading frame. The transgenic tobacco plants overexpressing TaARF6 were generated based on a genetic transformation approach mediated by Agobacterium-tumefaciens using the leaf discs as explants. Based on the culture methods of agar medium and hydroponic solution, the

  2. A G-Box-Binding Protein from Soybean Binds to the E1 Auxin-Response Element in the Soybean GH3 Promoter and Contains a Proline-Rich Repression Domain.

    Science.gov (United States)

    Liu, Z. B.; Hagen, G.; Guilfoyle, T. J.

    1997-10-01

    The E1 promoter fragment (-249 to -203) is one of three auxin-response elements (AuxREs) in the soybean (Glycine max L.) GH3 promoter (Z.-B. Liu, T. Ulmasov, X. Shi, G. Hagen, T.J. Guilfoyle [1994] Plant Cell 6: 645-657). Results presented here further characterize and delimit the AuxRE within the E1 fragment. The E1 fragment functioned as an AuxRE in transgenic tobacco (Nicotiana tabacum L.) plants, as well as in transfected protoplasts. The AuxRE within E1 contains a G-box, and this G-box was used to clone a G-box-binding factor (GBF) from soybean (SGBF-2). This 45-kD GBF contains an N-terminal proline-rich domain and a C-terminal basic/leucine zipper DNA-binding domain. Gel-mobility shift assays were used to characterize the binding specificity of SGBF-2. Antiserum raised against recombinant SGBF-2 was used to further characterize SGBF-2 and antigenically related GBFs in soybean nuclear extracts. Co-transfection assays with effector and reporter plasmids in carrot (Daucus carota L.) protoplasts indicated that the N-terminal proline-rich domain of SGBF-2 functioned as a repression domain in both basal and auxin-inducible transcription.

  3. Stem transcriptome reveals mechanisms to reduce the energetic cost of shade-avoidance responses in tomato.

    Science.gov (United States)

    Cagnola, Juan Ignacio; Ploschuk, Edmundo; Benech-Arnold, Tomás; Finlayson, Scott A; Casal, Jorge José

    2012-10-01

    While the most conspicuous response to low red/far-red ratios (R:FR) of shade light perceived by phytochrome is the promotion of stem growth, additional, less obvious effects may be discovered by studying changes in the stem transcriptome. Here, we report rapid and reversible stem transcriptome responses to R:FR in tomato (Solanum lycopersicum). As expected, low R:FR promoted the expression of growth-related genes, including those involved in the metabolism of cell wall carbohydrates and in auxin responses. In addition, genes involved in flavonoid synthesis, isoprenoid metabolism, and photosynthesis (dark reactions) were overrepresented in clusters showing reduced expression in the stem of low R:FR-treated plants. Consistent with these responses, low R:FR decreased the levels of flavonoids (anthocyanin, quercetin, kaempferol) and selected isoprenoid derivatives (chlorophyll, carotenoids) in the stem and severely reduced the photosynthetic capacity of this organ. However, lignin contents were unaffected. Low R:FR reduced the stem levels of jasmonate, which is a known inducer of flavonoid synthesis. The rate of stem respiration was also reduced in low R:FR-treated plants, indicating that by downsizing the stem photosynthetic apparatus and the levels of photoprotective pigments under low R:FR, tomato plants reduce the energetic cost of shade-avoidance responses.

  4. The restructuring of Shell Downstream; La restructuration de Shell Downstream

    Energy Technology Data Exchange (ETDEWEB)

    Maxwell, F.

    2005-01-15

    To facing a more and more competitive environment, the Group Shell began a restructuring. While the group was organized on horizontal national lines, it is creating today an integrated downstream activity. The word of this restructuring is profit. (A.L.B.)

  5. Continuous downstream processing of biopharmaceuticals.

    Science.gov (United States)

    Jungbauer, Alois

    2013-08-01

    Continuous manufacturing has been applied in many different industries but has been pursued reluctantly in biotechnology where the batchwise process is still the standard. A shift to continuous operation can improve productivity of a process and substantially reduce the footprint. Continuous operation also allows robust purification of labile biomolecules. A full set of unit operations is available to design continuous downstream processing of biopharmaceuticals. Chromatography, the central unit operation, is most advanced in respect to continuous operation. Here, the problem of 'batch' definition has been solved. This has also paved the way for implementation of continuous downstream processing from a regulatory viewpoint. Economic pressure, flexibility, and parametric release considerations will be the driving force to implement continuous manufacturing strategies in future.

  6. Downstream targets of WRKY33.

    Science.gov (United States)

    Petersen, Klaus; Fiil, Berthe Katrine; Mundy, John; Petersen, Morten

    2008-11-01

    Innate immunity signaling pathways in both animals and plants are regulated by mitogen-activated protein kinase (MAPK) cascades. In a recent publication we show that MPK4 and its substrate MKS1 interact with WRKY33 in vivo, and that WRKY33 is released from complexes with MPK4 upon infection. Transcriptome analysis of a wrky33 loss-of-function mutant identified a subset of defense-related genes as putative targets of WRKY33. These genes include PAD3 and CYP71A13, which encode cytochrome P450 monoxygenases required for synthesis of the antimicrobial phytoalexin camalexin. Chromatin immunoprecipitation confirmed that WRKY33 bound the promoter of PAD3 when plants were inoculated with pathogens. Here we further discuss the involvement of two other targets of WRKY33, NUDT6 and ROF2 in defense responses against invading pathogens.

  7. Downstream targets of WRKY33

    DEFF Research Database (Denmark)

    Petersen, Klaus; Fiil, Berthe Katrine; Mundy, John;

    2008-01-01

    Innate immunity signaling pathways in both animals and plants are regulated by mitogen-activated protein kinase (MAPK) cascades. In a recent publication we show that MPK4 and its substrate MKS1 interact with WRKY33 in vivo, and that WRKY33 is released from complexes with MPK4 upon infection....... Transcriptome analysis of a wrky33 loss-of-function mutant identified a subset of defense-related genes as putative targets of WRKY33. These genes include PAD3 and CYP71A13, which encode cytochrome P450 monoxygenases required for synthesis of the antimicrobial phytoalexin camalexin. Chromatin...... immunoprecipitation confirmed that WRKY33 bound the promoter of PAD3 when plants were inoculated with pathogens. Here we further discuss the involvement of two other targets of WRKY33, NUDT6 and ROF2 in defense responses against invading pathogens....

  8. Operational optimization in the downstream; Otimizacao operacional no downstream

    Energy Technology Data Exchange (ETDEWEB)

    Silberman, Luis; Cunha, Filipe Silveira Ramos da [Petroleo Ipiranga, Porto Alegre, RS (Brazil)

    2004-07-01

    On the present competitive down stream's market, there is a great necessity of optimization aiming to guarantee the best price and quality of our clients. Our goal is to attend these expectations while we guarantee an efficient operation. The greatest question is how far we are from the ideal model. This way, a lot of projects have been executed during the last years aiming the operational optimization of all our activities. We divide the projects in 4 areas: Logistic (new modals distribution), Transport (transport optimization - quality and more deliveries with less trucks), Client Support (Internet Ipiranga and Support Center), Distribution Terminals Productivity (automation and environment). This work intend to present our ideal, perfect and complete Downstream Operation model. We will talk about how close we are of this ideal model and we will present the projects that we had already developed and implanted on the automation of the terminals and the logistics area. (author)

  9. Web services for transcriptomics

    NARCIS (Netherlands)

    Neerincx, P.

    2009-01-01

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

  10. Transcriptome Analysis Reveals that Red and Blue Light Regulate Growth and Phytohormone Metabolism in Norway Spruce [Picea abies (L. Karst].

    Directory of Open Access Journals (Sweden)

    Fangqun OuYang

    Full Text Available The mechanisms by which different light spectra regulate plant shoot elongation vary, and phytohormones respond differently to such spectrum-associated regulatory effects. Light supplementation can effectively control seedling growth in Norway spruce. However, knowledge of the effective spectrum for promoting growth and phytohormone metabolism in this species is lacking. In this study, 3-year-old Norway spruce clones were illuminated for 12 h after sunset under blue or red light-emitting diode (LED light for 90 d, and stem increments and other growth traits were determined. Endogenous hormone levels and transcriptome differences in the current needles were assessed to identify genes related to the red and blue light regulatory responses. The results showed that the stem increment and gibberellin (GA levels of the seedlings illuminated by red light were 8.6% and 29.0% higher, respectively, than those of the seedlings illuminated by blue light. The indoleacetic acid (IAA level of the seedlings illuminated by red light was 54.6% lower than that of the seedlings illuminated by blue light, and there were no significant differences in abscisic acid (ABA or zeatin riboside [ZR] between the two groups of seedlings. The transcriptome results revealed 58,736,166 and 60,555,192 clean reads for the blue-light- and red-light-illuminated samples, respectively. Illumina sequencing revealed 21,923 unigenes, and 2744 (approximately 93.8% out of 2926 differentially expressed genes (DEGs were found to be upregulated under blue light. The main KEGG classifications of the DEGs were metabolic pathway (29%, biosynthesis of secondary metabolites (20.49% and hormone signal transduction (8.39%. With regard to hormone signal transduction, AUXIN-RESISTANT1 (AUX1, AUX/IAA genes, auxin-inducible genes, and early auxin-responsive genes [(auxin response factor (ARF and small auxin-up RNA (SAUR] were all upregulated under blue light compared with red light, which might have

  11. Next-generation transcriptome assembly

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey A.; Wang, Zhong

    2011-09-01

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

  12. CNOOC Advancing into Downstream of Petroleum Industry

    Institute of Scientific and Technical Information of China (English)

    1997-01-01

    @@ "China National Offshore Oil Corporation is starting to expand its business into the downstream sector after making achievements continuously in exploration and development," Wang Yan, president of the corporation,told reporter in an interview, adding that the downstream sector is the third development stage for China National Offshore Oil Corporation (CNOOC).

  13. Transcriptomics in ecotoxicology.

    Science.gov (United States)

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

    2010-06-01

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

  14. Anguillid herpesvirus 1 transcriptome

    NARCIS (Netherlands)

    Beurden, van S.J.; Gatherer, D.; Kerr, K.; Galbraith, J.; Herzyk, P.; Peeters, B.P.H.; Rottier, P.J.M.; Engelsma, M.Y.; Davidson, A.J.

    2012-01-01

    We used deep sequencing of poly(A) RNA to characterize the transcriptome of an economically important eel virus, anguillid herpesvirus 1 (AngHV1), at a stage during the lytic life cycle when infectious virus was being produced. In contrast to the transcription of mammalian herpesviruses, the overall

  15. Genome Wide Transcriptome Analysis reveals ABA mediated response in Arabidopsis during Gold (AuCl4- treatment

    Directory of Open Access Journals (Sweden)

    Devesh eShukla

    2014-11-01

    Full Text Available The unique physico-chemical properties of gold nanoparticles (AuNPs find manifold applications in diagnostics, medicine and catalysis. Chemical synthesis produces reactive AuNPs and generates hazardous by-products. Alternatively, plants can be utilized to produce AuNPs in an eco-friendly manner. To better control the biosynthesis of AuNPs, we need to first understand the detailed molecular response induced by AuCl4- In this study, we carried out global transcriptome analysis in root tissue of Arabidopsis grown for 12- hours in presence of gold solution (HAuCl4 using the novel unbiased Affymetrix exon array. Transcriptomics analysis revealed differential regulation of a total of 704 genes and 4900 exons. Of these, 492 and 212 genes were up- and downregulated, respectively. The validation of the expressed key genes, such as glutathione-S-transferases, auxin responsive genes, cytochrome P450 82C2, methyl transferases, transducin (G protein beta subunit, ERF transcription factor, ABC, and MATE transporters, was carried out through quantitative RT-PCR. These key genes demonstrated specific induction under AuCl4- treatment relative to other heavy metals, suggesting a unique plant-gold interaction. GO enrichment analysis reveals the upregulation of processes like oxidative stress, glutathione binding, metal binding, transport, and plant hormonal responses. Changes predicted in biochemical pathways indicated major modulation in glutathione mediated detoxification, flavones and derivatives, and plant hormone biosynthesis. Motif search analysis identified a highly significant enriched motif, ACGT, which is an abscisic acid responsive core element (ABRE, suggesting the possibility of ABA- mediated signaling. Identification of abscisic acid response element (ABRE points to the operation of a predominant signaling mechanism in response to AuCl4- exposure. Overall, this study presents a useful picture of plant-gold interaction with an identification of

  16. 苹果生长素响应因子(ARF)基因家族全基因组鉴定及表达分析%Genome-Wide Identiifcation and Expression Analysis ofAuxin Response Factor (ARF) Gene Family in Apple

    Institute of Scientific and Technical Information of China (English)

    李慧峰; 冉昆; 何平; 王海波; 常源升; 孙清荣; 程来亮; 李林光

    2015-01-01

    生长素响应因子(auxin response factor, ARF)基因在调控生长素响应基因和生长素信号转导途径以及其它多个生长发育过程具有重要作用。本研究利用Blast P程序比对并获得苹果ARF基因家族,通过DNAMAN 6.0、MEGA 5.0、WebLogo 3、MapInspect和MEME软件对苹果ARF基因进行分析,采用RT-PCR技术研究基因组织表达情况。结果表明,苹果基因组存在29个ARF基因,进化上可分为I、II、III、IV和V组,每组成员数目分别是4、5、10、6和4个。内含子和外显子结构分析表明,该基因家族由2~15个外显子构成。染色体分布结果显示, MdARF基因在染色体上分布不均匀。分别鉴定出4对和2对MdARF基因经历了串联复制和片段复制,14个MdARF基因经历了全基因组复制。保守元件分析表明,苹果ARF基因家族DBD区域、ARF区域、III元件和IV元件结构高度保守。半定量结果表明,大多数MdARF基因在根、茎、叶、花和果中均有表达。%Auxin response factor (ARF) genes play multiple important roles in the regulation of auxin response genes, auxin signal transduction pathway and other processes. In this study,ARF genes from apple (Malus domestica Borkh) genome were obtained via BlastP analysis, and their amino acid sequences were analyzed with DNAMAN 6.0, MEGA 5.0, WebLogo 3, MapInspect and MEME software, their expression patterns in different tissues were checked by RT-PCR analysis. The results showed that 29MdARF candidate genes were existed in apple genome. The results of phylogenetic analysis revealed thatMdARFgene family was divid-ed into ifve classes: Class I (four members), Class II (ifve members), Class III (ten members), Class IV (six members) and Class V (four members), respectively. The results of intron-exon structure analysis indicated that MdARF gene family members were composed of 2–15 exons. Chromosome mapping analysis revealed that MdARF genes were distributed unevenly on 15 chromosomes. Four

  17. Integrated metabolomics and transcriptomics reveal enhanced specialized metabolism in Medicago truncatula root border cells.

    Science.gov (United States)

    Watson, Bonnie S; Bedair, Mohamed F; Urbanczyk-Wochniak, Ewa; Huhman, David V; Yang, Dong Sik; Allen, Stacy N; Li, Wensheng; Tang, Yuhong; Sumner, Lloyd W

    2015-04-01

    Integrated metabolomics and transcriptomics of Medicago truncatula seedling border cells and root tips revealed substantial metabolic differences between these distinct and spatially segregated root regions. Large differential increases in oxylipin-pathway lipoxygenases and auxin-responsive transcript levels in border cells corresponded to differences in phytohormone and volatile levels compared with adjacent root tips. Morphological examinations of border cells revealed the presence of significant starch deposits that serve as critical energy and carbon reserves, as documented through increased β-amylase transcript levels and associated starch hydrolysis metabolites. A substantial proportion of primary metabolism transcripts were decreased in border cells, while many flavonoid- and triterpenoid-related metabolite and transcript levels were increased dramatically. The cumulative data provide compounding evidence that primary and secondary metabolism are differentially programmed in border cells relative to root tips. Metabolic resources normally destined for growth and development are redirected toward elevated accumulation of specialized metabolites in border cells, resulting in constitutively elevated defense and signaling compounds needed to protect the delicate root cap and signal motile rhizobia required for symbiotic nitrogen fixation. Elevated levels of 7,4'-dihydroxyflavone were further increased in border cells of roots exposed to cotton root rot (Phymatotrichopsis omnivora), and the value of 7,4'-dihydroxyflavone as an antimicrobial compound was demonstrated using in vitro growth inhibition assays. The cumulative and pathway-specific data provide key insights into the metabolic programming of border cells that strongly implicate a more prominent mechanistic role for border cells in plant-microbe signaling, defense, and interactions than envisioned previously.

  18. Transcriptomic response to differentiation induction

    Directory of Open Access Journals (Sweden)

    Dimitrov DS

    2006-02-01

    Full Text Available Abstract Background Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes. Methods We applied a transcriptomics analysis tool to elucidate the underlying pathways of leukocyte maturation at the genomic level in an established cellular model of leukemia by examining time-course data in two subclones of U-937 cells. Leukemias such as Acute Promyelocytic Leukemia (APL are characterized by a block in the hematopoietic stem cell maturation program at a point when expansion of clones which should be destined to mature into terminally-differentiated effector cells get locked into endless proliferation with few cells reaching maturation. Treatment with retinoic acid, depending on the precise genomic abnormality, often releases the responsible promyelocytes from this blockade but clinically can yield adverse sequellae in terms of potentially lethal side effects, referred to as retinoic acid syndrome. Results Briefly, the list of genes for temporal patterns of expression was pasted into the ABCC GRID Promoter TFSite Comparison Page website tool and the outputs for each pattern were examined for possible coordinated regulation by shared regelems (regulatory elements. We found it informative to use this novel web tool for identifying, on a genomic scale, genes regulated by drug treatment. Conclusion Improvement is needed in understanding the nature of the mutations responsible for controlling the maturation process and how these genes regulate downstream effects if there is to be better targeting of chemical interventions. Expanded implementation of the techniques and results reported here may better direct future efforts to improve treatment for diseases not restricted to APL.

  19. Downstream bioprocess characterisation within microfluidic devices

    DEFF Research Database (Denmark)

    Marques, Marco; Krühne, Ulrich; Szita, Nicolas

    2016-01-01

    Miniaturising bioprocess unit operation steps is a well-established approach to find novel routes for process intensification and improved process economics. While a number of microbioreactors have been presented over the last 15 years, miniaturised downstream unit operations (mDUO) are less deve...

  20. MITIGATION OF SEDIMENTATION HAZARDS DOWNSTREAM FROM RESERVOIRS

    Institute of Scientific and Technical Information of China (English)

    Ellen WOHL; Sara RATHBURN

    2003-01-01

    Many reservoirs currently in operation trap most or all of the sediment entering the reservoir,creating sediment-depleted conditions downstream. This may cause channel adjustment in the form of bank erosion, bed erosion, substrate coarsening, and channel planform change. Channel adjustment may also result from episodic sediment releases during reservoir operation, or from sediment evacuation following dam removal. Channel adjustment to increased sediment influx depends on the magnitude, frequency, duration and grain-size distribution of the sediment releases, and on the downstream channel characteristics. Channel adjustment may occur as a change in substrate sizedistribution, filling of pools, general bed aggradation, lateral instability, change in channel planform,and/or floodplain aggradation. The increased sediment availability may alter aquatic and riparian habitat, reduce water quality, distribute adsorbed contaminants along the river corridor, and provide germination sites for exotic vegetation. Mitigation of these sedimentation hazards requires: (1)mapping grain-size distribution within the reservoir and estimating the grain-size distributions of sediment that will be mobilized through time; (2) mapping shear stress and sediment transport capacity as a function of discharge on the basis of channel units for the length of the river likely to be affected; (3) mapping potential depositional zones, and aquatic habitat and "acceptable losses," along the downstream channel, and comparing these volumes to the total sediment volume stored in the reservoir as a means of estimating total transport capacity required to mobilize reservoir sediment delivered to the channel; (4) designing discharge and sediment release regime (magnitude, frequency,duration) to minimize adverse downstream impacts; and (5) developing plans to remove, treat, contain,or track contaminants, and to restrict establishment of exotic vegetation. The North Fork Poudre River in Colorado is used to

  1. TCW: transcriptome computational workbench.

    Directory of Open Access Journals (Sweden)

    Carol Soderlund

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

  2. India's Downstream Petroleum Sector

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2010-07-01

    This study provides a holistic examination of pricing and investment dynamics in India's downstream petroleum sector. It analyses the current pricing practices, highlights the tremendous fiscal cost of current pricing and regulatory arrangements, and examines the sectoral investment dynamics. It also looks at potential paths towards market-based reform along which the Indian government may move, while at the same time protecting energy market access for India's large poor population.

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

    Science.gov (United States)

    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.

  4. Fish reproductive guilds downstream of dams.

    Science.gov (United States)

    Vasconcelos, L P; Alves, D C; Gomes, L C

    2014-11-01

    Fish reproductive guilds were used to evaluate the responses of species with different reproductive strategies during two different periods of post-dam construction. The data used for the comparisons were collected in the upper Paraná River floodplain (Brazil), downstream of the Porto Primavera dam, 2 and 10 years after impoundment. The abundance (catch per unit effort, CPUE), species richness, evenness and structure of communities, all within reproductive guilds, were used to test the hypothesis that these metrics vary spatially and temporally. The influence of damming on species structure and the diversity of fish reproductive guilds varied spatiotemporally, and species with opportunistic reproductive strategies tended to be less affected. Conversely, long-distance migratory species responded more markedly to spatiotemporal variations, indicating that the ecosystem dynamics exert greater effects on populations of these species. Thus, the effects of a dam, even if attenuated, may extend over several years, especially downstream. This finding emphasizes the importance of maintaining large undammed tributaries downstream of reservoirs.

  5. Advances in Swine Transcriptomics

    Directory of Open Access Journals (Sweden)

    Christopher K. Tuggle , Yanfang Wang, Oliver Couture

    2007-01-01

    Full Text Available 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.

  6. Upstream and Downstream Influence in STBLI Instability

    Science.gov (United States)

    Martin, Pino; Priebe, Stephan; Helm, Clara

    2016-11-01

    Priebe and Martín (JFM, 2012) show that the low-frequency unsteadiness in shockwave and turbulent boundary layer interactions (STBLI) is governed by an inviscid instability. Priebe, Tu, Martín and Rowley (JFM, 2016) show that the instability is an inviscid centrifugal one, i.e Görtlerlike vortices. Previous works had given differing conclusions as to whether the low-frequency unsteadiness in STBLI is caused by an upstream or downstream mechanism. In this paper, we reconcile these opposite views and show that upstream and downstream correlations co-exist in the context of the nature of Görtler vortices. We find that the instability is similar to that in separated subsonic and laminar flows. Since the turbulence is modulated but passive to the global mode, the turbulent separated flows are amenable to linear global analysis. As such, the characteristic length and time scales, and the receptivity of the global mode might be determined, and low-order models that represent the low-frequency dynamics in STBLI might be developed. The centrifugal instability persists even under hypersonic conditions. This work is funded by the AFOSR Grant Number AF9550-15-1-0284 with Dr. Ivett Leyva.

  7. Downstream Thermal Evolution of Vortex Cores

    Science.gov (United States)

    Gómez-Barea, A.; Herrada, M. A.; Pérez-Saborid, M.; Barrero, A.

    1999-11-01

    The downstream evolution of the total temperature field in a quasi-incompressible axisymmetric vortex core has been computed. Starting at an initial station (z=0) with velocity profiles of the Burgers type and given temperature distributions, the numerical results of the evolution show that, according to experimental results, the total temperature in the near-axis region decreases substantially due to the work done by pressure and viscous forces together with the effect of both convection and conduction of heat. Depending on the values of the parameters characterizing the initial profiles and on the value of the Prandtl number, the vortex either breaks down or eventually reaches a self-similar regime. The results obtained shed light on the basic physics involved in the thermal separation phenomenon which appears inside Ranque-Hilsch vortex tubes.

  8. Channel changes downstream from a dam

    Science.gov (United States)

    Hadley, R.F.; Emmett, W.W.

    1998-01-01

    A flood-control dam was completed during 1979 on Bear Creek, a small tributary stream to the South Platte River in the Denver, Colorado, area. Before and after dam closure, repetitive surveys between 1977 and 1992 at five cross sections downstream of the dam documented changes in channel morphology. During this 15-year period, channel width increased slightly, but channel depth increased by more than 40 percent. Within the study reach, stream gradient decreased and median bed material sizes coarsened from sand in the pools and fine gravel on the riffle to a median coarse gravel throughout the reach. The most striking visual change was from a sparse growth of streamside grasses to a dense growth of riparian woody vegetation.

  9. Ammonia downstream from HH 80 North

    Science.gov (United States)

    Girart, Jose M.; Rodriguez, Luis F.; Anglada, Guillem; Estalella, Robert; Torrelles, Jose, M.; Marti, Josep; Pena, Miriam; Ayala, Sandra; Curiel, Salvador; Noriega-Crespo, Alberto

    1994-01-01

    HH 80-81 are two optically visible Herbig-Haro (HH) objects located about 5 minutes south of their exciting source IRAS 18162-2048. Displaced symmetrically to the north of this luminous IRAS source, a possible HH counterpart was recently detected as a radio continuum source with the very large array (VLA). This radio source, HH 80 North, has been proposed to be a member of the Herbig-Haro class since its centimeter flux density, angular size, spectral index, and morphology are all similar to those of HH 80. However, no object has been detected at optical wavelengths at the position of HH 80 North, possibly because of high extinction, and the confirmation of the radio continuum source as an HH object has not been possible. In the prototypical Herbig-Haro objects HH 1 and 2, ammonia emission has been detected downstream of the flow in both objects. This detection has been intepreted as a result of an enhancement in the ammonia emission produced by the radiation field of the shock associated with the HH object. In this Letter we report the detection of the (1,1) and (2,2) inversion transitions of ammonia downstream HH 80 North. This detection gives strong suppport to the interpretation of HH 80 North as a heavily obscured HH object. In addition, we suggest that ammonia emission may be a tracer of embedded Herbig-Haro objects in other regions of star formation. A 60 micrometer IRAS source could be associated with HH 80 North and with the ammonia condensation. A tentative explanation for the far-infrared emission as arising in dust heated by their optical and UV radiation of the HH object is presented.

  10. Regulation of auxin responses in tomato fruit development

    NARCIS (Netherlands)

    Jong, M. de

    2010-01-01

    The transformation from an ovary to a rapidly growing fruit includes molecular, biochemical and structural changes that must be tightly coordinated. Depending on the phase of fruit development, the temporal and spatial organization of these changes is mediated by phytohormones, such as auxin, gibber

  11. Valuable lessons-learned in transcriptomics experimentation.

    Science.gov (United States)

    Bruning, Oskar; Rauwerda, Han; Dekker, Rob J; de Leeuw, Wim C; Wackers, Paul F K; Ensink, Wim A; Jonker, Martijs J; Breit, Timo M

    2015-01-01

    We have collected several valuable lessons that will help improve transcriptomics experimentation. These lessons relate to experiment design, execution, and analysis. The cautions, but also the pointers, may help biologists avoid common pitfalls in transcriptomics experimentation and achieve better results with their transcriptome studies.

  12. Microbial production of scleroglucan and downstream processing

    Science.gov (United States)

    Castillo, Natalia A.; Valdez, Alejandra L.; Fariña, Julia I.

    2015-01-01

    Synthetic petroleum-based polymers and natural plant polymers have the disadvantage of restricted sources, in addition to the non-biodegradability of the former ones. In contrast, eco-sustainable microbial polysaccharides, of low-cost and standardized production, represent an alternative to address this situation. With a strong global market, they attracted worldwide attention because of their novel and unique physico-chemical properties as well as varied industrial applications, and many of them are promptly becoming economically competitive. Scleroglucan, a β-1,3-β-1,6-glucan secreted by Sclerotium fungi, exhibits high potential for commercialization and may show different branching frequency, side-chain length, and/or molecular weight depending on the producing strain or culture conditions. Water-solubility, viscosifying ability and wide stability over temperature, pH and salinity make scleroglucan useful for different biotechnological (enhanced oil recovery, food additives, drug delivery, cosmetic and pharmaceutical products, biocompatible materials, etc.), and biomedical (immunoceutical, antitumor, etc.) applications. It can be copiously produced at bioreactor scale under standardized conditions, where a high exopolysaccharide concentration normally governs the process optimization. Operative and nutritional conditions, as well as the incidence of scleroglucan downstream processing will be discussed in this chapter. The relevance of using standardized inocula from selected strains and experiences concerning the intricate scleroglucan scaling-up will be also herein outlined. PMID:26528259

  13. Microbial production of scleroglucan and downstream processing

    Directory of Open Access Journals (Sweden)

    Natalia Alejandra Castillo

    2015-10-01

    Full Text Available Synthetic petroleum-based polymers and natural plant polymers have the disadvantage of restricted sources, in addition to the non-biodegradability of the former ones. In contrast, eco-sustainable microbial polysaccharides, of low-cost and standardized production, represent an alternative to address this situation. With a strong global market, they attracted worldwide attention because of their novel and unique physico-chemical properties as well as varied industrial applications, and many of them are promptly becoming economically competitive. Scleroglucan, a beta-1,3-beta-1,6-glucan secreted by Sclerotium fungi, exhibits high potential for commercialization and may show different branching frequency, side-chain length and/or molecular weight depending on the producing strain or culture conditions. Water-solubility, viscosifying ability and wide stability over temperature, pH and salinity make scleroglucan useful for different biotechnological (enhanced oil recovery, food additives, drug delivery, cosmetic and pharmaceutical products, biocompatible materials, etc., and biomedical (immunoceutical, antitumor, etc. applications. It can be copiously produced at bioreactor scale under standardized conditions, where a high EPS concentration normally governs the process optimization. Operative and nutritional conditions, as well as the incidence of scleroglucan downstream processing will be discussed in this chapter. The relevance of using standardized inocula from selected strains and experiences concerning the intricate scleroglucan scaling-up will be also herein outlined.

  14. DOWNSTREAM ECOCIDE FROM UPSTREAM WATER PIRACY

    Directory of Open Access Journals (Sweden)

    Miah Muhammad Adel

    2012-01-01

    Full Text Available Upstream India and downstream Bangladesh share more than 50 international rivers. India has set up water diversion constructions in more than 50% of these rivers, the largest one being on the Bangladesh’s northwest upon the Ganges River, puts Bangladesh’s Gangetic ecosystem at stake. In some border rivers, India has set up groins on her side of river banks. Also, Indian side pumps Bangladesh river water stealthily from border-rivers. Further, India is constructing another dam and reservoir upstream on the Barak River on the northeast of Bangladesh. Furthermore, India has chalked out a grand plan for river networking. Exploration has been made to assess the degree of the ecosystem degradation both inland and on the coast due to all water diversion constructions around the border, except for the Tipaimukh Dam in which case estimation of projected ecosystem degradation has been mentioned. Finally, Indian grand plan of river networking plan has been briefly touched upon. Site visitations, observations, surveys, measurements and interviews of professionals were made in the project country. Relevant literatures on this issue were reviewed in electronic and print databases. Related published articles in electronic and print media were systematically searched following the key words for the case. Finally, both electronic and print news media have been closely followed to know the latest developments on this issue. The reduced flow of the Ganges in Bangladesh has caused scarcity of fresh water, species endangerment and extinction, obstruction to livestock raising, loss of livelihoods, people’s displacement, changes in crop production, reduction in navigable routes, extreme weather, increased flood occurrences, scarcity of potable water, groundwater contamination, reduction in coastal sediment deposition, deterioration of the Ganges water quality and inland intrusion of saline water front. Water diversion constructions in other rivers have

  15. Understanding cross-communication between aboveground and belowground tissues via transcriptome analysis of a sucking insect whitefly-infested pepper plants.

    Science.gov (United States)

    Park, Yong-Soon; Ryu, Choong-Min

    2014-01-03

    Plants have developed defensive machinery to protect themselves against herbivore and pathogen attacks. We previously reported that aboveground whitefly (Bemisia tabaci Genn.) infestation elicited induced resistance in leaves and roots and influenced the modification of the rhizosphere microflora. In this study, to obtain molecular evidence supporting these plant fitness strategies against whitefly infestation, we performed a 300 K pepper microarray analysis using leaf and root tissues of pepper (Capsicum annuum L.) applied with whitefly, benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH), and the combination of BTH+whitefly. We defined differentially expressed genes (DEGs) as genes exhibiting more than 2-fold change (1.0 based on log2 values) in expression in leaves and roots in response to each treatment compared to the control. We identified a total of 16,188 DEGs in leaves and roots. Of these, 6685, 6752, and 4045 DEGs from leaf tissue and 6768, 7705, and 7667 DEGs from root tissue were identified in the BTH, BTH+whitefly, and whitefly treatment groups, respectively. The total number of DEGs was approximately two-times higher in roots than in whitefly-infested leaves subjected to whitefly infestation. Among DEGs, whitefly feeding induced salicylic acid and jasmonic acid/ethylene-dependent signaling pathways in leaves and roots. Several transporters and auxin-responsive genes were upregulated in roots, which can explain why biomass increase is facilitated. Using transcriptome analysis, our study provides new insights into the molecular basis of whitefly-mediated intercommunication between aboveground and belowground plant tissues and provides molecular evidence that may explain the alteration of rhizosphere microflora and root biomass by whitefly infestation.

  16. Downstream Evolution of Longitudinal Embedded Vortices with Helical Structure

    DEFF Research Database (Denmark)

    Velte, Clara Marika; Okulov, Valery; Hansen, Martin Otto Laver

    2009-01-01

    In the present work the downstream development of device induced vortices with helical symmetry embedded in wall bounded flow on a bump is studied with the aid of Stereoscopic Particle Image Velocimetry (SPIV). The downstream evolution of characteristic parameters of helical vortices is studied...

  17. PageRank-based identification of signaling crosstalk from transcriptomics data: the case of Arabidopsis thaliana.

    Science.gov (United States)

    Omranian, Nooshin; Mueller-Roeber, Bernd; Nikoloski, Zoran

    2012-04-01

    The levels of cellular organization, from gene transcription to translation to protein-protein interaction and metabolism, operate via tightly regulated mutual interactions, facilitating organismal adaptability and various stress responses. Characterizing the mutual interactions between genes, transcription factors, and proteins involved in signaling, termed crosstalk, is therefore crucial for understanding and controlling cells' functionality. We aim at using high-throughput transcriptomics data to discover previously unknown links between signaling networks. We propose and analyze a novel method for crosstalk identification which relies on transcriptomics data and overcomes the lack of complete information for signaling pathways in Arabidopsis thaliana. Our method first employs a network-based transformation of the results from the statistical analysis of differential gene expression in given groups of experiments under different signal-inducing conditions. The stationary distribution of a random walk (similar to the PageRank algorithm) on the constructed network is then used to determine the putative transcripts interrelating different signaling pathways. With the help of the proposed method, we analyze a transcriptomics data set including experiments from four different stresses/signals: nitrate, sulfur, iron, and hormones. We identified promising gene candidates, downstream of the transcription factors (TFs), associated to signaling crosstalk, which were validated through literature mining. In addition, we conduct a comparative analysis with the only other available method in this field which used a biclustering-based approach. Surprisingly, the biclustering-based approach fails to robustly identify any candidate genes involved in the crosstalk of the analyzed signals. We demonstrate that our proposed method is more robust in identifying gene candidates involved downstream of the signaling crosstalk for species for which large transcriptomics data sets

  18. MATHEMATICAL MODELLING OF DEGRADATION AND FLUVIAL PROCESS DOWNSTREAM RESERVOIRS

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    To research into the problem of degradation and fluvial process downstream reservoirs and its influence on flood control and navigation, a 1-D mathematical model of degradation and fluvial process downstream the reservoir was established in this paper. The non-equilibrium transport of non-uniform suspended load, the non-uniform bedload transport and bed material sorting were considered in the model. Some techniques were suggested for some problems in calculation, such as the effective suspended load carrying capacity of the different reaches of bed materials, the coefficient of suspended load carrying capacity, the recovering coefficient of carrying capacity, the mixed layer thickness, the bedload transport width, bifurcation and confluence of main and branch channel, and the distribution of deposition and erosion along the cross section, etc. The model was tested by the data of degradation downstream the Danjiangkou reservoir on the Hanjiang River and the data of degradation downstream the Gezhouba Project on the Yangtze River.

  19. MATHEMATICAL MODEL OF RIVER BED CHANGE DOWNSTREAM OF XIAOLANGDI RESERVOIR

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A mathematical model of river bed change downstream of the Xiaolangdi Reservoir was developed based on the most recent achievement of sediment theory in the Yellow River. The model was verified by the comparison of computed results and measured data from 1986 to 1996. Numerical prediction of the erosion and deposition downstream of the Xiaolangdi Reservoir in its first operation year was carried out, and a series of suggestions were given for reservoir operation mode in its early operation period.

  20. Downstream-based Scheduling for Energy Conservation in Green EPONs

    KAUST Repository

    Chen, Shen

    2012-05-01

    Maximizing the optical network unit’s (ONU) sleep time is an effective approach for achieving maximum energy conservation in green Ethernet passive optical networks (EPONs). While overlapping downstream and upstream ONU transmissions can maximize the ONU sleep time, it jeopardizes the quality of service (QoS) performance of the network, especially for downstream traffic in case the overlapping is based on the upstream time slot. In this paper, we study the downstream traffic performance in green EPONs under the limited service discipline and the upstream-based overlapped time window. Specifically, we first derive the expected mean packet delay, and then present a closed-form expression of the ONU sleep time, setting identical upstream/downstream transmission cycle times based on a maximum downstream traffic delay re-quirement. With the proposed system model, we present a novel downstream bandwidth allocation scheme for energy conservation in green EPONs. Simulation results verify the proposed model and highlight the advantages of our scheme over conventional approaches.

  1. Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions.

    Science.gov (United States)

    Gong, Lei; Zhang, Hongxia; Gan, Xiaoyan; Zhang, Li; Chen, Yuchao; Nie, Fengjie; Shi, Lei; Li, Miao; Guo, Zhiqian; Zhang, Guohui; Song, Yuxia

    2015-01-01

    Drought stress can seriously affect tuberization, yield and quality of potato plant. However, the precise molecular mechanisms governing potato stolon's response to drought stress and water supply are not very well understood. In this work, a potato (Solanum tuberosum L.) variant, Ningshu 4, was subjected to severe drought stress treatment (DT) and re-watering treatment (RWT) at tuber bulking stage. Strand-specific cDNA libraries of stolon materials were constructed for paired-end transcriptome sequencing analyses and differentially expressed gene (DEG) examination. In comparison to untreated-control (CT) plants, 3189 and 1797 DEGs were identified in DT and RWT plants and 4154 solely expressed DEGs were screened out from these two comparison groups. Interestingly, 263 genes showed opposite expression patterns in DT and RWT plants. Among them, genes homologous to Protein Phosphatase 2C (PP2C), Aspartic protease in guard cell 1 (ASPG1), auxin-responsive protein, Arabidopsis pseudo response regualtor 2 (APRR2), GA stimulated transcripts in Arabidopsis 6 (GASA6), Calmodulin-like protein 19 (CML19), abscisic acid 8'-hydroxylases and calcium-transporting ATPase, et al. were related with drought-stress and water stimulus response. Sixteen DEGs involved in starch synthesis, accumulation and tuber formation exhibited significantly different expression upon re-watering. In addition, 1630, 1527 and 1596 transcription factor encoding genes were detected in CT, DT and RWT. DEGs of ERF, bHLH, MYB, NAC, WRKY, C2H2, bZIP and HD-ZIP families accounted for 50% in three comparison groups, respectively. Furthermore, characteristics of 565 gene ontology (GO) and 108 Kyoto Encyclopedia of Genes and Genomes pathways (KEGG) were analyzed with the 4154 DEGs. All these results suggest that the drought- and water-stimulus response could be implemented by the regulated expression of metabolic pathway DEGs, and these genes were involved in the endogenous hormone biosynthesis and signal

  2. Identifying master regulators of cancer and their downstream targets by integrating genomic and epigenomic features.

    Science.gov (United States)

    Gevaert, Olivier; Plevritis, Sylvia

    2013-01-01

    Vast amounts of molecular data characterizing the genome, epigenome and transcriptome are becoming available for a variety of cancers. The current challenge is to integrate these diverse layers of molecular biology information to create a more comprehensive view of key biological processes underlying cancer. We developed a biocomputational algorithm that integrates copy number, DNA methylation, and gene expression data to study master regulators of cancer and identify their targets. Our algorithm starts by generating a list of candidate driver genes based on the rationale that genes that are driven by multiple genomic events in a subset of samples are unlikely to be randomly deregulated. We then select the master regulators from the candidate driver and identify their targets by inferring the underlying regulatory network of gene expression. We applied our biocomputational algorithm to identify master regulators and their targets in glioblastoma multiforme (GBM) and serous ovarian cancer. Our results suggest that the expression of candidate drivers is more likely to be influenced by copy number variations than DNA methylation. Next, we selected the master regulators and identified their downstream targets using module networks analysis. As a proof-of-concept, we show that the GBM and ovarian cancer module networks recapitulate known processes in these cancers. In addition, we identify master regulators that have not been previously reported and suggest their likely role. In summary, focusing on genes whose expression can be explained by their genomic and epigenomic aberrations is a promising strategy to identify master regulators of cancer.

  3. Transcriptomic Analysis for Different Sex Types of Ricinus communis L. during Development from Apical Buds to Inflorescences by Digital Gene Expression Profiling.

    Science.gov (United States)

    Tan, Meilian; Xue, Jianfeng; Wang, Lei; Huang, Jiaxiang; Fu, Chunling; Yan, Xingchu

    2015-01-01

    The castor plant (Ricinus communis L.) is a versatile industrial oilseed crop with a diversity of sex patterns, its hybrid breeding for improving yield and high purity is still hampered by genetic instability of female and poor knowledge of sex expression mechanisms. To obtain some hints involved in sex expression and provide the basis for further insight into the molecular mechanisms of castor plant sex determination, we performed DGE analysis to investigate differences between the transcriptomes of apices and racemes derived from female (JXBM0705P) and monoecious (JXBM0705M) lines. A total of 18 DGE libraries were constructed from the apices and racemes of a wild monoecious line and its isogenic female derivative at three stages of apex development, in triplicate. Approximately 5.7 million clean tags per library were generated and mapped to the reference castor genome. Transcriptomic analysis showed that identical dynamic changes of gene expression were indicated in monoecious and female apical bud during its development from vegetation to reproduction, with more genes expressed at the raceme formation and infant raceme stages compare to the early leaf bud stage. More than 3000 of differentially expressed genes (DEGs) were detected in Ricinus apices at three developmental stages between two different sex types. A number of DEGs involved in hormone response and biosynthesis, such as auxin response and transport, transcription factors, signal transduction, histone demethylation/methylation, programmed cell death, and pollination, putatively associated with sex expression and reproduction were discovered, and the selected DEGs showed consistent expression between qRT-PCR validation and the DGE patterns. Most of those DEGs were suppressed at the early leaf stage in buds of the mutant, but then activated at the following transition stage (5-7-leaf stage) of buds in the mutant, and ultimately, the number of up-regulated DEGs was equal to that of down-regulation in the

  4. Transcriptomic analysis for different sex types of Ricinus communis L. during development from apical buds to inflorescences by digital gene expression profiling

    Directory of Open Access Journals (Sweden)

    Tan eMeilian

    2016-02-01

    Full Text Available The castor plant (Ricinus communis L. is a versatile industrial oilseed crop with a diversity of sex patterns, its hybrid breeding for improving yield and high purity is still hampered by genetic instability of female and poor knowledge of sex expression mechanisms. To obtain some hints involved in sex expression and provide the basis for further insight into the molecular mechanisms of castor plant sex determination, we performed DGE analysis to investigate differences between the transcriptomes of apices and racemes derived from female (JXBM0705P and monoecious (JXBM0705M lines. A total of 18 DGE libraries were constructed from the apices and racemes of a wild monoecious line and its isogenic female derivative at three stages of apex development, in triplicate. Approximately 5.7 million clean tags per library were generated and mapped to the reference castor genome. Transcriptomic analysis showed that identical dynamic changes of gene expression were indicated in monoecious and female apical bud during its development from vegetation to reproduction, with more genes expressed at the raceme formation and infant raceme stages compare to the early leaf bud stage. More than 3 thousands of differentially expressed genes (DEGs were detected in Ricinus apices at three developmental stages between two different sex types. A number of DEGs involved in hormone response and biosynthesis, especially auxin response and transport, transcription factors, signal transduction, histone demethylation/methylation, programmed cell death, and pollination, putatively associated with sex expression and reproduction were discovered, and the selected DEGs showed consistent expression between qRT-PCR validation and the DGE patterns. Most of those DEGs were suppressed at the early leaf stage in buds of the mutant, but then activated at the following transition stage (5-7-leaf stage of buds in the mutant, and ultimately, the number of up-regulated DEGs was equal to that

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

    Directory of Open Access Journals (Sweden)

    Murukarthick Jayakodi

    2014-10-01

    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.

  6. Developmental transcriptome of Aplysia californica'

    KAUST Repository

    Heyland, Andreas

    2010-12-06

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

  7. Experimental investigation of unsteady fan flow interaction with downstream struts

    Science.gov (United States)

    Ng, W. F.; Obrien, W. F.; Olsen, T. L.

    1986-07-01

    In the present study of the unsteady pressure field produced on fan rotor blades by interaction with downstream struts, a single stage, low speed axial-flow fan was instrumented with blade-mounted high frequency pressure transducers. In addition, stationary pressure problems were used to map out the flowfield. Fluctuating pressure measurements are presented for blade midspan and 85-percent span on both the suction and pressure surfaces of the rotor blades at several positions of the downstream struts, and for two different flow coefficients. The strut is found to produce an effect on the unsteady pressure field on the rotor blades; this effect exceeds that due to the stator at design rotor-stator-strut spacing, but it rapidly declines as the struts are moved downstream.

  8. Transition duct with divided upstream and downstream portions

    Energy Technology Data Exchange (ETDEWEB)

    McMahan, Kevin Weston; LeBegue, Jeffrey Scott; Maldonado, Jaime Javier; Dillard, Daniel Jackson; Flanagan, James Scott

    2015-07-14

    Turbine systems are provided. In one embodiment, a turbine system includes a transition duct comprising an inlet, an outlet, and a duct passage extending between the inlet and the outlet and defining a longitudinal axis, a radial axis, and a tangential axis. The outlet of the transition duct is offset from the inlet along the longitudinal axis and the tangential axis. The duct passage includes an upstream portion extending from the inlet and a downstream portion extending from the outlet. The turbine system further includes a rib extending from an outer surface of the duct passage, the rib dividing the upstream portion and the downstream portion.

  9. Distinct signal transduction pathways downstream of the (PRR revealed by microarray and ChIP-chip analyses.

    Directory of Open Access Journals (Sweden)

    Daniela Zaade

    Full Text Available The (prorenin receptor ((PRR signaling is involved in different pathophysiologies ranging from cardiorenal end-organ damage via diabetic retinopathy to tumorigenesis. We have previously shown that the transcription factor promyelocytic leukemia zinc finger (PLZF is an adaptor protein of the (PRR. Furthermore, recent publications suggest that major functions of the (PRR are mediated ligand-independently by its transmembrane and intracellular part, which acts as an accessory protein of V-ATPases. The transcriptome and recruitmentome downstream of the V-ATPase function and PLZF in the context of the (PRR are currently unknown. Therefore, we performed a set of microarray and chromatin-immunoprecipitation (ChIP-chip experiments using siRNA against the (PRR, stable overexpression of PLZF, the PLZF translocation inhibitor genistein and the specific V-ATPase inhibitor bafilomycin to dissect transcriptional pathways downstream of the (PRR. We were able to identify distinct and overlapping genetic signatures as well as novel real-time PCR-validated target genes of the different molecular functions of the (PRR. Moreover, bioinformatic analyses of our data confirm the role of (PRŔs signal transduction pathways in cardiovascular disease and tumorigenesis.

  10. Transcriptome analysis of Aedes aegypti transgenic mosquitoes with altered immunity.

    Directory of Open Access Journals (Sweden)

    Zhen Zou

    2011-11-01

    Full Text Available The mosquito immune system is involved in pathogen-elicited defense responses. The NF-κB factors REL1 and REL2 are downstream transcription activators of Toll and IMD immune pathways, respectively. We have used genome-wide microarray analyses to characterize fat-body-specific gene transcript repertoires activated by either REL1 or REL2 in two transgenic strains of the mosquito Aedes aegypti. Vitellogenin gene promoter was used in each transgenic strain to ectopically express either REL1 (REL1+ or REL2 (REL2+ in a sex, tissue, and stage specific manner. There was a significant change in the transcript abundance of 297 (79 up- and 218 down-regulated and 299 (123 up- and 176 down-regulated genes in fat bodies of REL1+ and REL2+, respectively. Over half of the induced genes had predicted functions in immunity, and a large group of these was co-regulated by REL1 and REL2. By generating a hybrid transgenic strain, which ectopically expresses both REL1 and REL2, we have shown a synergistic action of these NF-κB factors in activating immune genes. The REL1+ immune transcriptome showed a significant overlap with that of cactus (RNAi-depleted mosquitoes (50%. In contrast, the REL2+ -regulated transcriptome differed from the relatively small group of gene transcripts regulated by RNAi depletion of a putative inhibitor of the IMD pathway, caspar (35 up- and 140 down-regulated, suggesting that caspar contributes to regulation of a subset of IMD-pathway controlled genes. Infections of the wild type Ae. aegypti with Plasmodium gallinaceum elicited the transcription of a distinct subset of immune genes (76 up- and 25 down-regulated relative to that observed in REL1+ and REL2+ mosquitoes. Considerable overlap was observed between the fat body transcriptome of Plasmodium-infected mosquitoes and that of mosquitoes with transiently depleted PIAS, an inhibitor of the JAK-STAT pathway. PIAS gene silencing reduced Plasmodium proliferation in Ae. aegypti, indicating

  11. Downstream processing of Isochrysis galbana: a step towards microalgal biorefinery

    NARCIS (Netherlands)

    Gilbert-López, B.; Mendiola, J.A.; Fontecha, J.; Broek, van den L.A.M.; Sijtsma, L.; Cifuentes, A.; Herrero, M.; Ibáñez, E.

    2015-01-01

    An algae-based biorefinery relies on the efficient use of algae biomass through its fractionation of several valuable/bioactive compounds that can be used in industry. If this biorefinery includes green platforms as downstream processing technologies able to fulfill the requirements of green chemist

  12. Patents and Downstream Innovation Suppression - Facts or Fiction?

    DEFF Research Database (Denmark)

    Howells, John

    Merges and Nelson have proposed that pioneer patents have enabled their owners to 'block' or 'hold-up' downstream innovation in cases as important as the car, radio, aircraft and electric lighting (Merges and Nelson 1990, ; Merges and Nelson 1994). Merges and Nelson use their work to question...

  13. Modeling downstream fining in sand-bed rivers. II: Application

    Science.gov (United States)

    Wright, S.; Parker, G.

    2005-01-01

    In this paper the model presented in the companion paper, Wright and Parker (2005) is applied to a generic river reach typical of a large, sand-bed river flowing into the ocean in order to investigate the mechanisms controlling longitudinal profile development and downstream fining. Three mechanisms which drive downstream fining are studied: a delta prograding into standing water, sea-level rise, and tectonic subsidence. Various rates of sea-level rise (typical of the late Holocene) and tectonic subsidence are modeled in order to quantify their effects on the degree of profile concavity and downstream fining. Also, several other physical mechanisms which may affect fining are studied, including the relative importance of the suspended versus bed load, the effect of the loss of sediment overbank, and the influence of the delta bottom slope. Finally, sensitivity analysis is used to show that the grain-size distribution at the interface between the active layer and substrate has a significant effect on downstream fining. ?? 2005 International Association of Hydraulic Engineering and Research.

  14. Extreme wave phenomena in down-stream running modulated waves

    NARCIS (Netherlands)

    Andonowati,; Karjanto, N.; Groesen, van E.

    2006-01-01

    Modulational, Benjamin-Feir, instability is studied for the down-stream evolution of surface gravity waves. An explicit solution, the soliton on finite background, of the NLS equation in physical space is used to study various phenomena in detail. It is shown that for sufficiently long modulation le

  15. DNS and RANS Simulation of Dispersion Downstream of an Obstacle

    Science.gov (United States)

    2008-12-01

    DNS AND RANS SIMULATION OF DISPERSION DOWNSTREAM OF AN OBSTACLE Riccardo Rossi*, Gianluca Iaccarino** * Laboratorio di Termofluidodinamica...ORGANIZATION NAME(S) AND ADDRESS(ES) Laboratorio di Termofluidodinamica Computazionale, Seconda Facolt‘a di Ingegneria di Forl‘ý Universit‘a di Bologna

  16. Flow diagnostics downstream of a tribladed rotor model

    DEFF Research Database (Denmark)

    Naumov, I. V.; Rahmanov, V. V.; Okulov, Valery

    2012-01-01

    This paper presents results of a study of vortex wake structures and measurements of instantaneous 3D velocity fields downstream of a triblade turbine model. Two operation modes of flow around the rotor with different tip speed ratios were tested. Initially the wake structures were visualized and...

  17. Downstream-migrating fluvial point bars in the rock record

    Science.gov (United States)

    Ghinassi, Massimiliano; Ielpi, Alessandro; Aldinucci, Mauro; Fustic, Milovan

    2016-04-01

    Classical models developed for ancient fluvial point bars are based on the assumption that meander bends invariably increase their radius as meander-bend apices migrate in a direction transverse to the channel-belt axis (i.e., meander bend expansion). However, many modern meandering rivers are also characterized by down-valley migration of the bend apex, a mechanism that takes place without a significant change in meander radius and wavelength. Downstream-migrating fluvial point bars (DMFPB) are the dominant architectural element of these types of meander belts. Yet they are poorly known from ancient fluvial-channel belts, since their disambiguation from expansional point bars often requires fully-3D perspectives. This study aims to review DMFPB deposits spanning in age from Devonian to Holocene, and to discuss their main architectural and sedimentological features from published outcrop, borehole and 3D-seismic datasets. Fluvial successions hosting DMFPB mainly accumulated in low accommodation conditions, where channel belts were affected by different degrees of morphological (e.g., valleys) or tectonic (e.g., axial drainage of shortening basins) confinement. In confined settings, bends migrate downstream along the erosion-resistant valley flanks and little or no floodplain deposits are preserved. Progressive floor aggradation (e.g., valley filling) allow meander belts with DMFPB to decrease their degree of confinement. In less confined settings, meander bends migrate downstream mainly after impinging against older, erosion-resistant channel fill mud. By contrast, tectonic confinement is commonly associated with uplifted alluvial plains that prevented meander-bend expansion, in turn triggering downstream translation. At the scale of individual point bars, translational morphodynamics promote the preservation of downstream-bar deposits, whereas the coarser-grained upstream and central beds are less frequently preserved. However, enhanced preservation of upstream

  18. A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads

    Directory of Open Access Journals (Sweden)

    Stanley Kimbung Mbandi

    2014-02-01

    Full Text Available Downstream analyses of short-reads from next-generation sequencing platforms are often preceded by a pre-processing step that removes uncalled and wrongly called bases. Standard approaches rely on their associated base quality scores to retain the read or a portion of it when the score is above a predefined threshold. It is difficult to differentiate sequencing error from biological variation without a reference using quality scores. The effects of quality score based trimming have not been systematically studied in de novo transcriptome assembly. Using RNA-Seq data produced from Illumina, we teased out the effects of quality score base filtering or trimming on de novo transcriptome reconstruction. We showed that assemblies produced from reads subjected to different quality score thresholds contain truncated and missing transfrags when compared to those from untrimmed reads. Our data supports the fact that de novo assembling of untrimmed data is challenging for de Bruijn graph assemblers. However, our results indicates that comparing the assemblies from untrimmed and trimmed read subsets can suggest appropriate filtering parameters and enable selection of the optimum de novo transcriptome assembly in non-model organisms.

  19. Transcriptome analysis of ein3 eil1 mutants in response to iron deficiency.

    Science.gov (United States)

    Bauer, Petra; Blondet, Eddy

    2011-11-01

    Multiple transcriptome and proteome studies indicated that the micronutrient deficiency stress caused by lack of iron results in increased molecular responses for the mobilization and uptake of iron and also in altered metabolic adaptation and stress responses. Recently, we identified the ethylene-regulated transcription factors ETHYLENE INSENSITIVE3 (EIN3) and EIN3-LIKE1 (EIL1) as protein interaction partners of the Fe deficiency response regulator and transcription factor FER-LIKE FE DEFINCY-INDUCED TRANSCRPTION FACTOR1 (FIT). EIN3/EIL1 contribute to high level gene expression of FIT downstream genes and also promote FIT protein abundance. Transcriptome analyses showed that more genes were differentially regulated in ein3 eil1 mutants versus wild type upon iron deficiency than upon sufficient iron supply. Moreover, several of the differentially expressed genes are implicated in photo-oxidative stress responses in leaves. We therefore speculated that by enhancing Fe uptake through interaction with FIT and by re-organizing the photo-oxidative stress responses, EIN3/EIL1 might contribute to decreasing photo-oxidative stress that may occur under light conditions in response to Fe deficiency. Here, we present an additional analysis of our previously published transcriptome data of ein3 eil1 and wild type between sufficient iron supply and iron deficiency, respectively.

  20. Integrative investigation of metabolic and transcriptomic data

    Directory of Open Access Journals (Sweden)

    Önsan Z İlsen

    2006-04-01

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

  1. A novel virtual hub approach for multisource downstream service integration

    Science.gov (United States)

    Previtali, Mattia; Cuca, Branka; Barazzetti, Luigi

    2016-08-01

    A large development of downstream services is expected to be stimulated starting from earth observations (EO) datasets acquired by Copernicus satellites. An important challenge connected with the availability of downstream services is the possibility for their integration in order to create innovative applications with added values for users of different categories level. At the moment, the world of geo-information (GI) is extremely heterogeneous in terms of standards and formats used, thus preventing a facilitated access and integration of downstream services. Indeed, different users and data providers have also different requirements in terms of communication protocols and technology advancement. In recent years, many important programs and initiatives have tried to address this issue even on trans-regional and international level (e.g. INSPIRE Directive, GEOSS, Eye on Earth and SEIS). However, a lack of interoperability between systems and services still exists. In order to facilitate the interaction between different downstream services, a new architectural approach (developed within the European project ENERGIC OD) is proposed in this paper. The brokering-oriented architecture introduces a new mediation layer (the Virtual Hub) which works as an intermediary to bridge the gaps linked to interoperability issues. This intermediation layer de-couples the server and the client allowing a facilitated access to multiple downstream services and also Open Data provided by national and local SDIs. In particular, in this paper an application is presented integrating four services on the topic of agriculture: (i) the service given by Space4Agri (providing services based on MODIS and Landsat data); (ii) Gicarus Lab (providing sample services based on Landsat datasets) and (iii) FRESHMON (providing sample services for water quality) and services from a several regional SDIs.

  2. Downstream migrating antidunes or in-phase waves?

    Science.gov (United States)

    Núñez González, Francisco

    2014-05-01

    Late back in the beginning of the 20th century, Gilbert observed bedforms that migrated in opposite direction to flow. Since this feature was remarkable and inverse to the behavior of dunes (most often observed in rivers and flumes), he called the new species antidunes. Subsequent researchers identified other characteristic attributes of the new species, and it was later commonly accepted that a defining characteristic of antidunes was that undulations of bed and water profiles were roughly in-phase. Due to its generality, such definition has given place to some ambiguities, particularly when dealing with bedforms close to the critical-supercritical transition, as occurs with bedforms with bed and water profiles roughly in-phase but migrating downstream. Such bedforms are described by different researchers, but they are not always classified as antidunes. Some sedimentologists argue that given the depositional pattern of such streamwise migrating forms is different to that of upstream-migrating antidunes, the more generic term "in-phase waves" should be applied to consider them as a different class. The lack of a stability field for 2D downstream-migrating antidunes in the classical theoretical study of Kennedy in the early sixties, has also contributed to some confusion. According to such theoretical diagram, downstream-migrating antidunes could only exist being 3D, but empirical evidences -even from Kennedy- contradict this outcome. In this work, such results and other morphodynamic features of downstream-migrating antidunes will be discussed, in light of experimental data and a simple hydraulic analysis of the direction of movement of antidunes. An open question will be left to debate about the appropriateness of classifying downstream-migrating in-phase waves as antidunes, and it will be emphasized that finding consensus between different disciplines involved with the study of bedforms will be advantageous.

  3. DNA methylation and transcriptomic changes in response to different lights and stresses in 7B-1 male-sterile tomato.

    Science.gov (United States)

    Omidvar, Vahid; Fellner, Martin

    2015-01-01

    We reported earlier that 7B-1 mutant in tomato (Solanum lycopersicum L., cv. Rutgers), an ABA overproducer, is defective in blue light (B) signaling leading to B-specific resistance to abiotic and biotic stresses. Using a methylation-sensitive amplified polymorphism (MSAP) assay, a number of genes were identified, which were differentially methylated between 7B-1 and its wild type (WT) seedlings in white (W), blue (B), red (R) lights and dark (D) or in response to exogenous ABA and mannitol-induced stresses. The genomic methylation level was almost similar in different lights between 7B-1 and WT seedlings, while significant differences were observed in response to stresses in D, but not B. Using a cDNA-AFLP assay, several transcripts were identified, which were differentially regulated between 7B-1 and WT by B or D or in response to stresses. Blue light receptors cryptochrome 1 and 2 (CRY1 and CRY2) and phototropin 1 and 2 (PHOT1 and PHOT2) were not affected by the 7B-1 mutation at the transcriptional level, instead the mutation had likely affected downstream components of the light signaling pathway. 5-azacytidine (5-azaC) induced DNA hypomethylation, inhibited stem elongation and differentially regulated the expression of a number of genes in 7B-1. In addition, it was shown that mir167 and mir390 were tightly linked to auxin signaling pathway in 5-azaC-treated 7B-1 seedlings via the regulation of auxin-response factor (ARF) transcripts. Our data showed that DNA methylation remodeling is an active epigenetic response to different lights and stresses in 7B-1 and WT, and highlighted the differences in epigenetic and transcriptional regulation of light and stress responses between 7B-1 and WT. Furthermore, it shed lights on the crosstalk between DNA hypomethylation and miRNA regulation of ARFs expression. This information could also be used as a benchmark for future studies of male-sterility in other crops.

  4. DNA methylation and transcriptomic changes in response to different lights and stresses in 7B-1 male-sterile tomato.

    Directory of Open Access Journals (Sweden)

    Vahid Omidvar

    Full Text Available We reported earlier that 7B-1 mutant in tomato (Solanum lycopersicum L., cv. Rutgers, an ABA overproducer, is defective in blue light (B signaling leading to B-specific resistance to abiotic and biotic stresses. Using a methylation-sensitive amplified polymorphism (MSAP assay, a number of genes were identified, which were differentially methylated between 7B-1 and its wild type (WT seedlings in white (W, blue (B, red (R lights and dark (D or in response to exogenous ABA and mannitol-induced stresses. The genomic methylation level was almost similar in different lights between 7B-1 and WT seedlings, while significant differences were observed in response to stresses in D, but not B. Using a cDNA-AFLP assay, several transcripts were identified, which were differentially regulated between 7B-1 and WT by B or D or in response to stresses. Blue light receptors cryptochrome 1 and 2 (CRY1 and CRY2 and phototropin 1 and 2 (PHOT1 and PHOT2 were not affected by the 7B-1 mutation at the transcriptional level, instead the mutation had likely affected downstream components of the light signaling pathway. 5-azacytidine (5-azaC induced DNA hypomethylation, inhibited stem elongation and differentially regulated the expression of a number of genes in 7B-1. In addition, it was shown that mir167 and mir390 were tightly linked to auxin signaling pathway in 5-azaC-treated 7B-1 seedlings via the regulation of auxin-response factor (ARF transcripts. Our data showed that DNA methylation remodeling is an active epigenetic response to different lights and stresses in 7B-1 and WT, and highlighted the differences in epigenetic and transcriptional regulation of light and stress responses between 7B-1 and WT. Furthermore, it shed lights on the crosstalk between DNA hypomethylation and miRNA regulation of ARFs expression. This information could also be used as a benchmark for future studies of male-sterility in other crops.

  5. An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison.

    Science.gov (United States)

    Terrasson, Emmanuel; Buitink, Julia; Righetti, Karima; Ly Vu, Benoit; Pelletier, Sandra; Zinsmeister, Julia; Lalanne, David; Leprince, Olivier

    2013-01-01

    Desiccation tolerance (DT) is the capacity to withstand total loss of cellular water. It is acquired during seed filling and lost just after germination. However, in many species, a germinated seed can regain DT under adverse conditions such as osmotic stress. The genes, proteins and metabolites that are required to establish this DT is referred to as the desiccome. It includes both a range of protective mechanisms and underlying regulatory pathways that remain poorly understood. As a first step toward the identification of the seed desiccome of Medicago truncatula, using updated microarrays we characterized the overlapping transcriptomes associated with acquisition of DT in developing seeds and the re-establishment of DT in germinated seeds using a polyethylene glycol treatment (-1.7 MPa). The resulting list contained 740 and 2829 transcripts whose levels, respectively, increased and decreased with DT. Fourty-eight transcription factors (TF) were identified including MtABI3, MtABI5 and many genes regulating flowering transition and cell identity. A promoter enrichment analysis revealed a strong over-representation of ABRE elements together with light-responsive cis-acting elements. In Mtabi5 Tnt1 insertion mutants, DT could no longer be re-established by an osmotic stress. Transcriptome analysis on Mtabi5 radicles during osmotic stress revealed that 13 and 15% of the up-regulated and down-regulated genes, respectively, are mis-regulated in the mutants and might be putative downstream targets of MtABI5 implicated in the re-establishment of DT. Likewise, transcriptome comparisons of the desiccation sensitive Mtabi3 mutants and hairy roots ectopically expressing MtABI3 revealed that 35 and 23% of the up-regulated and down-regulated genes are acting downstream of MtABI3. Our data suggest that ABI3 and ABI5 have complementary roles in DT. Whether DT evolved by co-opting existing pathways regulating flowering and cellular phase transition and cell identity is discussed.

  6. Metabolomic Dynamic Analysis of Hypoxia in MDA-MB-231 and the Comparison with Inferred Metabolites from Transcriptomics Data

    Directory of Open Access Journals (Sweden)

    Yufeng Jane Tseng

    2013-05-01

    Full Text Available Hypoxia affects the tumor microenvironment and is considered important to metastasis progression and therapy resistance. Thus far, the majority of global analyses of tumor hypoxia responses have been limited to just a single omics level. Combining multiple omics data can broaden our understanding of tumor hypoxia. Here, we investigate the temporal change of the metabolite composition with gene expression data from literature to provide a more comprehensive insight into the system level in response to hypoxia. Nuclear magnetic resonance spectroscopy was used to perform metabolomic profiling on the MDA-MB-231 breast cancer cell line under hypoxic conditions. Multivariate statistical analysis revealed that the metabolic difference between hypoxia and normoxia was similar over 24 h, but became distinct over 48 h. Time dependent microarray data from the same cell line in the literature displayed different gene expressions under hypoxic and normoxic conditions mostly at 12 h or earlier. The direct metabolomic profiles show a large overlap with theoretical metabolic profiles deduced from previous transcriptomic studies. Consistent pathways are glycolysis/gluconeogenesis, pyruvate, purine and arginine and proline metabolism. Ten metabolic pathways revealed by metabolomics were not covered by the downstream of the known transcriptomic profiles, suggesting new metabolic phenotypes. These results confirm previous transcriptomics understanding and expand the knowledge from existing models on correlation and co-regulation between transcriptomic and metabolomics profiles, which demonstrates the power of integrated omics analysis.

  7. Patents and Downstream Innovation Suppresion - Facts or Fiction?

    DEFF Research Database (Denmark)

    Howells, John

    Merges and Nelson have proposed that pioneer patents of "broad" scope (where the claimed scope is typically broader than that strictly justified by the invention) enable their owners to "block" or "hold-up" downstream innovation.[1] They claim to have illustrated this thesis in such important cases...... of development as aircraft, the car, radio and electric lighting. Merges and Nelson quite logically use their work to question the value of Kitch's prospect theory of patents,[2] a theory that emphasises that the social value of patents is that they enable the coordination of technological development....... This article re-examines Merges and Nelson's illustrative historical-empirical evidence and finds their thesis of downstream innovation suppression to be unwarranted by their empirical evidence.[3] Instead, Merges and Nelson have selected a number of important historical cases in which the administration...

  8. Downstream plasma parameters in laminar shocks from ion kinetics

    Science.gov (United States)

    Gedalin, M.

    2016-10-01

    Ion dynamics in oblique shocks is governed by the macroscopic electric and magnetic fields of the shock front. In laminar shocks, these fields are time-independent and depend only on the coordinate along the shock normal. The shock ramp is narrow and the ion motion across the shock is manifestly non-adiabatic. The ion distribution just behind the ramp is significantly non-gyrotropic. Gyrotropy is achieved well behind the ramp mainly due to the gyrophase mixing. The asymptotic values of the ion density and temperature are determined by the eventual collisionless relaxation of the gyrating ion distribution. Given a distribution at the downstream edge of the ramp, the moments of the distribution after gyrophase mixing are derived using proper spatial averaging. The obtained expressions can be used for independent determination of the downstream plasma state and implementation in Rankine-Hugoniot relations.

  9. Upstream-downstream cooperation approach in Guanting Reservoir watershed

    Institute of Scientific and Technical Information of China (English)

    YANG Zhi-feng; ZHANG Wen-guo

    2005-01-01

    A case study is introduced and discussed concerning water dispute of misuse and pollution between up- and down-stream parts.The relations between water usage and local industrial structures are analyzed. Results show it is important to change industrial structures of the target region along with controlling water pollution by technical and engineering methods. Three manners of upstream-downstream cooperation are presented and discussed based on the actual conditions of Guangting Reservoir watershed, Two typical scenarios are supposed and studied along with the local plan on water resources development. The best solution for this cooperation presents a good way to help the upstream developing in a new pattern of eco-economy.

  10. Dead zone area at the downstream flow of barrages

    Directory of Open Access Journals (Sweden)

    Mohamed F. Sauida

    2016-12-01

    Full Text Available Flow separation is a natural phenomenon encountered at some cases downstream of barrages. The main flow is divided into current and dead zone flows. The percentage area of dead zone flow must be taken into consideration downstream of barrages, due to its negative effect on flow characteristics. Experimental studies were conducted in the Hydraulic Research Institute (HRI, on a physical regulator model with five vents. Theoretically the separation zone is described as a part of an ellipse which is practically verified by plotting velocity vectors. The results show that the percentage area of dead zone to the area through length of separation depends mainly on the expansion ratio [channel width to width of opened vents], with maximum value of 81% for operated side gates. A statistical analysis was derived, to predict the percentage area of dead zone flow to the area through length of separation.

  11. Supply Chain Modeling: Downstream Risk Assessment Methodology (DRAM)

    Science.gov (United States)

    2013-12-05

    Supply Chain Modeling: Downstream Risk Assessment Methodology (DRAM) Dr. Sean Barnett December 5, 2013 Institute for Defense Analyses Alexandria, Virginia DMSMS Conference 2013 These Slides are Unclassified and Not Proprietary Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the

  12. Unsteady Interaction Between a Transonic Turbine Stage and Downstream Components

    OpenAIRE

    Davis Roger; Yao Jixian; Clark John; Stetson Gary; Alonso Juan; Jameson Antony; Haldeman Charles; Dunn Michael

    2004-01-01

    Results from a numerical simulation of the unsteady flow through one quarter of the circumference of a transonic high-pressure turbine stage, transition duct, and low-pressure turbine first vane are presented and compared with experimental data. Analysis of the unsteady pressure field resulting from the simulation shows the effects of not only the rotor/stator interaction of the high-pressure turbine stage but also new details of the interaction between the blade and the downstream transition...

  13. Innovation Incentive of Downstream Firms in Stackelberg Duopoly Model

    Institute of Scientific and Technical Information of China (English)

    Guo Hongzhen; Yan Qingyou; Huang Wenjie

    2006-01-01

    The licensing strategies and innovation incentives of downstream firms in a Stackelberg duopoly model were analyzed under three respective assumptions that upstream industry is monopoly, duopoly, or perfect competition. It is found that the Stackelberg firm may license his drastic innovation by a fixed royalty rate which is lower than innovation size. The incentives of drastic innovation of Stackelberg firm facing input suppliers with market power decrease considerably even under royalty licensing,compared with facing perfectly competitive input market.

  14. De novo Transcriptome Analysis in Perennial Ryegrass

    DEFF Research Database (Denmark)

    Farrell, Jacqueline Danielle; Byrne, Stephen; Asp, Torben

    selection will be the availability of a reference genome, and efforts are underway within our group to deliver this. An important step in de novo assembly will be defining the gene set, and the availability of transcriptome sequencing data will greatly aid gene prediction and validation, and the development...... of functional markers for improved ryegrass breeding. Therefore, the goal of this study is to analyze a de novo assembly of the perennial ryegrass transcriptome from the same inbred genotype being used for de novo genome assembly. Furthermore, we also conducted de novo transcriptome assembly with other......Perennial ryegrass (Lolium perenne L.) is an important grass species for both forage and amenity purposes for temperate regions worldwide. It is envisaged that breeding efforts may be enhanced with the assistance of new breeding technologies such as genomic selection. A major step towards genomic...

  15. The Human Transcriptome: An Unfinished Story

    Directory of Open Access Journals (Sweden)

    Mihaela Pertea

    2012-06-01

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

  16. A consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: Assembly of the duck (Anas platyrhynchos transcriptome.

    Directory of Open Access Journals (Sweden)

    Joanna eMoreton

    2014-06-01

    Full Text Available For vertebrate organisms where a reference genome is not available, de novo transcriptome assembly enables a cost effective insight into the identification of tissue specific or differentially expressed genes and variation of the coding part of the genome. However, since there are a number of different tools and parameters that can be used to reconstruct transcripts, it is difficult to determine an optimal method. Here we suggest a pipeline based on (1 assessing the performance of three different assembly tools (2 using both single and multiple k-mer approaches (3 examining the influence of the number of reads used in the assembly (4 merging assemblies from different tools. We use an example dataset from the vertebrate Anas platyrhynchos domestica (Pekin duck. We find that taking a subset of data enables a robust assembly to be produced by multiple methods without the need for very high memory capacity. The use of reads mapped back to transcripts (RMBT and CEGMA (Core Eukaryotic Genes Mapping Approach provides useful metrics to determine the completeness of assembly obtained. For this dataset the use of multiple k-mers in the assembly generated a more complete assembly as measured by greater number of RMBT and CEGMA score. Merged single k-mer assemblies are generally smaller but consist of longer transcripts, suggesting an assembly consisting of fewer fragmented transcripts. We suggest that the use of a subset of reads during assembly allows the relatively rapid investigation of assembly characteristics and can guide the user to the most appropriate transcriptome for particular downstream use. Transcriptomes generated by the compared assembly methods and the final merged assembly are freely available for download at http://dx.doi.org/10.6084/m9.figshare.1032613.

  17. Transcriptomic Microenvironment of Lung Adenocarcinoma.

    Science.gov (United States)

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

    2017-03-01

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

  18. eQTL networks unveil enriched mRNA master integrators downstream of complex disease-associated SNPs.

    Science.gov (United States)

    Li, Haiquan; Pouladi, Nima; Achour, Ikbel; Gardeux, Vincent; Li, Jianrong; Li, Qike; Zhang, Hao Helen; Martinez, Fernando D; Garcia, Joe G N 'Skip'; Lussier, Yves A

    2015-12-01

    The causal and interplay mechanisms of Single Nucleotide Polymorphisms (SNPs) associated with complex diseases (complex disease SNPs) investigated in genome-wide association studies (GWAS) at the transcriptional level (mRNA) are poorly understood despite recent advancements such as discoveries reported in the Encyclopedia of DNA Elements (ENCODE) and Genotype-Tissue Expression (GTex). Protein interaction network analyses have successfully improved our understanding of both single gene diseases (Mendelian diseases) and complex diseases. Whether the mRNAs downstream of complex disease genes are central or peripheral in the genetic information flow relating DNA to mRNA remains unclear and may be disease-specific. Using expression Quantitative Trait Loci (eQTL) that provide DNA to mRNA associations and network centrality metrics, we hypothesize that we can unveil the systems properties of information flow between SNPs and the transcriptomes of complex diseases. We compare different conditions such as naïve SNP assignments and stringent linkage disequilibrium (LD) free assignments for transcripts to remove confounders from LD. Additionally, we compare the results from eQTL networks between lymphoblastoid cell lines and liver tissue. Empirical permutation resampling (p<0.001) and theoretic Mann-Whitney U test (p<10(-30)) statistics indicate that mRNAs corresponding to complex disease SNPs via eQTL associations are likely to be regulated by a larger number of SNPs than expected. We name this novel property mRNA hubness in eQTL networks, and further term mRNAs with high hubness as master integrators. mRNA master integrators receive and coordinate the perturbation signals from large numbers of polymorphisms and respond to the personal genetic architecture integratively. This genetic signal integration contrasts with the mechanism underlying some Mendelian diseases, where a genetic polymorphism affecting a single protein hub produces a divergent signal that affects a large

  19. Atypical RNAs in the coelacanth transcriptome.

    Science.gov (United States)

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

    2014-09-01

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

  20. Hydroeconomic optimization of reservoir management under downstream water quality constraints

    DEFF Research Database (Denmark)

    Davidsen, Claus; Liu, Suxia; Mo, Xingguo;

    2015-01-01

    low increase to 16.4. billion. CNY/year. Dilution plays an important role and increases the share of surface water allocations to users situated furthest downstream in the system. The modeling framework generates decision rules that result in the economically efficient strategy for complying with both...... a variant of stochastic dynamic programming known as the water value method. Nonlinearity arising from the water quality constraints is handled with an effective hybrid method combining genetic algorithms and linear programming. Untreated pollutant loads are represented by biochemical oxygen demand (BOD...

  1. Recent Molecular Advances on Downstream Plant Responses to Abiotic Stress

    Directory of Open Access Journals (Sweden)

    Cláudia Regina Batista de Souza

    2012-07-01

    Full Text Available Abiotic stresses such as extremes of temperature and pH, high salinity and drought, comprise some of the major factors causing extensive losses to crop production worldwide. Understanding how plants respond and adapt at cellular and molecular levels to continuous environmental changes is a pre-requisite for the generation of resistant or tolerant plants to abiotic stresses. In this review we aimed to present the recent advances on mechanisms of downstream plant responses to abiotic stresses and the use of stress-related genes in the development of genetically engineered crops.

  2. Enhanced mixing downstream of a pile in an estuarine flow

    Science.gov (United States)

    Lass, H. U.; Mohrholz, V.; Knoll, M.; Prandke, H.

    2008-11-01

    We studied the impact on stratification and mixing of a bridge pile in a stratified shear flow at the Western Bridge of the Great Belt Fixed Link, Denmark, in January and April 2006. Stratification was measured with high horizontal resolution by towed CTD chains and dissipation of turbulent kinetic energy was measured by a free-falling MSS 90 microstructure profiler equipped with shear probes. Background stratification and current were measured by standard CTD and a bottom-mounted ADCP, respectively. The spatial and temporal variability of the flow field close behind a single pile was measured by an ADCP mounted on a small catamaran tethered to this pile. A shear background flow of varying strength was observed with an inflow of up to 80 cm s - 1 in the surface layer and an outflow of 10 cm s - 1 in the bottom layer. The brackish surface layer was separated from the saline Kattegat water in the bottom layer by an intermediate layer resulting in a Brunt-Väisälä frequency of up to 100 cycles per hour (cph). The maximum Reynolds number ( Re) and internal Froude number ( Fr) were 4.6 × 10 6 and 1.3, respectively. Eddies occurred downstream of a pile with a characteristic diameter of the pile and a frequency corresponding to a von Kármán vortex street when near-surface Fr > 0.7. Enhanced mixing was observed in the von Kármán vortex streets, which caused an increase in salinity by a few psu in the surface mixed layer of the eddy up to 400 m downstream of the piles. Differential advection by cross-channel circulation smeared out laterally from the wakes' salinity anomalies and turbulence. The dissipation of turbulent kinetic energy in the intermediate layer increased by an order of magnitude downstream of the piles as a function of Fr when Fr > 0.7. This enhanced mixing reduced the mean potential energy anomaly downstream by some 10 Jm - 3 in the upper 15 m depth and caused an upstream-directed baroclinic pressure gradient of the same order as the barotropic

  3. Ion Effects in the DARHT-II Downstream Transport

    CERN Document Server

    Chan, Kwok-Chi D; Ekdahl, Carl; Genoni, Thomas C; Hughes, Thomas P; Schulze, Martin E

    2005-01-01

    The DARHT-II accelerator produces an 18-MeV, 2-kA, 2-μs electron beam pulse. After the accelerator, the pulse is delivered to the final focus on an x-ray producing target via a beam transport section called the Downstream Transport. Ions produced due to beam ionization of residual gases in the Downstream Transport can affect the beam dynamics. Ions generated by the head of the pulse will cause modification of space-charge forces at the tail of the pulse so that the beam head and tail will have different beam envelopes. They may also induce ion-hose instability at the tail of the pulse. If these effects are significant, the focusing requirements of beam head and tail at the final focus will become very different. The focusing of the complete beam pulse will be time dependent and difficult to achieve, leading to less efficient x-ray production. In this paper, we will describe the results of our calculations of these ion effects at different residual-gas pressure levels. Our goal is to determine the ma...

  4. PIV measurements and flow characteristics downstream of mangrove root models

    Science.gov (United States)

    Kazemi, Amirkhosro; Curet, Oscar

    2016-11-01

    Mangrove forests attracted attentions as a solution to protect coastal areas exposed to sea-level rising, frequent storms, and tsunamis. Mangrove forests found in tide-dominated flow regions are characterized by their massive and complex root systems, which play a prominent role in the structure of tidal flow currents. To understand the role of mangrove roots in flow structure, we modeled mangrove roots with rigid and flexible arrays of cylinders with different spacing between them as well as different configurations. In this work, we investigate the fluid dynamics downstream of the models using a 2-D time-resolved particle image velocimetry (PIV) and flow visualization. We carried out experiments for four different Reynolds number based on cylinder diameters ranges from 2200 to 12000. We present time-averaged and time-resolved flow parameters including velocity distribution, vorticity, streamline, Reynolds shear stress and turbulent kinetic energy. The results show that the flow structure has different vortex shedding downstream of the cylinders due to interactions of shear layers separating from cylinders surface. The spectral analysis of the measured velocity data is also performed to obtain Strouhal number of the unsteady flow in the cylinder wake.

  5. Natural Origin Lycopene and Its "Green" Downstream Processing.

    Science.gov (United States)

    Papaioannou, Emmanouil H; Liakopoulou-Kyriakides, Maria; Karabelas, Anastasios J

    2016-01-01

    Lycopene is an abundant natural carotenoid pigment with several biological functions (well-known for its antioxidant properties) which is under intensive investigation in recent years. Lycopene chemistry, its natural distribution, bioavailability, biological significance, and toxicological effects are briefly outlined in the first part of this review. The second, major part, deals with various modern downstream processing techniques, which are assessed in order to identify promising approaches for the recovery of lycopene and of similar lipophilic compounds. Natural lycopene is synthesized in plants and by microorganisms, with main representatives of these two categories (for industrial production) tomato and its by-products and the fungus Blakeslea trispora, respectively. Currently, there is a great deal of effort to develop efficient downstream processing for large scale production of natural-origin lycopene, with trends strongly indicating the necessity for "green" and mild extraction conditions. In this review, emphasis is placed on final product safety and ecofriendly processing, which are expected to totally dominate in the field of natural-origin lycopene extraction and purification.

  6. Downstream processing of biopharmaceutical proteins produced in plants

    Science.gov (United States)

    Buyel, Johannes Felix; Fischer, Rainer

    2014-01-01

    All biological platforms for the manufacture of biopharmaceutical proteins produce an initially turbid extract that must be clarified to avoid fouling sensitive media such as chromatography resins. Clarification is more challenging if the feed stream contains large amounts of dispersed particles, because these rapidly clog the filter media typically used to remove suspended solids. Charged polymers (flocculants) can increase the apparent size of the dispersed particles by aggregation, facilitating the separation of solids and liquids, and thus reducing process costs. However, many different factors can affect the behavior of flocculants, including the pH and conductivity of the medium, the size and charge distribution of the particulates, and the charge density and molecular mass of the polymer. Importantly, these properties can also affect the recovery of the target protein and the overall safety profile of the process. We therefore used a design of experiments approach to establish reliable predictive models that characterize the impact of flocculants during the downstream processing of biopharmaceutical proteins. We highlight strategies for the selection of flocculants during process optimization. These strategies will contribute to the quality by design aspects of process development and facilitate the development of safe and efficient downstream processes for plant-derived pharmaceutical proteins. PMID:24637706

  7. Vortex structures downstream a lobed nozzle/mixer

    Institute of Scientific and Technical Information of China (English)

    Hui Hu; Toshio Kobayashi

    2008-01-01

    An experimental study was conducted to investigate the evolutions of unsteady vortex structures downstream a lobed mixer/nozzle. A novel dual-plane stereoscopic PIV system was used to measure all 3-components of vorticity distributions to revealed both the large-scale streamwise vortices produced by the lobed mixer/nozzle and the Kelvin-Helmholtz vortex structures generated due to the Kelvin-Helmholtz instabilities simultaneously and quantitatively for the first time. The instantaneous and the ensemble-averaged vorticity distributions displayed quite different aspects about the evolutions of the unsteady vortex structures. While the ensemble-averaged vorticity distributions indicated the overall effect of the special geometry of the lobed nozzle/mixer on the enhanced mixing process, the instantaneous vorticity distributions elucidated many details about how the enhanced mixing process was conducted. In addition to quantitatively confirming conjectures of previous studies, further insight about the formation, evolution and interaction characteristics of the unsteady vortex structures downstream of the lobed mixer/nozzle were also uncovered quantitatively in the present study.

  8. Integrative Genomics Implicates EGFR as a Downstream Mediator in NKX2-1 Amplified Non-Small Cell Lung Cancer.

    Science.gov (United States)

    Clarke, Nicole; Biscocho, Jewison; Kwei, Kevin A; Davidson, Jean M; Sridhar, Sushmita; Gong, Xue; Pollack, Jonathan R

    2015-01-01

    NKX2-1, encoding a homeobox transcription factor, is amplified in approximately 15% of non-small cell lung cancers (NSCLC), where it is thought to drive cancer cell proliferation and survival. However, its mechanism of action remains largely unknown. To identify relevant downstream transcriptional targets, here we carried out a combined NKX2-1 transcriptome (NKX2-1 knockdown followed by RNAseq) and cistrome (NKX2-1 binding sites by ChIPseq) analysis in four NKX2-1-amplified human NSCLC cell lines. While NKX2-1 regulated genes differed among the four cell lines assayed, cell proliferation emerged as a common theme. Moreover, in 3 of the 4 cell lines, epidermal growth factor receptor (EGFR) was among the top NKX2-1 upregulated targets, which we confirmed at the protein level by western blot. Interestingly, EGFR knockdown led to upregulation of NKX2-1, suggesting a negative feedback loop. Consistent with this finding, combined knockdown of NKX2-1 and EGFR in NCI-H1819 lung cancer cells reduced cell proliferation (as well as MAP-kinase and PI3-kinase signaling) more than knockdown of either alone. Likewise, NKX2-1 knockdown enhanced the growth-inhibitory effect of the EGFR-inhibitor erlotinib. Taken together, our findings implicate EGFR as a downstream effector of NKX2-1 in NKX2-1 amplified NSCLC, with possible clinical implications, and provide a rich dataset for investigating additional mediators of NKX2-1 driven oncogenesis.

  9. Integrative Genomics Implicates EGFR as a Downstream Mediator in NKX2-1 Amplified Non-Small Cell Lung Cancer.

    Directory of Open Access Journals (Sweden)

    Nicole Clarke

    Full Text Available NKX2-1, encoding a homeobox transcription factor, is amplified in approximately 15% of non-small cell lung cancers (NSCLC, where it is thought to drive cancer cell proliferation and survival. However, its mechanism of action remains largely unknown. To identify relevant downstream transcriptional targets, here we carried out a combined NKX2-1 transcriptome (NKX2-1 knockdown followed by RNAseq and cistrome (NKX2-1 binding sites by ChIPseq analysis in four NKX2-1-amplified human NSCLC cell lines. While NKX2-1 regulated genes differed among the four cell lines assayed, cell proliferation emerged as a common theme. Moreover, in 3 of the 4 cell lines, epidermal growth factor receptor (EGFR was among the top NKX2-1 upregulated targets, which we confirmed at the protein level by western blot. Interestingly, EGFR knockdown led to upregulation of NKX2-1, suggesting a negative feedback loop. Consistent with this finding, combined knockdown of NKX2-1 and EGFR in NCI-H1819 lung cancer cells reduced cell proliferation (as well as MAP-kinase and PI3-kinase signaling more than knockdown of either alone. Likewise, NKX2-1 knockdown enhanced the growth-inhibitory effect of the EGFR-inhibitor erlotinib. Taken together, our findings implicate EGFR as a downstream effector of NKX2-1 in NKX2-1 amplified NSCLC, with possible clinical implications, and provide a rich dataset for investigating additional mediators of NKX2-1 driven oncogenesis.

  10. The transcriptome of Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Roos David S

    2005-12-01

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

  11. The renal transcriptome in experimental hypertension

    NARCIS (Netherlands)

    Wesseling, S.

    2007-01-01

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

  12. Transcriptome Encyclopedia of Early Human Development.

    Science.gov (United States)

    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.

  13. The transcriptome landscape of early maize meiosis

    Science.gov (United States)

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

  14. Transcriptome analysis of the Capra hircus ovary.

    Directory of Open Access Journals (Sweden)

    Zhong Quan Zhao

    Full Text Available 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.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.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.

  15. Large Wood Storage Does Not Decrease Downstream Through a Watershed

    Science.gov (United States)

    Vaughan, M.; Pasternack, G. B.; Senter, A. E.; Dahlke, H. E.

    2013-12-01

    The storage of large wood in streams at the watershed scale has long been characterized as decreasing downstream due to a transport limitation in headwater streams, and a supply limitation in larger rivers. The objective of this study was to test this hypothesis through a field study in the Upper Yuba River watershed in Northern California, USA. While most studies surveyed within the wetted channel at selected reaches of different sizes, this study measured overbank deposits of large wood in addition to those in-channel to reflect the total storage within the active river corridor, and used a stratified random sampling scheme to see if relations held at the watershed scale. The watershed is large (2,874 km2), mountainous, mostly forested, and has been dramatically altered by human activities primarily related to gold mining. One hundred fourteen field sites of varied drainage area sizes were visited, inventoried for large wood (length > 1 m, diameter > 10 cm) storage within the active river corridor, and the volume storage per river length was calculated. Inclusion of floodplains in field surveys illuminates the fact that the distribution of large wood changes within the active river corridor, while the total storage does not decrease downstream. Among many watershed-scale control variables, such as drainage area, stream order, and upslope distance, the local amount of shrub cover and bankfull channel width were the only significant predictors of large wood storage in a multiple linear regression model, both with positive coefficients. A critical literature review was also conducted to investigate the evidence for the common conceptual model. Findings were that (1) the observed downstream trend of large wood storage is largely a function of the methods employed by each study, (2) the use of storage per channel area has confounded the commonly held conceptual model, due to its correlation with channel width, and (3) there is little evidence to support the hypothesis

  16. Calmodulin as a downstream gene of octopamine-OAR α1 signalling mediates olfactory attraction in gregarious locusts.

    Science.gov (United States)

    Xu, L; Li, L; Yang, P; Ma, Z

    2017-02-01

    The migratory locust (Locusta migratoria) shows aggregative traits in nymph marching bands and swarm formations through mutual olfactory attraction of conspecifics. However, olfactory preference in different nymph stages in gregarious locusts is not sufficiently explored. In this study, we found that the nymph olfactory preference for gregarious volatiles exhibited obvious variations at different developmental stages. The gregarious locusts show attractive response to conspecific volatiles from the third stadium. Transcriptome comparison between third- and fourth-stadium nymphs showed that the G protein-coupled receptor (GPCR) pathways are significantly enriched. Amongst the genes present in GPCR pathways, the expression level of calmodulin in locust brains significantly increased from the third- to the fourth-stadium nymphs. Amongst the four octopamine receptors (OARs) belonging to the GPCR family, only OAR α1 showed similar expression patterns to those of calmodulin, and knockdown of OAR α1 reduced the expression level of calmodulin. RNA interference of calmodulin decreased locomotion and induced the loss of olfactory attraction in gregarious locusts. Moreover, the activation of OAR α1 in calmodulin-knockdown locusts did not induce olfactory attraction of the nymphs to gregarious volatiles. Thus, calmodulin as a downstream gene of octopamine-OAR α1 (OA-OAR α1) signalling mediates olfactory attraction in gregarious locusts. Overall, this study provides novel insights into the mechanism of OA-OAR α1 signalling involved in olfactory attraction of gregarious locusts.

  17. Ethiopia's Grand Renaissance Dam: Implications for Downstream Riparian Countries

    Science.gov (United States)

    Zhang, Y.; Block, P. J.; Hammond, M.; King, A.

    2013-12-01

    Ethiopia has begun seriously developing their significant hydropower potential by launching construction of the Grand Ethiopian Renaissance Dam (GERD) on the Blue Nile River to facilitate local and regional growth. Although this has required substantial planning on Ethiopia's part, no policy dictating the reservoir filling rate strategy has been publicly issued. This filling stage will have clear implications on downstream flows in Sudan and Egypt, complicated by evaporative losses, climate variability, and climate change. In this study, various filling policies and future climate states are simultaneously explored to infer potential streamflow reductions at Lake Nasser, providing regional decision-makers with a set of plausible, justifiable, and comparable outcomes. Schematic of the model framework Box plots of 2017-2032 percent change in annual average streamflow at Lake Nasser for each filling policy constructed from the 100 time-series and weighted precipitation changes. All values are relative to the no dam policy and no changes to future precipitation.

  18. 'Patents and Downstream Innovation Suppression - Fact or Fiction?'

    DEFF Research Database (Denmark)

    Howells, John

    1977), a theory that is a version of the classic justification for the award of the exclusive right - that it should protect the incentive to develop property. Merges and Nelson insist that their thesis should be supported by empirical evidence and they turn to historical accounts as an important form...... of that empirical evidence. They present alleged historical examples of downstream innovation suppression in such important technologies as: Edison's carbon filament light bulb; the automobile; radio; aircraft; the transistor; the computer. This paper presents a contrary interpretation of the role of patents......), when adequate historical context is included in the analysis, the more common problem is revealed to be that the patents at issue were not administered, for example by courts or the US Patent Office, to maintain their prospect function i.e, their ability to enable the coordination of development...

  19. Continuous downstream processing for high value biological products: A Review.

    Science.gov (United States)

    Zydney, Andrew L

    2016-03-01

    There is growing interest in the possibility of developing truly continuous processes for the large-scale production of high value biological products. Continuous processing has the potential to provide significant reductions in cost and facility size while improving product quality and facilitating the design of flexible multi-product manufacturing facilities. This paper reviews the current state-of-the-art in separations technology suitable for continuous downstream bioprocessing, focusing on unit operations that would be most appropriate for the production of secreted proteins like monoclonal antibodies. This includes cell separation/recycle from the perfusion bioreactor, initial product recovery (capture), product purification (polishing), and formulation. Of particular importance are the available options, and alternatives, for continuous chromatographic separations. Although there are still significant challenges in developing integrated continuous bioprocesses, recent technological advances have provided process developers with a number of attractive options for development of truly continuous bioprocessing operations.

  20. Efficient industry configurations in downstream gas markets. An empirical assessment

    Energy Technology Data Exchange (ETDEWEB)

    Casarin, Ariel A. [IAE Escuela de Direccion y Negocios, Universidad Austral, Buenos Aires (Argentina)

    2007-03-15

    This paper examines the production technology of the downstream gas industry in order to provide some useful insights into its efficient structure by looking at the optimal size of firms and the productive efficiency reasons for and against their vertical integration. The analysis is based on a restricted cost function model estimated using firm level data for Argentina and Great Britain. The findings provide evidence for the presence of vertical diseconomies between stages. Results indicate that a single transmitter is able to produce the industry's output at lower costs for large market sizes and that several regional firms are able to operate without sacrificing scale economies if gas distribution is integrated with supply. The findings also indicate that a gas retailer experiences constant returns to scale when it supplies a large customer base. Liberalisation could thus result in oligopolistic industry configurations. (Author)

  1. Interactive Learning-driven Innovation in Upstream-Downstream Relations

    DEFF Research Database (Denmark)

    Machikita, Tomohiro; Ueki, Yasushi

    2012-01-01

    This paper presents a simple framework of the innovations that result from interfirm learning through exchanges of engineers in upstream-downstream relations within a production chain. To examine the framework, we empirically investigate the impact of mutual knowledge exchanges on product...... and process innovation using a survey of firm's self-reporting customer and supplier data in Indonesia, the Philippines, Thailand and Vietnam. Evidence from interconnected firms within a production chain suggests that firms with mutual exchanges between engineers and customers achieved product innovations...... with new technologies and new markets. However, this is not true for simple improvement of products or process innovation. Mutual exchanges with engineers between producers and suppliers within a chain can be expected to play an important role in the case of costly innovation and in situations unknown...

  2. Trends in Upstream and Downstream Process Development for Antibody Manufacturing

    Directory of Open Access Journals (Sweden)

    Petra Gronemeyer

    2014-10-01

    Full Text Available A steady increase of product titers and the corresponding change in impurity composition represent a challenge for development and optimization of antibody production processes. Additionally, increasing demands on product quality result in higher complexity of processes and analytics, thereby increasing the costs for product work-up. Concentration and composition of impurities are critical for efficient process development. These impurities can show significant variations, which primarily depend on culture conditions. They have a major impact on the work-up strategy and costs. The resulting “bottleneck” in downstream processing requires new optimization, technology and development approaches. These include the optimization and adaptation of existing unit operations respective to the new separation task, the assessment of alternative separation technologies and the search for new methods in process development. This review presents an overview of existing methods for process optimization and integration and indicates new approaches for future developments.

  3. Simultaneous isolation of DNA, RNA, and proteins for genetic, epigenetic, transcriptomic, and proteomic analysis.

    Science.gov (United States)

    Radpour, Ramin; Sikora, Michal; Grussenmeyer, Thomas; Kohler, Corina; Barekati, Zeinab; Holzgreve, Wolfgang; Lefkovits, Ivan; Zhong, Xiao Yan

    2009-11-01

    Analysis of DNA, RNA, and proteins for downstream genetic, epigenetic, transcriptomic, and proteomic analysis holds an important place in the field of medical care and life science. This is often hampered by the limited availability of sample material. For this reason, there exists an increasing interest for simultaneous isolation of DNA, RNA and proteins from a single sample aliquot. Several kit-systems allowing such a procedure have been introduced to the market. We present an approach using the AllPrep method for simultaneous isolation of DNA, RNA and proteins from several human specimens, such as whole blood, buffy coat, serum, plasma and tissue samples. The quantification and qualification of the isolated molecular species were assessed by different downstream methods: NanoDrop for measuring concentration and purity of all molecular species; DNA and RNA LabChip for fractionation analysis of nucleic acids; quantitative PCR for quantification analysis of DNA and RNA; thymidine-specific cleavage mass array on MALDI-TOF silico-chip for epigenetic analysis; Protein LabChip and two-dimensional (2D) gel electrophoresis for proteomic analysis. With our modified method, we can simultaneously isolate DNA, RNA and/or proteins from one single sample aliquot. We could overcome to some method limitations like low quality or DNA fragmentation using reamplification strategy for performing high-throughput downstream assays. Fast and easy performance of the procedure makes this method interesting for all fields of downstream analysis, especially when using limited sample resources. The cost-effectiveness of the procedure when material is abundantly available has not been addressed. This methodological improvement enables to execute such experiments that were not performable with standard procedure, and ensures reproducible outcome.

  4. A Copernicus downstream service for surface displacement monitoring in Germany

    Science.gov (United States)

    Cahyadi Kalia, Andre; Frei, Michaela; Lege, Thomas

    2016-04-01

    SAR Interferometry is a powerful technique able to detect and monitor various surface displacements caused by e.g. gravitative mass movement, subrosion, groundwater extraction, fluid injection, natural gas extraction. These processes can e.g. cause damage to buildings, infrastructure, affect ecosystems, agriculture and the economic use of the geological underground by influencing the hydro(geo)logical setting. Advanced techniques of interferometric processing (Persistent Scatterer Interferometry, PSI) allow highly precise displacement measurements (mm precision) by analyzing stacks of SAR imagery. The PSI mapping coverage can be increased to entire nations by using several adjacent satellite tracks. In order to assist the operational use of this technique a German-wide, officially approved, PSI dataset is under development. The intention of this presentation is to show i) the concept of the Copernicus downstream service for surface displacement monitoring in Germany and ii) a pilot study to exemplarily demonstrate the workflow and potential products from the Copernicus downstream service. The pilot study is focusing on the built up of an officially approved wide-area PSI dataset. The study area covers an area of more than 30.000 km² and is located in the Northwest German Basin. Several natural processes (e.g. compaction of marine sediments, peat loss) and anthropogenic activities (e.g. natural gas extraction, rock salt mining) are causing surface displacements in the study area. The PSI analysis is based on six ERS-1/-2 data stacks covering the timespan from 1992 until 2001. Each data stack consists of 49 to 73 ERS-1/-2 SAR images. A comparison of the PSI results with thematic data (e.g. volume and location of extracted natural gas) strongly indicates that a part of the detected land subsidence is caused by natural gas extraction. Furthermore, land subsidence caused by e.g. fluid injection and rock salt mining were successfully detected by the PSI analysis.

  5. Calpains are downstream effectors of bax-dependent excitotoxic apoptosis.

    Science.gov (United States)

    D'Orsi, Beatrice; Bonner, Helena; Tuffy, Liam P; Düssmann, Heiko; Woods, Ina; Courtney, Michael J; Ward, Manus W; Prehn, Jochen H M

    2012-02-01

    Excitotoxicity resulting from excessive Ca(2+) influx through glutamate receptors contributes to neuronal injury after stroke, trauma, and seizures. Increased cytosolic Ca(2+) levels activate a family of calcium-dependent proteases with papain-like activity, the calpains. Here we investigated the role of calpain activation during NMDA-induced excitotoxic injury in embryonic (E16-E18) murine cortical neurons that (1) underwent excitotoxic necrosis, characterized by immediate deregulation of Ca(2+) homeostasis, a persistent depolarization of mitochondrial membrane potential (Δψ(m)), and insensitivity to bax-gene deletion, (2) underwent excitotoxic apoptosis, characterized by recovery of NMDA-induced cytosolic Ca(2+) increases, sensitivity to bax gene deletion, and delayed Δψ(m) depolarization and Ca(2+) deregulation, or (3) that were tolerant to excitotoxic injury. Interestingly, treatment with the calpain inhibitor calpeptin, overexpression of the endogenous calpain inhibitor calpastatin, or gene silencing of calpain protected neurons against excitotoxic apoptosis but did not influence excitotoxic necrosis. Calpeptin failed to exert a protective effect in bax-deficient neurons but protected bid-deficient neurons similarly to wild-type cells. To identify when calpains became activated during excitotoxic apoptosis, we monitored calpain activation dynamics by time-lapse fluorescence microscopy using a calpain-sensitive Förster resonance energy transfer probe. We observed a delayed calpain activation that occurred downstream of mitochondrial engagement and directly preceded neuronal death. In contrast, we could not detect significant calpain activity during excitotoxic necrosis or in neurons that were tolerant to excitotoxic injury. Oxygen/glucose deprivation-induced injury in organotypic hippocampal slice cultures confirmed that calpains were specifically activated during bax-dependent apoptosis and in this setting function as downstream cell-death executioners.

  6. Downstream evolution of unconfined vortices: mechanical and thermal aspects

    Science.gov (United States)

    Pérez-Saborid, M.; Herrada, M. A.; Gómez-Barea, A.; Barrero, A.

    2002-11-01

    We present a numerical study of the downstream evolution (mechanical and thermal) of vortex-jet cores whose velocity and temperature fields far from the axis match a family of inviscid and non-conducting vortices. The far-velocity field is rotational, except for a particular case which corresponds to the well-known Long's vortex. The evolution of the vortex core depends on both the conditions at a certain upstream station, characterized by the dimensionless value of the velocity at the axis, and a dimensionless swirling parameter L defined as the ratio of the values of the azimuthal and axial velocities outside the vortex core. This numerical study, based on the quasi-cylindrical approximation (QC) of the Navier Stokes equations, determines the conditions under which the vortex evolution proceeds smoothly, eventually reaching an asymptotic self-similar behaviour as described in the literature (Fernández-Feria, Fernández de la Mora & Barrero 1995; Herrada, Pérez-Saborid & Barrero 1999), or breaks in a non-slender solution (vortex breakdown). In particular, the critical value L = Lb(a) beyond which vortex breakdown occurs downstream is a function of a dimensionless parameter a characterizing the axial momentum of the vortex jet at an initial upstream station. It is found numerically that for very large values of a this vortex breakdown criterion tends to an asymptote which is precisely the value L = L* predicted by the self-similar analysis, and beyond which a self-similar structure of the vortex core does not exist. In addition, the computation of the total temperature field provides useful information on the physical mechanisms responsible for the thermal separation phenomenon observed in Ranque Hilsch tubes and other swirling jet devices. In particular, the mechanical work of viscous forces which gives rise to an intense loss of kinetic energy during the initial stages of the evolution has been identified as the physical mechanism responsible for thermal

  7. Transcriptome analysis of cortical tissue reveals shared sets of downregulated genes in autism and schizophrenia

    Science.gov (United States)

    Ellis, S E; Panitch, R; West, A B; Arking, D E

    2016-01-01

    Autism (AUT), schizophrenia (SCZ) and bipolar disorder (BPD) are three highly heritable neuropsychiatric conditions. Clinical similarities and genetic overlap between the three disorders have been reported; however, the causes and the downstream effects of this overlap remain elusive. By analyzing transcriptomic RNA-sequencing data generated from post-mortem cortical brain tissues from AUT, SCZ, BPD and control subjects, we have begun to characterize the extent of gene expression overlap between these disorders. We report that the AUT and SCZ transcriptomes are significantly correlated (P<0.001), whereas the other two cross-disorder comparisons (AUT–BPD and SCZ–BPD) are not. Among AUT and SCZ, we find that the genes differentially expressed across disorders are involved in neurotransmission and synapse regulation. Despite the lack of global transcriptomic overlap across all three disorders, we highlight two genes, IQSEC3 and COPS7A, which are significantly downregulated compared with controls across all three disorders, suggesting either shared etiology or compensatory changes across these neuropsychiatric conditions. Finally, we tested for enrichment of genes differentially expressed across disorders in genetic association signals in AUT, SCZ or BPD, reporting lack of signal in any of the previously published genome-wide association study (GWAS). Together, these studies highlight the importance of examining gene expression from the primary tissue involved in neuropsychiatric conditions—the cortical brain. We identify a shared role for altered neurotransmission and synapse regulation in AUT and SCZ, in addition to two genes that may more generally contribute to neurodevelopmental and neuropsychiatric conditions. PMID:27219343

  8. Frontal Cortex Transcriptome Analysis of Mice Exposed to Electronic Cigarettes During Early Life Stages

    Directory of Open Access Journals (Sweden)

    Dana E. Lauterstein

    2016-04-01

    Full Text Available Electronic cigarettes (e-cigarettes, battery-powered devices containing nicotine, glycerin, propylene glycol, flavorings, and other substances, are increasing in popularity. They pose a potential threat to the developing brain, as nicotine is a known neurotoxicant. We hypothesized that exposure to e-cigarettes during early life stages induce changes in central nervous system (CNS transcriptome associated with adverse neurobiological outcomes and long-term disease states. To test the hypothesis, pregnant C57BL/6 mice were exposed daily (via whole body inhalation throughout gestation (3 h/day; 5 days/week to aerosols produced from e-cigarettes either with nicotine (13–16 mg/mL or without nicotine; following birth, pups and dams were exposed together to e-cigarette aerosols throughout lactation beginning at postnatal day (PND 4–6 and using the same exposure conditions employed during gestational exposure. Following exposure, frontal cortex recovered from ~one-month-old male and female offspring were excised and analyzed for gene expression by RNA Sequencing (RNA-Seq. Comparisons between the treatment groups revealed that e-cigarette constituents other than nicotine might be partly responsible for the observed biological effects. Transcriptome alterations in both offspring sexes and treatment groups were all significantly associated with downstream adverse neurobiological outcomes. Results from this study demonstrate that e-cigarette exposure during early life alters CNS development potentially leading to chronic neuropathology.

  9. Frontal Cortex Transcriptome Analysis of Mice Exposed to Electronic Cigarettes During Early Life Stages.

    Science.gov (United States)

    Lauterstein, Dana E; Tijerina, Pamella B; Corbett, Kevin; Akgol Oksuz, Betul; Shen, Steven S; Gordon, Terry; Klein, Catherine B; Zelikoff, Judith T

    2016-04-12

    Electronic cigarettes (e-cigarettes), battery-powered devices containing nicotine, glycerin, propylene glycol, flavorings, and other substances, are increasing in popularity. They pose a potential threat to the developing brain, as nicotine is a known neurotoxicant. We hypothesized that exposure to e-cigarettes during early life stages induce changes in central nervous system (CNS) transcriptome associated with adverse neurobiological outcomes and long-term disease states. To test the hypothesis, pregnant C57BL/6 mice were exposed daily (via whole body inhalation) throughout gestation (3 h/day; 5 days/week) to aerosols produced from e-cigarettes either with nicotine (13-16 mg/mL) or without nicotine; following birth, pups and dams were exposed together to e-cigarette aerosols throughout lactation beginning at postnatal day (PND) 4-6 and using the same exposure conditions employed during gestational exposure. Following exposure, frontal cortex recovered from ~one-month-old male and female offspring were excised and analyzed for gene expression by RNA Sequencing (RNA-Seq). Comparisons between the treatment groups revealed that e-cigarette constituents other than nicotine might be partly responsible for the observed biological effects. Transcriptome alterations in both offspring sexes and treatment groups were all significantly associated with downstream adverse neurobiological outcomes. Results from this study demonstrate that e-cigarette exposure during early life alters CNS development potentially leading to chronic neuropathology.

  10. Improving transcriptome assembly through error correction of high-throughput sequence reads.

    Science.gov (United States)

    Macmanes, Matthew D; Eisen, Michael B

    2013-01-01

    The study of functional genomics, particularly in non-model organisms, has been dramatically improved over the last few years by the use of transcriptomes and RNAseq. While these studies are potentially extremely powerful, a computationally intensive procedure, the de novo construction of a reference transcriptome must be completed as a prerequisite to further analyses. The accurate reference is critically important as all downstream steps, including estimating transcript abundance are critically dependent on the construction of an accurate reference. Though a substantial amount of research has been done on assembly, only recently have the pre-assembly procedures been studied in detail. Specifically, several stand-alone error correction modules have been reported on and, while they have shown to be effective in reducing errors at the level of sequencing reads, how error correction impacts assembly accuracy is largely unknown. Here, we show via use of a simulated and empiric dataset, that applying error correction to sequencing reads has significant positive effects on assembly accuracy, and should be applied to all datasets. A complete collection of commands which will allow for the production of Reptile corrected reads is available at https://github.com/macmanes/error_correction/tree/master/scripts and as File S1.

  11. Transcriptome data - Initial stage of dough fermentation - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available DGBY Transcriptome data - Initial stage of dough fermentation Data detail Data name Transcriptome data - Initial...Policy | Contact Us Transcriptome data - Initial stage of dough fermentation - DGBY | LSDB Archive ...

  12. Transcriptomic studies on liver toxicity of acetaminophen.

    Science.gov (United States)

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

    2014-09-01

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

  13. Application of next-generation sequencing for comparative transcriptome analysis

    OpenAIRE

    Shin, Heesun

    2010-01-01

    I have used novel whole transcriptome sequence data generated from massively parallel high-throughput next generation sequencing technologies, namely 454 pyrosequencing and Illumina sequencing, to perform comparative transcriptome analyses of C. elegans populations in specific biological conditions and developmental stages. Firstly, I have conducted transcriptome profiling of C. elegans in its first larval (L1) stage using data generated from the Roche 454 sequencing platform. I have used thi...

  14. Corrosion impact of reductant on DWPF and downstream facilities

    Energy Technology Data Exchange (ETDEWEB)

    Mickalonis, J. I. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Imrich, K. J. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Jantzen, C. M. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Murphy, T. H. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Wilderman, J. E. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2014-12-01

    Glycolic acid is being evaluated as an alternate reductant in the preparation of high level waste for the Defense Waste Processing Facility (DWPF) at the Savannah River Site (SRS). During processing, the glycolic acid is not completely consumed and small quantities of the glycolate anion are carried forward to other high level waste (HLW) facilities. The impact of the glycolate anion on the corrosion of the materials of construction throughout the waste processing system has not been previously evaluated. A literature review had revealed that corrosion data in glycolate-bearing solution applicable to SRS systems were not available. Therefore, testing was recommended to evaluate the materials of construction of vessels, piping and components within DWPF and downstream facilities. The testing, conducted in non-radioactive simulants, consisted of both accelerated tests (electrochemical and hot-wall) with coupons in laboratory vessels and prototypical tests with coupons immersed in scale-up and mock-up test systems. Eight waste or process streams were identified in which the glycolate anion might impact the performance of the materials of construction. These streams were 70% glycolic acid (DWPF feed vessels and piping), SRAT/SME supernate (Chemical Processing Cell (CPC) vessels and piping), DWPF acidic recycle (DWPF condenser and recycle tanks and piping), basic concentrated recycle (HLW tanks, evaporators, and transfer lines), salt processing (ARP, MCU, and Saltstone tanks and piping), boric acid (MCU separators), and dilute waste (HLW evaporator condensate tanks and transfer line and ETF components). For each stream, high temperature limits and worst-case glycolate concentrations were identified for performing the recommended tests. Test solution chemistries were generally based on analytical results of actual waste samples taken from the various process facilities or of prototypical simulants produced in the laboratory. The materials of construction for most vessels

  15. Transcriptome architecture across tissues in the pig

    Directory of Open Access Journals (Sweden)

    Folch Josep M

    2008-04-01

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

  16. Transcriptomics of the Bed Bug (Cimex lectularius)

    OpenAIRE

    Xiaodong Bai; Praveen Mamidala; Swapna P Rajarapu; Jones, Susan C.; Omprakash Mittapalli

    2011-01-01

    BACKGROUND: Bed bugs (Cimex lectularius) are blood-feeding insects poised to become one of the major pests in households throughout the United States. Resistance of C. lectularius to insecticides/pesticides is one factor thought to be involved in its sudden resurgence. Despite its high-impact status, scant knowledge exists at the genomic level for C. lectularius. Hence, we subjected the C. lectularius transcriptome to 454 pyrosequencing in order to identify potential genes involved in pestici...

  17. High-resolution transcriptome of human macrophages.

    Directory of Open Access Journals (Sweden)

    Marc Beyer

    Full Text Available Macrophages are dynamic cells integrating signals from their microenvironment to develop specific functional responses. Although, microarray-based transcriptional profiling has established transcriptional reprogramming as an important mechanism for signal integration and cell function of macrophages, current knowledge on transcriptional regulation of human macrophages is far from complete. To discover novel marker genes, an area of great need particularly in human macrophage biology but also to generate a much more thorough transcriptome of human M1- and M1-like macrophages, we performed RNA sequencing (RNA-seq of human macrophages. Using this approach we can now provide a high-resolution transcriptome profile of human macrophages under classical (M1-like and alternative (M2-like polarization conditions and demonstrate a dynamic range exceeding observations obtained by previous technologies, resulting in a more comprehensive understanding of the transcriptome of human macrophages. Using this approach, we identify important gene clusters so far not appreciated by standard microarray techniques. In addition, we were able to detect differential promoter usage, alternative transcription start sites, and different coding sequences for 57 gene loci in human macrophages. Moreover, this approach led to the identification of novel M1-associated (CD120b, TLR2, SLAMF7 as well as M2-associated (CD1a, CD1b, CD93, CD226 cell surface markers. Taken together, these data support that high-resolution transcriptome profiling of human macrophages by RNA-seq leads to a better understanding of macrophage function and will form the basis for a better characterization of macrophages in human health and disease.

  18. Blood Transcriptomics and Metabolomics for Personalized Medicine

    Science.gov (United States)

    2015-10-31

    progress in human immunology , where transcriptomics of isolated cell populations provided necessary information [15–17]. Nonetheless, a review on “blood...databases are biased towards cancer , under- representing the immunology in white blood cells. Second, many path- ways are based on tissues other than blood...metabolomics in oncology: a review . Clin Cancer Res 2009;15. [52] Armitage EG. Metabolomics in cancer biomarker discovery: current trends and fu- ture

  19. Comparative analysis of the transcriptomes of Populus

    Energy Technology Data Exchange (ETDEWEB)

    Tuskan, Gerald A [ORNL; Davis, John M [University of Florida

    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.

  20. Reshaping of the maize transcriptome by domestication.

    Science.gov (United States)

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

    2012-07-17

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

  1. p53 regulates the cardiac transcriptome

    Science.gov (United States)

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

    2017-01-01

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

  2. Flume experiments on scour downstream of wood stream restoration structures

    Science.gov (United States)

    Pagliara, Stefano; Kurdistani, Sahameddin Mahmoudi

    2017-02-01

    River restoration aims to improve physical natural form and processes of a river. Techniques to control the riverbed, stabilize channel alignment, protect stream banks, and rebuild the natural habitat are an important part of river restoration projects. Rivers can be stabilized and habitat restored through techniques such as rebuilding meanders and pool-riffle sequences and managing large wood. Structures that limit channel width to accelerate the normal flows through the constricted section are referred to as stream deflectors. Single-wing, double-wing and triangular deflectors are the most commonly used types of this measure. Log-frame deflectors consist of a triangular log frame filled with rock. Deflector constructions singly or in series in low gradient meandering streams, divert base flows toward the center of the channel and, under certain conditions, increase the depth and velocity of flow thereby creating scour pools and enhancing fish habitat. Scour characteristics and morphologies downstream of log-frame deflectors have been analyzed at the hydraulic laboratory of the University of Pisa. All experiments have been carried out in clear water conditions. The results showed that the tailwater depth plays an important role on scour characteristics. In addition, it was experimentally proven that using log-frame deflectors instead of log-deflectors result in a better river bank protection. In this case, for all the tested hydraulic conditions, the scour hole never occurred close to the channel bank. Useful empirical relationships have been proposed in order to evaluate the main features of the scour geometry.

  3. Synthetic Routes to Methylerythritol Phosphate Pathway Intermediates and Downstream Isoprenoids

    Science.gov (United States)

    Jarchow-Choy, Sarah K; Koppisch, Andrew T; Fox, David T

    2014-01-01

    Isoprenoids constitute the largest class of natural products with greater than 55,000 identified members. They play essential roles in maintaining proper cellular function leading to maintenance of human health, plant defense mechanisms against predators, and are often exploited for their beneficial properties in the pharmaceutical and nutraceutical industries. Most impressively, all known isoprenoids are derived from one of two C5-precursors, isopentenyl diphosphate (IPP) or dimethylallyl diphosphate (DMAPP). In order to study the enzyme transformations leading to the extensive structural diversity found within this class of compounds there must be access to the substrates. Sometimes, intermediates within a biological pathway can be isolated and used directly to study enzyme/pathway function. However, the primary route to most of the isoprenoid intermediates is through chemical catalysis. As such, this review provides the first exhaustive examination of synthetic routes to isoprenoid and isoprenoid precursors with particular emphasis on the syntheses of intermediates found as part of the 2C-methylerythritol 4-phosphate (MEP) pathway. In addition, representative syntheses are presented for the monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), triterpenes (C30) and tetraterpenes (C40). Finally, in some instances, the synthetic routes to substrate analogs found both within the MEP pathway and downstream isoprenoids are examined. PMID:25009443

  4. Downstream process development in biotechnological itaconic acid manufacturing.

    Science.gov (United States)

    Magalhães, Antonio Irineudo; de Carvalho, Júlio Cesar; Medina, Jesus David Coral; Soccol, Carlos Ricardo

    2017-01-01

    Itaconic acid is a promising chemical that has a wide range of applications and can be obtained in large scale using fermentation processes. One of the most important uses of this biomonomer is the environmentally sustainable production of biopolymers. Separation of itaconic acid from the fermented broth has a considerable impact in the total production cost. Therefore, optimization and high efficiency downstream processes are technological challenges to make biorefineries sustainable and economically viable. This review describes the current state of the art in recovery and purification for itaconic acid production via bioprocesses. Previous studies on the separation of itaconic acid relying on operations such as crystallization, precipitation, extraction, electrodialysis, diafiltration, pertraction, and adsorption. Although crystallization is a typical method of itaconic acid separation from fermented broth, other methods such as membrane separation and reactive extraction are promising as a recovery steps coupled to the fermentation, potentially enhancing the overall process yield. Another approach is adsorption in fixed bed columns, which efficiently separates itaconic acid. Despite recent advances in separation and recovery methods, there is still space for improvement in IA recovery and purification.

  5. Downstream effects of a hydroelectric reservoir on aquatic plant assemblages.

    Science.gov (United States)

    Bernez, Ivan; Haury, Jacques; Ferreira, Maria Teresa

    2002-03-16

    Macrophytes were studied downstream of the Rophémel hydroelectric dam on the River Rance (Côtes d'Armor Department, western France) to assess the effects of hydroelectric functioning on river macrophyte communities. We studied ten representative sections of the hydro-peaking channel on five occasions in 1995 and 1996, on a 15-km stretch of river. Floristic surveys were carried out on sections 50 m in length, and genera of macroalgae, species of bryophyta, hydrophytes, and emergent rhizophytes were identified. For the aquatic bryophytes and spermatophytes section of our study, we compared our results with 19th century floristic surveys, before the dam was built. During the vegetative growth period, the hydro-peaking frequency was low. The plant richness was highest near the dam. The macrophyte communities were highly modified according to the distance to the dam. The frequency and magnitude of hydro-peaking was related to the aquatic macrophyte richness in an Intermediate Disturbance Hypothesis position. However, the results of the eco-historical comparison with 19th century floristic surveys point to the original nature of the flora found at the site. Some floral patterns, seen during both periods and at an interval of 133 years, were indicative of the ubiquity of the aquatic flora and of the plants" adaptability. This demonstrates the importance of taking river basin history into account in such biological surveys.

  6. Downstream Effects of a Hydroelectric Reservoir on Aquatic Plant Assemblages

    Directory of Open Access Journals (Sweden)

    Ivan Bernez

    2002-01-01

    Full Text Available Macrophytes were studied downstream of the Rophémel hydroelectric dam on the River Rance (Côtes d’Armor Department, western France to assess the effects of hydroelectric functioning on river macrophyte communities. We studied ten representative sections of the hydro-peaking channel on five occasions in 1995 and 1996, on a 15-km stretch of river. Floristic surveys were carried out on sections 50 m in length, and genera of macroalgae, species of bryophyta, hydrophytes, and emergent rhizophytes were identified. For the aquatic bryophytes and spermatophytes section of our study, we compared our results with 19th century floristic surveys, before the dam was built. During the vegetative growth period, the hydro-peaking frequency was low. The plant richness was highest near the dam. The macrophyte communities were highly modified according to the distance to the dam. The frequency and magnitude of hydro-peaking was related to the aquatic macrophyte richness in an Intermediate Disturbance Hypothesis position. However, the results of the eco-historical comparison with 19th century floristic surveys point to the original nature of the flora found at the site. Some floral patterns, seen during both periods and at an interval of 133 years, were indicative of the ubiquity of the aquatic flora and of the plants’ adaptability. This demonstrates the importance of taking river basin history into account in such biological surveys.

  7. Hydroeconomic optimization of reservoir management under downstream water quality constraints

    Science.gov (United States)

    Davidsen, Claus; Liu, Suxia; Mo, Xingguo; Holm, Peter E.; Trapp, Stefan; Rosbjerg, Dan; Bauer-Gottwein, Peter

    2015-10-01

    A hydroeconomic optimization approach is used to guide water management in a Chinese river basin with the objectives of meeting water quantity and water quality constraints, in line with the China 2011 No. 1 Policy Document and 2015 Ten-point Water Plan. The proposed modeling framework couples water quantity and water quality management and minimizes the total costs over a planning period assuming stochastic future runoff. The outcome includes cost-optimal reservoir releases, groundwater pumping, water allocation, wastewater treatments and water curtailments. The optimization model uses a variant of stochastic dynamic programming known as the water value method. Nonlinearity arising from the water quality constraints is handled with an effective hybrid method combining genetic algorithms and linear programming. Untreated pollutant loads are represented by biochemical oxygen demand (BOD), and the resulting minimum dissolved oxygen (DO) concentration is computed with the Streeter-Phelps equation and constrained to match Chinese water quality targets. The baseline water scarcity and operational costs are estimated to 15.6 billion CNY/year. Compliance to water quality grade III causes a relatively low increase to 16.4 billion CNY/year. Dilution plays an important role and increases the share of surface water allocations to users situated furthest downstream in the system. The modeling framework generates decision rules that result in the economically efficient strategy for complying with both water quantity and water quality constraints.

  8. An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison

    Directory of Open Access Journals (Sweden)

    Emmanuel eTerrasson

    2013-12-01

    Full Text Available Desiccation tolerance (DT is the capacity to withstand total loss of cellular water. It is acquired during seed filling and lost just after germination. However, in many species, a germinated seed can regain DT under adverse conditions such as osmotic stress. The genes, proteins and metabolites that are required to establish this DT is referred to as the desiccome. It includes both a range of protective mechanisms and underlying regulatory pathways that remain poorly understood. As a first step towards the identification of the seed desiccome of Medicago truncatula, using updated microarrays we characterised the overlapping transcriptomes associated with acquisition of DT in developing seeds and the re-establishment of DT in germinated seeds using a polyethylene glycol treatment (-1.7 MPa. The resulting list contained 740 and 2829 transcripts whose levels respectively increased and decreased with DT. Fourty-eight transcription factors were identified including MtABI3, MtABI5 and many genes regulating flowering transition and cell identity. A promoter enrichment analysis revealed a strong over-representation of ABRE elements together with light-responsive cis-acting elements. In Mtabi5 Tnt1 insertion mutants, DT could no longer be re-established by an osmotic stress. Transcriptome analysis on Mtabi5 radicles during osmotic stress revealed that 13 and 15 % of the up-regulated and down-regulated genes, respectively, are mis-regulated in the mutants and might be putative downstream targets of MtABI5 implicated in the re-establishment of DT. Likewise, transcriptome comparisons of the desiccation sensitive Mtabi3 mutants and hairy roots ectopically expressing MtABI3 revealed that 35% and 23% of the up-regulated and down-regulated genes are acting downstream of MtABI3. Our data suggest that ABI3 and ABI5 have complementary roles in DT. Whether DT evolved by co-opting existing pathways regulating flowering and cellular phase transition and cell identity

  9. iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences

    Directory of Open Access Journals (Sweden)

    Zheng Yi

    2011-11-01

    Full Text Available Abstract Background Expressed Sequence Tags (ESTs have played significant roles in gene discovery and gene functional analysis, especially for non-model organisms. For organisms with no full genome sequences available, ESTs are normally assembled into longer consensus sequences for further downstream analysis. However current de novo EST assembly programs often generate large number of assembly errors that will negatively affect the downstream analysis. In order to generate more accurate consensus sequences from ESTs, tools are needed to reduce or eliminate errors from de novo assemblies. Results We present iAssembler, a pipeline that can assemble large-scale ESTs into consensus sequences with significantly higher accuracy than current existing assemblers. iAssembler employs MIRA and CAP3 assemblers to generate initial assemblies, followed by identifying and correcting two common types of transcriptome assembly errors: 1 ESTs from different transcripts (mainly alternatively spliced transcripts or paralogs are incorrectly assembled into same contigs; and 2 ESTs from same transcripts fail to be assembled together. iAssembler can be used to assemble ESTs generated using the traditional Sanger method and/or the Roche-454 massive parallel pyrosequencing technology. Conclusion We compared performances of iAssembler and several other de novo EST assembly programs using both Roche-454 and Sanger EST datasets. It demonstrated that iAssembler generated significantly more accurate consensus sequences than other assembly programs.

  10. Wind-Driven Ecological Flow Regimes Downstream from Hydropower Dams

    Science.gov (United States)

    Kern, J.; Characklis, G. W.

    2012-12-01

    Conventional hydropower can be turned on and off quicker and less expensively than thermal generation (coal, nuclear, or natural gas). These advantages enable hydropower utilities to respond to rapid fluctuations in energy supply and demand. More recently, a growing renewable energy sector has underlined the need for flexible generation capacity that can complement intermittent renewable resources such as wind power. While wind power entails lower variable costs than other types of generation, incorporating it into electric power systems can be problematic. Due to variable and unpredictable wind speeds, wind power is difficult to schedule and must be used when available. As a result, integrating large amounts of wind power into the grid may result in atypical, swiftly changing demand patterns for other forms of generation, placing a premium on sources that can be rapidly ramped up and down. Moreover, uncertainty in wind power forecasts will stipulate increased levels of 'reserve' generation capacity that can respond quickly if real-time wind supply is less than expected. These changes could create new hourly price dynamics for energy and reserves, altering the short-term financial signals that hydroelectric dam operators use to schedule water releases. Traditionally, hourly stream flow patterns below hydropower dams have corresponded in a very predictable manner to electricity demand, whose primary factors are weather (hourly temperature) and economic activity (workday hours). Wind power integration has the potential to yield more variable, less predictable flows at hydro dams, flows that at times could resemble reciprocal wind patterns. An existing body of research explores the impacts of standard, demand-following hydroelectric dams on downstream ecological flows; but weighing the benefits of increased reliance on wind power against further impacts to ecological flows may be a novel challenge for the environmental community. As a preliminary step in meeting this

  11. Extraction and downstream processing of plant-derived recombinant proteins.

    Science.gov (United States)

    Buyel, J F; Twyman, R M; Fischer, R

    2015-11-01

    Plants offer the tantalizing prospect of low-cost automated manufacturing processes for biopharmaceutical proteins, but several challenges must be addressed before such goals are realized and the most significant hurdles are found during downstream processing (DSP). In contrast to the standardized microbial and mammalian cell platforms embraced by the biopharmaceutical industry, there are many different plant-based expression systems vying for attention, and those with the greatest potential to provide inexpensive biopharmaceuticals are also the ones with the most significant drawbacks in terms of DSP. This is because the most scalable plant systems are based on the expression of intracellular proteins in whole plants. The plant tissue must therefore be disrupted to extract the product, challenging the initial DSP steps with an unusually high load of both particulate and soluble contaminants. DSP platform technologies can accelerate and simplify process development, including centrifugation, filtration, flocculation, and integrated methods that combine solid-liquid separation, purification and concentration, such as aqueous two-phase separation systems. Protein tags can also facilitate these DSP steps, but they are difficult to transfer to a commercial environment and more generic, flexible and scalable strategies to separate target and host cell proteins are preferable, such as membrane technologies and heat/pH precipitation. In this context, clarified plant extracts behave similarly to the feed stream from microbes or mammalian cells and the corresponding purification methods can be applied, as long as they are adapted for plant-specific soluble contaminants such as the superabundant protein RuBisCO. Plant-derived pharmaceutical proteins cannot yet compete directly with established platforms but they are beginning to penetrate niche markets that allow the beneficial properties of plants to be exploited, such as the ability to produce 'biobetters' with tailored

  12. Transcriptome complexity in a genome-reduced bacterium

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  13. Downstream boundary effects on the frequency of self-excited oscillations in transonic diffuser flows

    Science.gov (United States)

    Hsieh, T.

    1986-10-01

    Investigation of downstream boundary effects on the frequency of self-excited oscillations in two-dimensional, separated transonic diffuser flows were conducted numerically by solving the compressible, Reynolds-averaged, thin-layer Navier-Stokes equation with two equation turbulence models. It was found that the flow fields are very sensitive to the location of the downstream boundary. Extension of the diffuser downstream boundary significantly reduces the frequency and amplitude of oscillations for pressure, velocity, and shock. The existence of a suction slot in the experimental setpup obscures the physical downstream boundary and therefore presents a difficulty for quantitative comparisons between computation and experiment.

  14. Exploring the shallow end; estimating information content in transcriptomics studies

    Directory of Open Access Journals (Sweden)

    Daniel J Kliebenstein

    2012-09-01

    Full Text Available Transcriptomics is a major platform to study organismal biology. The advent of new parallel sequencing technologies has opened up a new avenue of transcriptomics with ever deeper and deeper sequencing to identify and quantify each and every transcript in a sample. However, this may not be the best usage of the parallel sequencing technology for all transcriptomics experiments. I utilized the Shannon Entropy approach to estimate the information contained within a transcriptomics experiment and tested the ability of shallow RNAseq to capture the majority of this information. This analysis showed that it was possible to capture nearly all of the network or genomic information present in a variety of transcriptomics experiments using a subset of the most abundant 5000 transcripts or less within any given sample. Thus, it appears that it should be possible and affordable to conduct large scale factorial analysis with a high degree of replication using parallel sequencing technologies.

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

    Directory of Open Access Journals (Sweden)

    Stahl Ulf

    2010-05-01

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

  16. Oxidative stress and its downstream signaling in aging eyes

    Directory of Open Access Journals (Sweden)

    Pinazo-Durán MD

    2014-04-01

    Full Text Available María Dolores Pinazo-Durán,1,* Roberto Gallego-Pinazo,2,* Jose Javier García-Medina,1,3,* Vicente Zanón-Moreno,1,4 Carlo Nucci,5 Rosa Dolz-Marco,2 Sebastián Martínez-Castillo,2 Carmen Galbis-Estrada,1 Carla Marco-Ramírez,1 Maria Isabel López-Gálvez,6,* David J Galarreta,6,* Manuel Díaz-Llópis4,*1Ophthalmic Research Unit "Santiago Grisolía", Valencia, Spain; 2Department of Ophthalmology, Macula Section, The University and Polytechnic Hospital La Fe, Valencia, Spain; 3Department of Ophthalmology, University Hospital Reina Sofia, Murcia, Spain; 4Faculty of Medicine, University of Valencia, Spain; 5University of Rome Tor Vergata, Rome, Italy; 6Instituto de Oftalmobiología Aplicada (IOBA, Valladolid, Spain *Members of the Spanish Net of Ocular Pathology of the Instituto de Salud Carlos III (Madrid, OFTAREDBackground: Oxidative stress (OS and its biomarkers are the biochemical end point of the imbalance between reactive oxygen species (ROS production and the ability of the antioxidant (AOX biological systems to fight against oxidative injury.Objective: We reviewed the role of OS and its downstream signaling in aging eyes.Methods: A search of the literature and current knowledge on the physiological and pathological mechanisms of OS were revisited in relation to the eyes and the aging process. Most prevalent ocular diseases have been analyzed herein in relation to OS and nutraceutic supplements, such as dry-eye disorders, glaucoma, age-related macular degeneration, and diabetic retinopathy.Results: Clinical, biochemical, and molecular data from anterior and posterior eye segment diseases point to OS as the common pathogenic mechanism in the majority of these ocular disorders, many of which are pathologies causing visual impairment, blindness, and subsequent loss of life quality. Studies with nutraceutic supplements in aging eye-related pathologies have also been reviewed.Conclusion: OS, nutritional status, and nutraceutic supplements have

  17. Transcriptomic dissection of tongue squamous cell carcinoma

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    Schwartz Joel L

    2008-02-01

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

  18. The adult boar testicular and epididymal transcriptomes

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    Guyonnet Benoît

    2009-08-01

    Full Text Available Abstract Background Mammalians gamete production takes place in the testis but when they exit this organ, although spermatozoa have acquired a specialized and distinct morphology, they are immotile and infertile. It is only after their travel in the epididymis that sperm gain their motility and fertility. Epididymis is a crescent shaped organ adjacent to the testis that can be divided in three gross morphological regions, head (caput, body (corpus and tail (cauda. It contains a long and unique convoluted tubule connected to the testis via the efferent ducts and finished by joining the vas deferens in its caudal part. Results In this study, the testis, the efferent ducts (vas efferens, VE, nine distinct successive epididymal segments and the deferent duct (vas deferens, VD of four adult boars of known fertility were isolated and their mRNA extracted. The gene expression of each of these samples was analyzed using a pig generic 9 K nylon microarray (AGENAE program; GEO accession number: GPL3729 spotted with 8931 clones derived from normalized cDNA banks from different pig tissues including testis and epididymis. Differentially expressed transcripts were obtained with moderated t-tests and F-tests and two data clustering algorithms based either on partitioning around medoid (top down PAM or hierarchical clustering (bottom up HCL were combined for class discovery and gene expression analysis. Tissue clustering defined seven transcriptomic units: testis, vas efferens and five epididymal transcriptomic units. Meanwhile transcripts formed only four clusters related to the tissues. We have then used a specific statistical method to sort out genes specifically over-expressed (markers in testis, VE or in each of the five transcriptomic units of the epididymis (including VD. The specific regional expression of some of these genes was further validated by PCR and Q-PCR. We also searched for specific pathways and functions using available gene ontology

  19. Transcriptome-wide dynamics of RNA pseudouridylation.

    Science.gov (United States)

    Karijolich, John; Yi, Chengqi; Yu, Yi-Tao

    2015-10-01

    Pseudouridylation is the most abundant internal post-transcriptional modification of stable RNAs, with fundamental roles in the biogenesis and function of spliceosomal small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNAs). Recently, the first transcriptome-wide maps of RNA pseudouridylation were published, greatly expanding the catalogue of known pseudouridylated RNAs. These data have further implicated RNA pseudouridylation in the cellular stress response and, moreover, have established that mRNAs are also targets of pseudouridine synthases, potentially representing a novel mechanism for expanding the complexity of the cellular proteome.

  20. Crx broadly modulates the pineal transcriptome

    DEFF Research Database (Denmark)

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

    2011-01-01

    Cone-rod homeobox (Crx) encodes Crx, a transcription factor expressed selectively in retinal photoreceptors and pinealocytes, the major cell type of the pineal gland. In this study, the influence of Crx on the mammalian pineal gland was studied by light and electron microscopy and by use......-regulation of 745 genes (p pineal glands of wild......-type animals; only eight of these were also day/night expressed in the Crx-/- pineal gland. However, in the Crx-/- pineal gland 41 genes exhibited differential night/day expression that was not seen in wild-type animals. These findings indicate that Crx broadly modulates the pineal transcriptome and also...

  1. Transcriptome marker diagnostics using big data.

    Science.gov (United States)

    Han, Henry; Liu, Ying

    2016-02-01

    The big omics data are challenging translational bioinformatics in an unprecedented way for its complexities and volumes. How to employ big omics data to achieve a rivalling-clinical, reproducible disease diagnosis from a systems approach is an urgent problem to be solved in translational bioinformatics and machine learning. In this study, the authors propose a novel transcriptome marker diagnosis to tackle this problem using big RNA-seq data by viewing whole transcriptome as a profile marker systematically. The systems diagnosis not only avoids the reproducibility issue of the existing gene-/network-marker-based diagnostic methods, but also achieves rivalling-clinical diagnostic results by extracting true signals from big RNA-seq data. Their method demonstrates a better fit for personalised diagnostics by attaining exceptional diagnostic performance via using systems information than its competitive methods and prepares itself as a good candidate for clinical usage. To the best of their knowledge, it is the first study on this topic and will inspire the more investigations in big omics data diagnostics.

  2. Chicken sperm transcriptome profiling by microarray analysis.

    Science.gov (United States)

    Singh, R P; Shafeeque, C M; Sharma, S K; Singh, R; Mohan, J; Sastry, K V H; Saxena, V K; Azeez, P A

    2016-03-01

    It has been confirmed that mammalian sperm contain thousands of functional RNAs, and some of them have vital roles in fertilization and early embryonic development. Therefore, we attempted to characterize transcriptome of the sperm of fertile chickens using microarray analysis. Spermatozoal RNA was pooled from 10 fertile males and used for RNA preparation. Prior to performing the microarray, RNA quality was assessed using a bioanalyzer, and gDNA and somatic cell RNA contamination was assessed by CD4 and PTPRC gene amplification. The chicken sperm transcriptome was cross-examined by analysing sperm and testes RNA on a 4 × 44K chicken array, and results were verified by RT-PCR. Microarray analysis identified 21,639 predominantly nuclear-encoded transcripts in chicken sperm. The majority (66.55%) of the sperm transcripts were shared with the testes, while surprisingly, 33.45% transcripts were detected (raw signal intensity greater than 50) only in the sperm and not in the testes. The greatest proportion of up-regulated transcripts were responsible for signal transduction (63.20%) followed by embryonic development (56.76%) and cell structure (56.25%). Of the 20 most abundant transcripts, 18 remain uncharacterized, whereas the least abundant genes were mostly associated with the ribosome. These findings lay a foundation for more detailed investigations on sperm RNAs in chickens to identify sperm-based biomarkers for fertility.

  3. The meiotic transcriptome architecture of plants

    Directory of Open Access Journals (Sweden)

    Stefanie eDukowic-Schulze

    2014-06-01

    Full Text Available 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 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 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 that addressed the transcriptome of female meiosis. For this review, we compiled 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 and how to follow up on them in the future.

  4. Analysis of a human brain transcriptome map

    Directory of Open Access Journals (Sweden)

    Greene Jonathan R

    2002-04-01

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

  5. Single-species microarrays and comparative transcriptomics.

    Directory of Open Access Journals (Sweden)

    Frédéric J J Chain

    Full Text Available BACKGROUND: Prefabricated expression microarrays are currently available for only a few species but methods have been proposed to extend their application to comparisons between divergent genomes. METHODOLOGY/PRINCIPAL FINDINGS: Here we demonstrate that the hybridization intensity of genomic DNA is a poor basis on which to select unbiased probes on Affymetrix expression arrays for studies of comparative transcriptomics, and that doing so produces spurious results. We used the Affymetrix Xenopus laevis microarray to evaluate expression divergence between X. laevis, X. borealis, and their F1 hybrids. When data are analyzed with probes that interrogate only sequences with confirmed identity in both species, we recover results that differ substantially analyses that use genomic DNA hybridizations to select probes. CONCLUSIONS/SIGNIFICANCE: Our findings have implications for the experimental design of comparative expression studies that use single-species microarrays, and for our understanding of divergent expression in hybrid clawed frogs. These findings also highlight important limitations of single-species microarrays for studies of comparative transcriptomics of polyploid species.

  6. The Human Blood Metabolome-Transcriptome Interface

    Science.gov (United States)

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

    2015-01-01

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

  7. The Human Blood Metabolome-Transcriptome Interface.

    Directory of Open Access Journals (Sweden)

    Jörg Bartel

    2015-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Danieli Gian

    2011-02-01

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

  9. The developmental transcriptome of Drosophila melanogaster

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-12-02

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

  10. Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes

    Directory of Open Access Journals (Sweden)

    Kyoungwoo Nam

    2016-02-01

    Full Text Available 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.

  11. Elucidating and mining the Tulipa and Lilium transcriptomes.

    Science.gov (United States)

    Moreno-Pachon, Natalia M; Leeggangers, Hendrika A C F; Nijveen, Harm; Severing, Edouard; Hilhorst, Henk; Immink, Richard G H

    2016-10-01

    Genome sequencing remains a challenge for species with large and complex genomes containing extensive repetitive sequences, of which the bulbous and monocotyledonous plants tulip and lily are examples. In such a case, sequencing of only the active part of the genome, represented by the transcriptome, is a good alternative to obtain information about gene content. In this study we aimed to generate a high quality transcriptome of tulip and lily and to make this data available as an open-access resource via a user-friendly web-based interface. The Illumina HiSeq 2000 platform was applied and the transcribed RNA was sequenced from a collection of different lily and tulip tissues, respectively. In order to obtain good transcriptome coverage and to facilitate effective data mining, assembly was done using different filtering parameters for clearing out contamination and noise of the RNAseq datasets. This analysis revealed limitations of commonly applied methods and parameter settings used in de novo transcriptome assembly. The final created transcriptomes are publicly available via a user friendly Transcriptome browser ( http://www.bioinformatics.nl/bulbs/db/species/index ). The usefulness of this resource has been exemplified by a search for all potential transcription factors in lily and tulip, with special focus on the TCP transcription factor family. This analysis and other quality parameters point out the quality of the transcriptomes, which can serve as a basis for further genomics studies in lily, tulip, and bulbous plants in general.

  12. Mercury exposure in terrestrial birds far downstream of an historical point source

    Energy Technology Data Exchange (ETDEWEB)

    Jackson, Allyson K., E-mail: allyson.jackson@briloon.org [Biodiversity Research Institute, 19 Flaggy Meadow Road, Gorham, ME 04038 (United States); Institute for Integrative Bird Behavior Studies, Department of Biology, College of William and Mary, PO Box 8795, Williamsburg, VA 23187 (United States); Evers, David C.; Folsom, Sarah B. [Biodiversity Research Institute, 19 Flaggy Meadow Road, Gorham, ME 04038 (United States); Condon, Anne M. [U.S. Fish and Wildlife Service, 6669 Short Lane, Gloucester, VA 23061 (United States); Diener, John; Goodrick, Lizzie F. [Biodiversity Research Institute, 19 Flaggy Meadow Road, Gorham, ME 04038 (United States); McGann, Andrew J. [Institute for Integrative Bird Behavior Studies, Department of Biology, College of William and Mary, PO Box 8795, Williamsburg, VA 23187 (United States); Schmerfeld, John [U.S. Fish and Wildlife Service, 6669 Short Lane, Gloucester, VA 23061 (United States); Cristol, Daniel A. [Institute for Integrative Bird Behavior Studies, Department of Biology, College of William and Mary, PO Box 8795, Williamsburg, VA 23187 (United States)

    2011-12-15

    Mercury (Hg) is a persistent environmental contaminant found in many freshwater and marine ecosystems. Historical Hg contamination in rivers can impact the surrounding terrestrial ecosystem, but there is little known about how far downstream this contamination persists. In 2009, we sampled terrestrial forest songbirds at five floodplain sites up to 137 km downstream of an historical source of Hg along the South and South Fork Shenandoah Rivers (Virginia, USA). We found that blood total Hg concentrations remained elevated over the entire sampling area and there was little evidence of decline with distance. While it is well known that Hg is a pervasive and long-lasting aquatic contaminant, it has only been recently recognized that it also biomagnifies effectively in floodplain forest food webs. This study extends the area of concern for terrestrial habitats near contaminated rivers for more than 100 km downstream from a waterborne Hg point source. - Highlights: > We report blood mercury levels for terrestrial songbirds downstream of contamination. > Blood mercury levels remain elevated above reference for at least 137 km downstream. > Trends vary based on foraging guild and migration strategy. > Mercury affects terrestrial biota farther downstream than previously documented. - Blood mercury levels of forest songbirds remain elevated above reference levels for at least 137 km downstream of historical point source.

  13. GH3-Mediated Auxin Conjugation Can Result in Either Transient or Oscillatory Transcriptional Auxin Responses.

    Science.gov (United States)

    Mellor, Nathan; Bennett, Malcolm J; King, John R

    2016-02-01

    The conjugation of the phytohormone auxin to amino acids via members of the gene family GH3 is an important component in the auxin-degradation pathway in the model plant species Arabidopsis thaliana, as well as many other plant species. Since the GH3 genes are themselves up-regulated in response to auxin, providing a negative feedback on intracellular auxin levels, it is hypothesised that the GH3s have a role in auxin homoeostasis. To investigate this, we develop a mathematical model of auxin signalling and response that includes the auxin-inducible negative feedback from GH3 on the rate of auxin degradation. In addition, we include a positive feedback on the rate of auxin input via the auxin influx transporter LAX3, shown previously to be expressed in response to auxin and to have an important role during lateral root emergence. In the absence of the LAX3 positive feedback, we show that the GH3 negative feedback suffices to generate a transient transcriptional response to auxin in the shape of damped oscillations of the model system. When LAX3 positive feedback is present, sustained oscillations of the system are possible. Using steady-state analyses, we identify and discuss key parameters affecting the oscillatory behaviour of the model. The transient peak of auxin and subsequent transcriptional response caused by the up-regulation of GH3 represents a possible protective homoeostasis mechanism that may be used by plant cells in response to excess auxin.

  14. Cell-Cell Communication in Yeast Using Auxin Biosynthesis and Auxin Responsive CRISPR Transcription Factors.

    Science.gov (United States)

    Khakhar, Arjun; Bolten, Nicholas J; Nemhauser, Jennifer; Klavins, Eric

    2016-04-15

    An engineering framework for synthetic multicellular systems requires a programmable means of cell-cell communication. Such a communication system would enable complex behaviors, such as pattern formation, division of labor in synthetic microbial communities, and improved modularity in synthetic circuits. However, it remains challenging to build synthetic cellular communication systems in eukaryotes due to a lack of molecular modules that are orthogonal to the host machinery, easy to reconfigure, and scalable. Here, we present a novel cell-to-cell communication system in Saccharomyces cerevisiae (yeast) based on CRISPR transcription factors and the plant hormone auxin that exhibits several of these features. Specifically, we engineered a sender strain of yeast that converts indole-3-acetamide (IAM) into auxin via the enzyme iaaH from Agrobacterium tumefaciens. To sense auxin and regulate transcription in a receiver strain, we engineered a reconfigurable library of auxin-degradable CRISPR transcription factors (ADCTFs). Auxin-induced degradation is achieved through fusion of an auxin-sensitive degron (from IAA corepressors) to the CRISPR TF and coexpression with an auxin F-box protein. Mirroring the tunability of auxin perception in plants, our family of ADCTFs exhibits a broad range of auxin sensitivities. We characterized the kinetics and steady-state behavior of the sender and receiver independently as well as in cocultures where both cell types were exposed to IAM. In the presence of IAM, auxin is produced by the sender cell and triggers deactivation of reporter expression in the receiver cell. The result is an orthogonal, rewireable, tunable, and, arguably, scalable cell-cell communication system for yeast and other eukaryotic cells.

  15. An INDEHISCENT-Controlled Auxin Response Specifies the Separation Layer in Early Arabidopsis Fruit

    NARCIS (Netherlands)

    van Gelderen, Kasper; van Rongen, Martin; Liu, An'an; Otten, Anne; Offringa, Remko

    2016-01-01

    Seed dispersal is an important moment in the life cycle of a plant species. In Arabidopsis thaliana, it is dependent on transcription factor INDEHISCENT (IND)-mediated specification of a separation layer in the dehiscence zone found in the margin between the valves (carpel walls) and the central rep

  16. A novel sensor to map auxin response and distribution at high spatio-temporal resolution.

    Science.gov (United States)

    Brunoud, Géraldine; Wells, Darren M; Oliva, Marina; Larrieu, Antoine; Mirabet, Vincent; Burrow, Amy H; Beeckman, Tom; Kepinski, Stefan; Traas, Jan; Bennett, Malcolm J; Vernoux, Teva

    2012-01-15

    Auxin is a key plant morphogenetic signal but tools to analyse dynamically its distribution and signalling during development are still limited. Auxin perception directly triggers the degradation of Aux/IAA repressor proteins. Here we describe a novel Aux/IAA-based auxin signalling sensor termed DII-VENUS that was engineered in the model plant Arabidopsis thaliana. The VENUS fast maturing form of yellow fluorescent protein was fused in-frame to the Aux/IAA auxin-interaction domain (termed domain II; DII) and expressed under a constitutive promoter. We initially show that DII-VENUS abundance is dependent on auxin, its TIR1/AFBs co-receptors and proteasome activities. Next, we demonstrate that DII-VENUS provides a map of relative auxin distribution at cellular resolution in different tissues. DII-VENUS is also rapidly degraded in response to auxin and we used it to visualize dynamic changes in cellular auxin distribution successfully during two developmental responses, the root gravitropic response and lateral organ production at the shoot apex. Our results illustrate the value of developing response input sensors such as DII-VENUS to provide high-resolution spatio-temporal information about hormone distribution and response during plant growth and development.

  17. TCP15 modulates cytokinin and auxin responses during gynoecium development in Arabidopsis.

    Science.gov (United States)

    Lucero, Leandro E; Uberti-Manassero, Nora G; Arce, Agustín L; Colombatti, Francisco; Alemano, Sergio G; Gonzalez, Daniel H

    2015-10-01

    We studied the role of Arabidopsis thaliana TCP15, a member of the TEOSINTE BRANCHED1-CYCLOIDEA-PCF (TCP) transcription factor family, in gynoecium development. Plants that express TCP15 from the 35S CaMV promoter (35S:TCP15) develop flowers with defects in carpel fusion and a reduced number of stigmatic papillae. In contrast, the expression of TCP15 fused to a repressor domain from its own promoter causes the development of outgrowths topped with stigmatic papillae from the replum. 35S:TCP15 plants show lower levels of the auxin indoleacetic acid and reduced expression of the auxin reporter DR5 and the auxin biosynthesis genes YUCCA1 and YUCCA4, suggesting that TCP15 is a repressor of auxin biosynthesis. Treatment of plants with cytokinin enhances the developmental effects of expressing TCP15 or its repressor form. In addition, treatment of a knock-out double mutant in TCP15 and the related gene TCP14 with cytokinin causes replum enlargement, increased development of outgrowths, and the induction of the auxin biosynthesis genes YUCCA1 and YUCCA4. A comparison of the phenotypes observed after cytokinin treatment of plants with altered expression levels of TCP15 and auxin biosynthesis genes suggests that TCP15 modulates gynoecium development by influencing auxin homeostasis. We propose that the correct development of the different tissues of the gynoecium requires a balance between auxin levels and cytokinin responses, and that TCP15 participates in a feedback loop that helps to adjust this balance.

  18. Expression pattern of the CsPK3 auxin-responsive protein kinase gene.

    Science.gov (United States)

    Chono, M; Suzuki, Y; Nemoto, K; Yamane, H; Murofushi, N; Yamaguchi, I

    2001-03-01

    We have previously cloned a cDNA of a putative serine/threonine protein kinase gene named CsPK3 from cucumber, the mRNA level of which was up-regulated by auxin and down-regulated by light irradiation. To examine the CsPK3 gene expression in detail, we cloned a genomic DNA of CsPK3 gene and made transgenic tobacco (Nicotiana tabacum L. cv. Petit Havana SR1) plants containing the fused CsPK3 promoter-beta-glucuronidase gene. The beta-glucuronidase expression was detected in the shoot apex, vascular tissues, and the outermost layer of cortex. The histological distribution of CsPK3 mRNA in cucumber seedlings was supported by in situ hybridization, where the positive signals were observed in similar tissues as those observed by beta-glucuronidase staining. The responsiveness of the CsPK3 gene to auxin and light was also confirmed for beta-glucuronidase activity. The pattern of beta-glucuronidase staining changed during the development of the tobacco seedlings. The results of our experiment showed that CsPK3 was expressed in a wide variety of tissues and cells in which the developmental and growth controls by auxin are suggested.

  19. Thorium impact on tobacco root transcriptome.

    Science.gov (United States)

    Mazari, Kateřina; Landa, Přemysl; Přerostová, Sylva; Müller, Karel; Vaňková, Radomíra; Soudek, Petr; Vaněk, Tomáš

    2017-03-05

    Thorium is natural actinide metal with potential use in nuclear energetics. Contamination by thorium, originated from mining activities or spills, represents environmental risk due to its radioactivity and chemical toxicity. A promising approach for cleaning of contaminated areas is phytoremediation, which need to be based, however, on detail understanding of the thorium effects on plants. In this study we investigated transcriptomic response of tobacco roots exposed to 200μM thorium for one week. Thorium application resulted in up-regulation of 152 and down-regulation of 100 genes (p-value thorium disturbed phosphate uptake or signaling. Also expression of iron responsive genes was influenced. Negative regulation of several aquaporins indicated disturbance of water homeostasis. Genes potentially involved in thorium transport could be zinc-induced facilitator ZIF2, plant cadmium resistance PCR2, and ABC transporter ABCG40. This study provides the first insight at the processes in plants exposed to thorium.

  20. Transcriptome changes during intestinal cell differentiation

    DEFF Research Database (Denmark)

    Tadjali, Mehrdad; Seidelin, Jakob B; Olsen, Jørgen;

    2002-01-01

    in the transcriptome was observed during the differentiation of the Caco-2 cells. 8762 of the 18149 genes analysed were expressed above background level in the undifferentiated Caco-2 cells, whereas only 5767 genes were expressed above background in differentiated Caco-2 cells. This pattern of expression was caused...... by a general down-regulation of genes in the low abundance class. Similar results were found using mouse small intestinal crypt and villus cells, suggesting that the phenomenon also occurs in the intestine in vivo. The expression data were subsequently used in a search for markers for subsets of epithelial...... cells by performing reverse transcriptase-polymerase chain reaction on RNA extracted from laser dissected intestinal crypt and villi. In a screen of eight transcripts one - SART3 - was identified as a marker for human colonic crypts....

  1. Transcriptome response to nitrogen starvation in rice

    Indian Academy of Sciences (India)

    Hongmei Cai; Yongen Lu; Weibo Xie; Tong Zhu; Xingming Lian

    2012-09-01

    Nitrogen is an essential mineral nutrient required for plant growth and development. Insufficient nitrogen (N) supply triggers extensive physiological and biochemical changes in plants. In this study, we used Affymetrix GeneChip rice genome arrays to analyse the dynamics of rice transcriptome under N starvation. N starvation induced or suppressed transcription of 3518 genes, representing 10.88% of the genome. These changes, mostly transient, affected various cellular metabolic pathways, including stress response, primary and secondary metabolism, molecular transport, regulatory process and organismal development. 462 or 13.1% transcripts for N starvation expressed similarly in root and shoot. Comparative analysis between rice and Arabidopsis identified 73 orthologous groups that responded to N starvation, demonstrated the existence of conserved N stress coupling mechanism among plants. Additional analysis of transcription profiles of microRNAs revealed differential expression of miR399 and miR530 under N starvation, suggesting their potential roles in plant nutrient homeostasis.

  2. Transcriptome changes during intestinal cell differentiation

    DEFF Research Database (Denmark)

    Tadjali, Mehrdad; Seidelin, Jakob B; Olsen, Jørgen Lillelund;

    2002-01-01

    The expression of 18149 genes have been analysed during the differentiation of the human intestinal cell line Caco-2. cDNA probes from undifferentiated and differentiated Caco-2 cells were separately hybridised to EST DNAs spotted in an array on a nylon membrane. A remarkable change...... in the transcriptome was observed during the differentiation of the Caco-2 cells. 8762 of the 18149 genes analysed were expressed above background level in the undifferentiated Caco-2 cells, whereas only 5767 genes were expressed above background in differentiated Caco-2 cells. This pattern of expression was caused...... by a general down-regulation of genes in the low abundance class. Similar results were found using mouse small intestinal crypt and villus cells, suggesting that the phenomenon also occurs in the intestine in vivo. The expression data were subsequently used in a search for markers for subsets of epithelial...

  3. Probabilistic Transcriptome Assembly and Variant Graph Genotyping

    DEFF Research Database (Denmark)

    Sibbesen, Jonas Andreas

    the resulting sequencing data should be interpreted. This has over the years spurred the development of many probabilistic methods that are capable of modelling dierent aspects of the sequencing process. Here, I present two of such methods that were developed to each tackle a dierent problem in bioinformatics......, together with an application of the latter method to a large Danish sequencing project. The rst is a probabilistic method for transcriptome assembly that is based on a novel generative model of the RNA sequencing process and provides condence estimates on the assembled transcripts. We show...... that this approach outperforms existing state-of-the-art methods measured using sensitivity and precision on both simulated and real data. The second is a novel probabilistic method that uses exact alignment of k-mers to a set of variants graphs to provide unbiased estimates of genotypes in a population...

  4. Assisted transcriptome reconstruction and splicing orthology

    Directory of Open Access Journals (Sweden)

    Samuel Blanquart

    2016-11-01

    Full Text Available Abstract Background Transcriptome reconstruction, defined as the identification of all protein isoforms that may be expressed by a gene, is a notably difficult computational task. With real data, the best methods based on RNA-seq data identify barely 21 % of the expressed transcripts. While waiting for algorithms and sequencing techniques to improve — as has been strongly suggested in the literature — it is important to evaluate assisted transcriptome prediction; this is the question of how alternative transcription in one species performs as a predictor of protein isoforms in another relatively close species. Most evidence-based gene predictors use transcripts from other species to annotate a genome, but the predictive power of procedures that use exclusively transcripts from external species has never been quantified. The cornerstone of such an evaluation is the correct identification of pairs of transcripts with the same splicing patterns, called splicing orthologs. Results We propose a rigorous procedural definition of splicing orthologs, based on the identification of all ortholog pairs of splicing sites in the nucleotide sequences, and alignments at the protein level. Using our definition, we compared 24 382 human transcripts and 17 909 mouse transcripts from the highly curated CCDS database, and identified 11 122 splicing orthologs. In prediction mode, we show that human transcripts can be used to infer over 62 % of mouse protein isoforms. When restricting the predictions to transcripts known eight years ago, the percentage grows to 74 %. Using CCDS timestamped releases, we also analyze the evolution of the number of splicing orthologs over the last decade. Conclusions Alternative splicing is now recognized to play a major role in the protein diversity of eukaryotic organisms, but definitions of spliced isoform orthologs are still approximate. Here we propose a definition adapted to the subtle variations of conserved alternative

  5. Integrative analysis of the mouse embryonic transcriptome.

    Science.gov (United States)

    Singh, Amar V; Knudsen, Kenneth B; Knudsen, Thomas B

    2007-04-10

    Monitoring global gene expression provides insight into how genes and regulatory signals work together to guide embryo development. The fields of developmental biology and teratology are now confronted with the need for automated access to a reference library of gene-expression signatures that benchmark programmed (genetic) and adaptive (environmental) regulation of the embryonic transcriptome. Such a library must be constructed from highly-distributed microarray data. Birth Defects Systems Manager (BDSM), an open access knowledge management system, provides custom software to mine public microarray data focused on developmental health and disease. The present study describes tools for seamless data integration in the BDSM library (MetaSample, MetaChip, CIAeasy) using the QueryBDSM module. A field test of the prototype was run using published microarray data series derived from a variety of laboratories, experiments, microarray platforms, organ systems, and developmental stages. The datasets focused on several developing systems in the mouse embryo, including preimplantation stages, heart and nerve development, testis and ovary development, and craniofacial development. Using BDSM data integration tools, a gene-expression signature for 346 genes was resolved that accurately classified samples by organ system and developmental sequence. The module builds a potential for the BDSM approach to decipher a large number developmental processes through comparative bioinformatics analysis of embryological systems at-risk for specific defects, using multiple scenarios to define the range of probabilities leading from molecular phenotype to clinical phenotype. We conclude that an integrative analysis of global gene-expression of the developing embryo can form the foundation for constructing a reference library of signaling pathways and networks for normal and abnormal regulation of the embryonic transcriptome. These tools are available free of charge from the web-site http

  6. The human airway epithelial basal cell transcriptome.

    Directory of Open Access Journals (Sweden)

    Neil R Hackett

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

  7. Toxicogenomics of bromobenzene hepatotoxicity: a combined transcriptomics and proteomics approach

    NARCIS (Netherlands)

    Heijne, W.H.M.; Stierum, R.H.; Slijper, M.; Bladeren, van P.J.; Ommen, van B.

    2003-01-01

    Toxicogenomics is a novel approach integrating the expression analysis of thousands of genes (transcriptomics) or proteins (proteomics) with classical methods in toxicology. Effects at the molecular level are related to pathophysiological changes of the organisms, enabling detailed comparison of mec

  8. New insights into domestication of carrot from root transcriptome analyses

    NARCIS (Netherlands)

    Rong, J.; Lammers, Y.; Strasburg, J.L.; Schidlo, N.S.; Ariyurek, Y.; Jong, de T.J.; Klinkhamer, P.G.L.; Smulders, M.J.M.; Vrieling, K.

    2014-01-01

    Background - Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified genes under selection based on transcriptome analyses. Results - The root transcr

  9. Single-cell transcriptomics enters the age of mass production

    NARCIS (Netherlands)

    Junker, Jan Philipp; van Oudenaarden, Alexander

    2015-01-01

    Two publications in the current issue of Cell introduce novel methods for high-throughput single-cell transcriptomics by using droplet microfluidics and sophisticated barcoding schemes for transcriptional profiling of thousands of individual cells.

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

    Science.gov (United States)

    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.

  11. The Escherichia coli transcriptome linked to growth fitness

    Directory of Open Access Journals (Sweden)

    Bei-Wen Ying

    2016-03-01

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

  12. Toxicogenomics of bromobenzene hepatotoxicity: A combined transcriptomics and proteomics approach

    NARCIS (Netherlands)

    Heijne, W.H.M.; Stierum, R.H.; Slijper, M.; Bladeren, P.J. van; Ommen, B. van

    2003-01-01

    Toxicogenomics is a novel approach integrating the expression analysis of thousands of genes (transcriptomics) or proteins (proteomics) with classical methods in toxicology. Effects at the molecular level are related to pathophysiological changes of the organisms, enabling detailed comparison of mec

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

    Indian Academy of Sciences (India)

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

    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.

  14. Antibiotic resistance in Aeromonas upstream and downstream of a water resource recovery facility.

    Science.gov (United States)

    Cisar, Cindy R; Henderson, Samantha K; Askew, Maegan L; Risenhoover, Hollie G; McAndrews, Chrystle R; Kennedy, S Dawn; Paine, C Sue

    2014-09-01

    Aeromonas strains isolated from sediments upstream and downstream of a water resource recovery facility (WRRF) over a two-year time period were tested for susceptibility to 13 antibiotics. Incidence of resistance to antibiotics, antibiotic resistance phenotypes, and diversity (based on resistance phenotypes) were compared in the two populations. At the beginning of the study, the upstream and downstream Aeromonas populations were different for incidence of antibiotic resistance (p resistance phenotypes (p antibiotic resistance in Aeromonas in stream sediments fluctuates considerably over time and (2) suggest that WRRF effluent does not, when examined over the long- term, affect antibiotic resistance in Aeromonas in downstream sediment.

  15. Single cell transcriptome analysis using next generation sequencing.

    OpenAIRE

    Blattner, M.

    2010-01-01

    The heterogeneity of tissues, especially in cancer research, is a central issue in transcriptome analysis. In recent years, research has primarily focused on the development of methods for single cell analysis. Single cell analysis aims at gaining (novel) insights into biological processes of healthy and diseased cells. Some of the challenges in transcriptome analysis concern low abundance of sample starting material, necessary sample amplification steps and subsequent analysis. In this study...

  16. Single-cell transcriptome analysis of endometrial tissue

    OpenAIRE

    Krjutškov, K.; Katayama, S .; Saare, M; Vera-Rodriguez, M.; Lubenets, D.; Samuel, K.; Laisk-Podar, T.; Teder, H.; Einarsdottir, E.; Salumets, A.; Kere, J.

    2016-01-01

    STUDY QUESTION How can we study the full transcriptome of endometrial stromal and epithelial cells at the single-cell level? SUMMARY ANSWER By compiling and developing novel analytical tools for biopsy, tissue cryopreservation and disaggregation, single-cell sorting, library preparation, RNA sequencing (RNA-seq) and statistical data analysis. WHAT IS KNOWN ALREADY Although single-cell transcriptome analyses from various biopsied tissues have been published recently, corresponding protocols fo...

  17. Characterisation of Caenorhabditis elegans sperm transcriptome and proteome

    OpenAIRE

    Ma, Xuan; Zhu, Yingjie; Li, Chunfang; Xue, Peng; Zhao, Yanmei; Chen, Shilin; Yang, Fuquan; Miao, Long

    2014-01-01

    Background Although sperm is transcriptionally and translationally quiescent, complex populations of RNAs, including mRNAs and non-coding RNAs, exist in sperm. Previous microarray analysis of germ cell mutants identified hundreds of sperm genes in Caenorhabditis elegans. To take a more comprehensive view on C. elegans sperm genes, here, we isolate highly pure sperm cells and employ high-throughput technologies to obtain sperm transcriptome and proteome. Results First, sperm transcriptome cons...

  18. Tissue-Specific Transcriptomics in the Field Cricket Teleogryllus oceanicus

    OpenAIRE

    Bailey, Nathan William; Veltsos, Paris; Tan, Yew-Foon; Millar, A. Harvey; Ritchie, Michael Gordon; Simmons, Leigh W.

    2013-01-01

    This work was supported by a Natural Environment Research Council Junior Postdoctoral Fellowship (NE/G014906/1) and Pacific Rim Foundation funding (08-T-PRRP-05-0029) to N.W.B. Field crickets (family Gryllidae) frequently are used in studies of behavioral genetics, sexual selection, and sexual conflict, but there have been no studies of transcriptomic differences among different tissue types. We evaluated transcriptome variation among testis, accessory gland, and the remaining whole-body p...

  19. SoyXpress: A database for exploring the soybean transcriptome

    OpenAIRE

    Cheng Kei; Strömvik Martina V

    2008-01-01

    Abstract Background Experiments using whole transcriptome microarrays produce massive amounts of data. To gain a comprehensive understanding of this gene expression data it needs to be integrated with other available information such as gene function and metabolic pathways. Bioinformatics tools are essential to handle, organize and interpret the results. To date, no database provides whole transcriptome analysis capabilities integrated with terms describing biological functions for soybean (G...

  20. Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis

    Science.gov (United States)

    Dijkstra, Annereinou R.; Alkema, Wynand; Starrenburg, Marjo J. C.; van Hijum, Sacha A. F. T.; Bron, Peter A.

    2016-01-01

    Recently, we demonstrated that fermentation conditions have a strong impact on subsequent survival of Lactococcus lactis strain MG1363 during heat and oxidative stress, two important parameters during spray drying. Moreover, employment of a transcriptome-phenotype matching approach revealed groups of genes associated with robustness towards heat and/or oxidative stress. To investigate if other strains have similar or distinct transcriptome signatures for robustness, we applied an identical transcriptome-robustness phenotype matching approach on the L. lactis strains IL1403, KF147 and SK11, which have previously been demonstrated to display highly diverse robustness phenotypes. These strains were subjected to an identical fermentation regime as was performed earlier for strain MG1363 and consisted of twelve conditions, varying in the level of salt and/or oxygen, as well as fermentation temperature and pH. In the exponential phase of growth, cells were harvested for transcriptome analysis and assessment of heat and oxidative stress survival phenotypes. The variation in fermentation conditions resulted in differences in heat and oxidative stress survival of up to five 10-log units. Effects of the fermentation conditions on stress survival of the L. lactis strains were typically strain-dependent, although the fermentation conditions had mainly similar effects on the growth characteristics of the different strains. By association of the transcriptomes and robustness phenotypes highly strain-specific transcriptome signatures for robustness towards heat and oxidative stress were identified, indicating that multiple mechanisms exist to increase robustness and, as a consequence, robustness of each strain requires individual optimization. However, a relatively small overlap in the transcriptome responses of the strains was also identified and this generic transcriptome signature included genes previously associated with stress (ctsR and lplL) and novel genes, including nan

  1. Four Arabidopsis AREB/ABF transcription factors function predominantly in gene expression downstream of SnRK2 kinases in abscisic acid signalling in response to osmotic stress.

    Science.gov (United States)

    Yoshida, Takuya; Fujita, Yasunari; Maruyama, Kyonoshin; Mogami, Junro; Todaka, Daisuke; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko

    2015-01-01

    Under osmotic stress conditions such as drought and high salinity, the plant hormone abscisic acid (ABA) plays important roles in stress-responsive gene expression mainly through three bZIP transcription factors, AREB1/ABF2, AREB2/ABF4 and ABF3, which are activated by SNF1-related kinase 2s (SnRK2s) such as SRK2D/SnRK2.2, SRK2E/SnRK2.6 and SRK2I/SnRK2.3 (SRK2D/E/I). However, since the three AREB/ABFs are crucial, but not exclusive, for the SnRK2-mediated gene expression, transcriptional pathways governed by SRK2D/E/I are not fully understood. Here, we show that a bZIP transcription factor, ABF1, is a functional homolog of AREB1, AREB2 and ABF3 in ABA-dependent gene expression in Arabidopsis. Despite lower expression levels of ABF1 than those of the three AREB/ABFs, the areb1 areb2 abf3 abf1 mutant plants displayed increased sensitivity to drought and decreased sensitivity to ABA in primary root growth compared with the areb1 areb2 abf3 mutant. Genome-wide transcriptome analyses revealed that expression of downstream genes of SRK2D/E/I, which include many genes functioning in osmotic stress responses and tolerance such as transcription factors and LEA proteins, was mostly impaired in the quadruple mutant. Thus, these results indicate that the four AREB/ABFs are the predominant transcription factors downstream of SRK2D/E/I in ABA signalling in response to osmotic stress during vegetative growth.

  2. Bioactive Carbohydrates and Peptides in Foods: An Overview of Sources, Downstream Processing Steps and Associated Bioactivities.

    Science.gov (United States)

    Hayes, Maria; Tiwari, Brijesh K

    2015-09-17

    Bioactive peptides and carbohydrates are sourced from a myriad of plant, animal and insects and have huge potential for use as food ingredients and pharmaceuticals. However, downstream processing bottlenecks hinder the potential use of these natural bioactive compounds and add cost to production processes. This review discusses the health benefits and bioactivities associated with peptides and carbohydrates of natural origin and downstream processing methodologies and novel processes which may be used to overcome these.

  3. Theory and observations of Ekman flux in the chlorophyll distribution downstream of South Georgia.

    OpenAIRE

    Venables, Hugh; Meredith, Michael Paul

    2009-01-01

    A large phytoplankton bloom occurs downstream of South Georgia, an island on the northern edge of the Scotia Sea, Atlantic sector of the Southern Ocean. This is due to natural iron fertilisation being advected downstream in the Antarctic Circumpolar Current. Mapping of SeaWiFS chl-a in dynamic height/longitude space reveals the trajectory of surface water under the dual influences of geostrophic flow and Ekman flux. A theoretical estimate of the trajectory shows good agreement with observatio...

  4. Development of an idealised downstream cyclone: Eulerian and Lagrangian perspective on the kinetic energy

    OpenAIRE

    Papritz, Lukas; Schemm, Sebastian

    2013-01-01

    In this idealised modelling study, the development of a downstream cyclone, which closely follows the life-cycle of a Shapiro-Keyser cyclone, is addressed from a quasi-geostrophic kinetic energy perspective. To this end a simulation of a dry, highly idealised, dispersive baroclinic wave, developing a primary and a downstream cyclone, is performed. Kinetic energy and processes contributing to its tendency – in particular baroclinic conversion and ageostrophic geopotential fluxes – are investig...

  5. User experience network. Erroneous downstream occlusion alarms may disable Smiths Medical CADD-Solis infusion pumps.

    Science.gov (United States)

    2010-10-01

    Due to an issue in manufacturing, downstream occlusion (DSO) sensors in some Smiths Medical CADD-Solis infusion pumps may drift out of calibration, potentially resulting in erroneous alarms that disable the units. Hospitals experiencing the problem should return affected units to Smiths Medical for recalibration (free of charge) and should consider testing all their CADD-Solis pumps during routine maintenance to ensure that they alarm appropriately for downstream occlusions.

  6. Relaxation response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways.

    Directory of Open Access Journals (Sweden)

    Manoj K Bhasin

    Full Text Available The relaxation response (RR is the counterpart of the stress response. Millennia-old practices evoking the RR include meditation, yoga and repetitive prayer. Although RR elicitation is an effective therapeutic intervention that counteracts the adverse clinical effects of stress in disorders including hypertension, anxiety, insomnia and aging, the underlying molecular mechanisms that explain these clinical benefits remain undetermined. To assess rapid time-dependent (temporal genomic changes during one session of RR practice among healthy practitioners with years of RR practice and also in novices before and after 8 weeks of RR training, we measured the transcriptome in peripheral blood prior to, immediately after, and 15 minutes after listening to an RR-eliciting or a health education CD. Both short-term and long-term practitioners evoked significant temporal gene expression changes with greater significance in the latter as compared to novices. RR practice enhanced expression of genes associated with energy metabolism, mitochondrial function, insulin secretion and telomere maintenance, and reduced expression of genes linked to inflammatory response and stress-related pathways. Interactive network analyses of RR-affected pathways identified mitochondrial ATP synthase and insulin (INS as top upregulated critical molecules (focus hubs and NF-κB pathway genes as top downregulated focus hubs. Our results for the first time indicate that RR elicitation, particularly after long-term practice, may evoke its downstream health benefits by improving mitochondrial energy production and utilization and thus promoting mitochondrial resiliency through upregulation of ATPase and insulin function. Mitochondrial resiliency might also be promoted by RR-induced downregulation of NF-κB-associated upstream and downstream targets that mitigates stress.

  7. Relaxation response induces temporal transcriptome changes in energy metabolism, insulin secretion and inflammatory pathways.

    Science.gov (United States)

    Bhasin, Manoj K; Dusek, Jeffery A; Chang, Bei-Hung; Joseph, Marie G; Denninger, John W; Fricchione, Gregory L; Benson, Herbert; Libermann, Towia A

    2013-01-01

    The relaxation response (RR) is the counterpart of the stress response. Millennia-old practices evoking the RR include meditation, yoga and repetitive prayer. Although RR elicitation is an effective therapeutic intervention that counteracts the adverse clinical effects of stress in disorders including hypertension, anxiety, insomnia and aging, the underlying molecular mechanisms that explain these clinical benefits remain undetermined. To assess rapid time-dependent (temporal) genomic changes during one session of RR practice among healthy practitioners with years of RR practice and also in novices before and after 8 weeks of RR training, we measured the transcriptome in peripheral blood prior to, immediately after, and 15 minutes after listening to an RR-eliciting or a health education CD. Both short-term and long-term practitioners evoked significant temporal gene expression changes with greater significance in the latter as compared to novices. RR practice enhanced expression of genes associated with energy metabolism, mitochondrial function, insulin secretion and telomere maintenance, and reduced expression of genes linked to inflammatory response and stress-related pathways. Interactive network analyses of RR-affected pathways identified mitochondrial ATP synthase and insulin (INS) as top upregulated critical molecules (focus hubs) and NF-κB pathway genes as top downregulated focus hubs. Our results for the first time indicate that RR elicitation, particularly after long-term practice, may evoke its downstream health benefits by improving mitochondrial energy production and utilization and thus promoting mitochondrial resiliency through upregulation of ATPase and insulin function. Mitochondrial resiliency might also be promoted by RR-induced downregulation of NF-κB-associated upstream and downstream targets that mitigates stress.

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

    Directory of Open Access Journals (Sweden)

    Rodd F Helen

    2011-04-01

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

  9. Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata, and a comparison of assembler performance

    Directory of Open Access Journals (Sweden)

    Rotter Björn

    2011-06-01

    Full Text Available Abstract Background Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. Results A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig performance in the mt genome comparison. While VELVET produced the highest overall number of contigs, a large fraction of these were of small size (BLAST searches and the mt genome alignment. The best overall contig performance resulted from the NGEN assembly. It produced the second largest number of contigs, which on average were comparable to the OASES contigs but gave the highest number of gene hits in two out of four BLAST searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of BLAST hits. Conclusion Our results document the first de novo transcriptome assembly of a non-model species using Illumina sequencing data. We show that de novo transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig quality

  10. Transcriptome analysis of zebrafish embryogenesis using microarrays.

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    Sinnakaruppan Mathavan

    2005-08-01

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

  11. Gingival tissue transcriptomes in experimental gingivitis

    Science.gov (United States)

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

    2012-01-01

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

  12. A transcriptome approach to ecdysozoan phylogeny.

    Science.gov (United States)

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

    2014-11-01

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

  13. Neuropeptide receptor transcriptome reveals unidentified neuroendocrine pathways.

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    Naoki Yamanaka

    Full Text Available 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.

  14. Transcriptomic analysis of Salmonella desiccation resistance.

    Science.gov (United States)

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

    2012-12-01

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

  15. Transcriptomic evidence for modulation of host inflammatory responses during febrile Plasmodium falciparum malaria

    Science.gov (United States)

    Tran, Tuan M.; Jones, Marcus B.; Ongoiba, Aissata; Bijker, Else M.; Schats, Remko; Venepally, Pratap; Skinner, Jeff; Doumbo, Safiatou; Quinten, Edwin; Visser, Leo G.; Whalen, Elizabeth; Presnell, Scott; O’Connell, Elise M.; Kayentao, Kassoum; Doumbo, Ogobara K.; Chaussabel, Damien; Lorenzi, Hernan; Nutman, Thomas B.; Ottenhoff, Tom H. M.; Haks, Mariëlle C.; Traore, Boubacar; Kirkness, Ewen F.; Sauerwein, Robert W.; Crompton, Peter D.

    2016-01-01

    Identifying molecular predictors and mechanisms of malaria disease is important for understanding how Plasmodium falciparum malaria is controlled. Transcriptomic studies in humans have so far been limited to retrospective analysis of blood samples from clinical cases. In this prospective, proof-of-principle study, we compared whole-blood RNA-seq profiles at pre-and post-infection time points from Malian adults who were either asymptomatic (n = 5) or febrile (n = 3) during their first seasonal PCR-positive P. falciparum infection with those from malaria-naïve Dutch adults after a single controlled human malaria infection (n = 5). Our data show a graded activation of pathways downstream of pro-inflammatory cytokines, with the highest activation in malaria-naïve Dutch individuals and significantly reduced activation in malaria-experienced Malians. Newly febrile and asymptomatic infections in Malians were statistically indistinguishable except for genes activated by pro-inflammatory cytokines. The combined data provide a molecular basis for the development of a pyrogenic threshold as individuals acquire immunity to clinical malaria. PMID:27506615

  16. Transcriptome Analyses Reveal Candidate Genes Potentially Involved in Al Stress Response in Alfalfa

    Science.gov (United States)

    Liu, Wenxian; Xiong, Conghui; Yan, Longfeng; Zhang, Zhengshe; Ma, Lichao; Wang, Yanrong; Liu, Yajie; Liu, Zhipeng

    2017-01-01

    Alfalfa is the most extensively cultivated forage legume, yet most alfalfa cultivars are not aluminum tolerant, and the molecular mechanisms underlying alfalfa responses to Al stress are largely unknown. In this study, we aimed to understand how alfalfa responds to Al stress by identifying and analyzing Al-stress-responsive genes in alfalfa roots at the whole-genome scale. The transcriptome changes in alfalfa roots under Al stress for 4, 8, or 24 h were analyzed using Illumina high-throughput sequencing platforms. A total of 2464 differentially expressed genes (DEGs) were identified, and most were up-regulated at early (4 h) and/or late (24 h) Al exposure time points rather than at the middle exposure time point (8 h). Metabolic pathway enrichment analysis demonstrated that the DEGs involved in ribosome, protein biosynthesis, and process, the citrate cycle, membrane transport, and hormonal regulation were preferentially enriched and regulated. Biosynthesis inhibition and signal transduction downstream of auxin- and ethylene-mediated signals occur during alfalfa responses to root growth inhibition. The internal Al detoxification mechanisms play important roles in alfalfa roots under Al stress. These findings provide valuable information for identifying and characterizing important components in the Al signaling network in alfalfa and enhance understanding of the molecular mechanisms underlying alfalfa responses to Al stress. PMID:28217130

  17. Transcriptome analysis of cadmium-treated roots in maize (Zea mays L.

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    Runqing Yue

    2016-08-01

    Full Text Available Cadmium (Cd is a heavy metal and is highly toxic to all plant species. However, the underlying molecular mechanism controlling the effects of auxin on the Cd stress response in maize is largely unknown. In this study, the transcriptome produced by maize ‘Zheng 58’ root responses to Cd stress was sequenced using Illumina sequencing technology. In our study, six RNA-seq libraries yielded a total of 244 million clean short reads and 30.37 Gb of sequence data. A total of 6342 differentially expressed genes (DEGs were grouped into 908 Gene Ontology (GO categories and 198 Kyoto Encyclopedia of Genes and Genomes terms. GO term enrichment analysis indicated that various auxin signaling pathway-related GO terms were significantly enriched in DEGs. Comparison of the transcript abundances for auxin biosynthesis, transport, and downstream response genes revealed a universal expression response under Cd treatment. Furthermore, our data showed that free indole-3-acetic acid (IAA levels were significantly reduced; but IAA oxidase activity was up-regulated after Cd treatment in maize roots. The analysis of Cd activity in maize roots under different Cd and auxin conditions confirmed that auxin affected Cd accumulation in maize seedlings. These results will improve our understanding of the complex molecular mechanisms underlying the response to Cd stress in maize roots.

  18. Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

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    Iraola Susana

    2011-06-01

    Full Text Available Abstract Background Epidermal Growth Factor (EGF is a key regulatory growth factor activating many processes relevant to normal development and disease, affecting cell proliferation and survival. Here we use a combined approach to study the EGF dependent transcriptome of HeLa cells by using multiple long oligonucleotide based microarray platforms (from Agilent, Operon, and Illumina in combination with digital gene expression profiling (DGE with the Illumina Genome Analyzer. Results By applying a procedure for cross-platform data meta-analysis based on RankProd and GlobalAncova tests, we establish a well validated gene set with transcript levels altered after EGF treatment. We use this robust gene list to build higher order networks of gene interaction by interconnecting associated networks, supporting and extending the important role of the EGF signaling pathway in cancer. In addition, we find an entirely new set of genes previously unrelated to the currently accepted EGF associated cellular functions. Conclusions We propose that the use of global genomic cross-validation derived from high content technologies (microarrays or deep sequencing can be used to generate more reliable datasets. This approach should help to improve the confidence of downstream in silico functional inference analyses based on high content data.

  19. Extraction of venom and venom gland microdissections from spiders for proteomic and transcriptomic analyses.

    Science.gov (United States)

    Garb, Jessica E

    2014-11-03

    Venoms are chemically complex secretions typically comprising numerous proteins and peptides with varied physiological activities. Functional characterization of venom proteins has important biomedical applications, including the identification of drug leads or probes for cellular receptors. Spiders are the most species rich clade of venomous organisms, but the venoms of only a few species are well-understood, in part due to the difficulty associated with collecting minute quantities of venom from small animals. This paper presents a protocol for the collection of venom from spiders using electrical stimulation, demonstrating the procedure on the Western black widow (Latrodectus hesperus). The collected venom is useful for varied downstream analyses including direct protein identification via mass spectrometry, functional assays, and stimulation of venom gene expression for transcriptomic studies. This technique has the advantage over protocols that isolate venom from whole gland homogenates, which do not separate genuine venom components from cellular proteins that are not secreted as part of the venom. Representative results demonstrate the detection of known venom peptides from the collected sample using mass spectrometry. The venom collection procedure is followed by a protocol for dissecting spider venom glands, with results demonstrating that this leads to the characterization of venom-expressed proteins and peptides at the sequence level.

  20. Transcriptomic profiling of human hippocampal progenitor cells treated with antidepressants and its application in drug repositioning

    Science.gov (United States)

    Powell, Timothy R; Murphy, Tytus; Lee, Sang H; Price, Jack; Thuret, Sandrine; Breen, Gerome

    2017-01-01

    Current pharmacological treatments for major depressive disorder (MDD) are ineffective in a significant proportion of patients, and the identification of new antidepressant compounds has been difficult. ‘Connectivity mapping’ is a method that can be used to identify drugs that elicit similar downstream effects on mRNA levels when compared to current treatments, and thus may point towards possible repositioning opportunities. We investigated genome-wide transcriptomic changes to human hippocampal progenitor cells treated with therapeutically relevant concentrations of a tricyclic antidepressant (nortriptyline) and a selective serotonin reuptake inhibitor (escitalopram). We identified mRNA changes common to both drugs to create an ‘antidepressant mRNA signature’. We used this signature to probe the Library of Integrated Network-based Cellular Signatures (LINCS) and to identify other compounds that elicit similar changes to mRNA in neural progenitor cells. Results from LINCS revealed that the tricyclic antidepressant clomipramine elicited mRNA changes most similar to our mRNA signature, and we identified W-7 and vorinostat as functionally relevant drug candidates, which may have repositioning potential. Our results are encouraging and represent the first attempt to use connectivity mapping for drug repositioning in MDD. PMID:28208023

  1. Comparative Transcriptomics Indicates a Role for SHORT VEGETATIVE PHASE (SVP Genes in Mimulus guttatus Vernalization Response

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    Jill C. Preston

    2016-05-01

    Full Text Available The timing of reproduction in response to variable environmental conditions is critical to plant fitness, and is a major driver of taxon differentiation. In the yellow monkey flower, Mimulus guttatus, geographically distinct North American populations vary in their photoperiod and chilling (vernalization requirements for flowering, suggesting strong local adaptation to their surroundings. Previous analyses revealed quantitative trait loci (QTL underlying short-day mediated vernalization responsiveness using two annual M. guttatus populations that differed in their vernalization response. To narrow down candidate genes responsible for this variation, and to reveal potential downstream genes, we conducted comparative transcriptomics and quantitative PCR (qPCR in shoot apices of parental vernalization responsive IM62, and unresponsive LMC24 inbred lines grown under different photoperiods and temperatures. Our study identified several metabolic, hormone signaling, photosynthetic, stress response, and flowering time genes that are differentially expressed between treatments, suggesting a role for their protein products in short-day-mediated vernalization responsiveness. Only a small subset of these genes intersected with candidate genes from the previous QTL study, and, of the main candidates tested with qPCR under nonpermissive conditions, only SHORT VEGETATIVE PHASE (SVP gene expression met predictions for a population-specific short-day-repressor of flowering that is repressed by cold.

  2. Transcriptomic analysis of dystrophin RNAi knockdown reveals a central role for dystrophin in muscle differentiation and contractile apparatus organization

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    Graham Ian R

    2010-06-01

    . Therefore, it becomes apparent that any gene therapy approaches for DMD should target early stages in muscle development to attain a maximum clinical benefit. With a clear and specific definition of the transcriptome of dystrophin deficiency, manipulation of identified dysregulated molecules downstream of dystrophin may lead to novel ameliorative approaches for DMD.

  3. Transcriptome profiling of Elettaria cardamomum (L. Maton (small cardamom

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    F. Nadiya

    2017-03-01

    Full Text Available Elettaria cardamomum (L. Maton, known as ‘queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base and 24,889,197 (75 base raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild and SRX1141276 (cultivars. The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

  4. De novo transcriptome of the Hemimetabolous German cockroach (Blattella germanica.

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    Xiaojie Zhou

    Full Text Available 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.

  5. Evaluating de Bruijn graph assemblers on 454 transcriptomic data.

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    Xianwen Ren

    Full Text Available Next generation sequencing (NGS technologies have greatly changed the landscape of transcriptomic studies of non-model organisms. Since there is no reference genome available, de novo assembly methods play key roles in the analysis of these data sets. Because of the huge amount of data generated by NGS technologies for each run, many assemblers, e.g., ABySS, Velvet and Trinity, are developed based on a de Bruijn graph due to its time- and space-efficiency. However, most of these assemblers were developed initially for the Illumina/Solexa platform. The performance of these assemblers on 454 transcriptomic data is unknown. In this study, we evaluated and compared the relative performance of these de Bruijn graph based assemblers on both simulated and real 454 transcriptomic data. The results suggest that Trinity, the Illumina/Solexa-specialized transcriptomic assembler, performs the best among the multiple de Bruijn graph assemblers, comparable to or even outperforming the standard 454 assembler Newbler which is based on the overlap-layout-consensus algorithm. Our evaluation is expected to provide helpful guidance for researchers to choose assemblers when analyzing 454 transcriptomic data.

  6. Analysis of the Citrullus colocynthis transcriptome during water deficit stress.

    Science.gov (United States)

    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.

  7. Transcriptome profiling of Elettaria cardamomum (L.) Maton (small cardamom).

    Science.gov (United States)

    Nadiya, F; Anjali, N; Thomas, Jinu; Gangaprasad, A; Sabu, K K

    2017-03-01

    Elettaria cardamomum (L.) Maton, known as 'queen of spices, is a perennial herbaceous monocot of the family Zingiberaceae, native to southern India. Cardamom is an economically valuable spice crop and used widely in culinary and medicinal purposes. In the present study, using Ion Proton RNA sequencing technology, we performed transcriptome sequencing and de novo transcriptome assembly of a wild and five cultivar genotypes of cardamom. RNA-seq generated a total of 22,811,983 (92 base) and 24,889,197 (75 base) raw reads accounting for approximately 8.21GB and 7.65GB of sequence data for wild and cultivar genotypes of cardamom respectively. The raw data were submitted to SRA database of NCBI under the accession numbers SRX1141272 (wild) and SRX1141276 (cultivars). The raw reads were quality filtered and assembled using MIRA assembler resulted with 112,208 and 264,161contigs having N50 value 616 and 664 for wild and cultivar cardamom respectively. The assembled unigenes were functionally annotated using several databases including PlantCyc for pathway annotation. This work represents the first report on cardamom transcriptome sequencing. In order to generate a comprehensive reference transcriptome, we further assembled the raw reads of wild and cultivar genotypes which might enrich the plant transcriptome database and trigger advanced research in cardamom genomics.

  8. Downstream Intensification Effects Associated with CO2 Laser Mitigation of Fused Silica

    Energy Technology Data Exchange (ETDEWEB)

    Matthews, M J; Bass, I L; Guss, G M; Widmayer, C C; Ravizza, F L

    2007-10-29

    Mitigation of 351nm laser-induced damage sites on fused silica exit surfaces by selective CO{sub 2} treatment has been shown to effectively arrest the exponential growth responsible for limiting the lifetime of optics in high-fluence laser systems. However, the perturbation to the optical surface profile following the mitigation process introduces phase contrast to the beam, causing some amount of downstream intensification with the potential to damage downstream optics. Control of the laser treatment process and measurement of the associated phase modulation is essential to preventing downstream 'fratricide' in damage-mitigated optical systems. In this work we present measurements of the surface morphology, intensification patterns and damage associated with various CO{sub 2} mitigation treatments on fused silica surfaces. Specifically, two components of intensification pattern, one on-axis and another off-axis can lead to damage of downstream optics and are related to rims around the ablation pit left from the mitigation process. It is shown that control of the rim structure around the edge of typical mitigation sites is crucial in preventing damage to downstream optics.

  9. Influence of Downstream Flow on Conduction Phase of Coaxial Plasma Opening Switch

    Institute of Scientific and Technical Information of China (English)

    XU Xiang; WANG Younian

    2008-01-01

    Plasma behaviour and the scaling relations in a coaxial plasma opening switch (POS) using hydrogen plasma are studied self-consistently based on the two-dimensional magnetohydro-dynamic (MHD) equations in conjunction with the generalized Ohm's law. The vacuum region on the right of POS is included in the model and the influence of downstream flow on the conduction characteristics is discussed. It is found that with the penetration of magnetic field, the pure hydro-gen plasma is pushed downstream significantly; and POS still conducts current after the magnetic field arrives at the load edge of POS, which is different from the previous experimental results in a multispecies POS. It is because that the noticeable downstream plasma in the pure hydrogen POS may continue to conduct the current, while in the multispecies POS, the downstream plasma is unimportant so that the conduction phase ends soon after the magnetic field reaches the load edge. The scaling relation obtained from the simulations including the downstream region is consistent with the experimental results.

  10. Assessing downstream flood impacts due to a potential GLOF from Imja Tsho in Nepal

    Science.gov (United States)

    Somos-Valenzuela, M. A.; McKinney, D. C.; Byers, A. C.; Rounce, D. R.; Portocarrero, C.; Lamsal, D.

    2015-03-01

    Glacial-dominated areas pose unique challenges to downstream communities in adapting to recent and continuing global climate change, including increased threats of glacial lake outburst floods (GLOFs) that can increase risk due to flooding of downstream communities and cause substantial impacts on regional social, environmental and economic systems. The Imja glacial lake (or Imja Tsho) in Nepal, which has the potential to generate a GLOF, was studied using a two-dimensional debris-flow inundation model in order to evaluate the effectiveness of proposed measures to reduce possible flooding impacts to downstream communities by lowering the lake level. The results indicate that only minor flood impact reduction is achieved in the downstream community of Dingboche with modest (~3 m) lake lowering. Lowering the lake by 10 m shows a significant reduction in inundated area. However, lowering the lake by 20 m almost eliminates all flood impact at Dingboche. Further downstream at Phakding, the impact of the GLOF is significant and similar reductions in inundation are likely as a result of lake lowering.

  11. Assessing downstream flood impacts due to a potential GLOF from Imja Lake in Nepal

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    M. A. Somos-Valenzuela

    2014-11-01

    Full Text Available Glacial-dominated areas pose unique challenges to downstream communities in adapting to recent and continuing global climate change, including increased threats of glacial lake outburst floods (GLOFs that can increase risk due to flooding of downstream communities and cause substantial impacts on regional social, environmental and economic systems. The Imja glacial lake in Nepal, with potential to generate a GLOF, was studied using a two-dimensional debris flow inundation model in order to evaluate the effectiveness of proposed measures to reduce possible flooding impacts to downstream communities by lowering the lake level. The results indicate that only minor flood impact reduction is achieved in the downstream community of Dingboche with modest (~3 m lake lowering. Lowering the lake by 10 m shows a significant reduction in inundated area. However, lowering the lake by 20 m almost eliminates all flood impact at Dingboche. Further downstream at Phakding, the impact of the GLOF is significant and similar reductions in inundation are likely as a result of lake lowering.

  12. The testes transcriptome derived from the New World Screwworm, Cochliomyia hominivorax TSA

    Science.gov (United States)

    In a collaboration with National Center for Genome Resources researchers, we sequenced and assembled the testes transcriptome derived from the Pacora, Panama, production plant strain of the New World Screwworm, Cochliomyia hominivorax. This transcriptome contains 4,149 unigenes and the Transcriptome...

  13. Transcriptomic Response to Nitric Oxide Treatment in Larix olgensis Henry

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    Xiaoqing Hu

    2015-12-01

    Full Text Available 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.

  14. Transcriptomic Response to Nitric Oxide Treatment in Larix olgensis Henry.

    Science.gov (United States)

    Hu, Xiaoqing; Yang, Jingli; Li, Chenghao

    2015-12-02

    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.

  15. De novo transcriptome assembly of shrimp Palaemon serratus

    Directory of Open Access Journals (Sweden)

    Alejandra Perina

    2017-03-01

    Full Text Available The shrimp Palaemon serratus is a coastal decapod crustacean with a high commercial value. It is harvested for human consumption. In this study, we used Illumina sequencing technology (HiSeq 2000 to sequence, assemble and annotate the transcriptome of P. serratus. RNA was isolated from muscle of adults individuals and, from a pool of larvae. A total number of 4 cDNA libraries were constructed, using the TruSeq RNA Sample Preparation Kit v2. The raw data in this study was deposited in NCBI SRA database with study accession number of SRP090769. The obtained data were subjected to de novo transcriptome assembly using Trinity software, and coding regions were predicted by TransDecoder. We used Blastp and Sma3s to annotate the identified proteins. The transcriptome data could provide some insight into the understanding of genes involved in the larval development and metamorphosis.

  16. Genomic and Transcriptomic Analyses of Foodborne Bacterial Pathogens

    Science.gov (United States)

    Zhang, Wei; Dudley, Edward G.; Wade, Joseph T.

    DNA microarrays (often interchangeably called DNA chips or DNA arrays) are among the most popular analytical tools for high-throughput comparative genomic and transcriptomic analyses of foodborne bacterial pathogens. A typical DNA microarray contains hundreds to millions of small DNA probes that are chemically attached (or "printed") onto the surface of a microscopic glass slide. Depending on the specific "printing" and probe synthesis technologies for different microarray platforms, such DNA probes can be PCR amplicons or in situ synthesized short oligonucleotides. DNA microarray technologies have revolutionized the way that we investigate the biology of foodborne bacterial pathogens. The major advantage of these technologies is that DNA microarrays allow comparison of subtle genomic or transcriptomic variations between two bacterial samples, such as genomic variations between two different bacterial strains or transcriptomic alterations of same bacterial strain under two different treatments. Some applications of comparative genomic hybridization microarrays and global gene expression microarrays have been covered in previous chapters of this book.

  17. Transcriptome complexity in a genome-reduced bacterium.

    Science.gov (United States)

    Güell, Marc; van Noort, Vera; Yus, Eva; Chen, Wei-Hua; Leigh-Bell, Justine; Michalodimitrakis, Konstantinos; Yamada, Takuji; Arumugam, Manimozhiyan; Doerks, Tobias; Kühner, Sebastian; Rode, Michaela; Suyama, Mikita; Schmidt, Sabine; Gavin, Anne-Claude; Bork, Peer; Serrano, Luis

    2009-11-27

    To study basic principles of transcriptome organization in bacteria, we analyzed one of the smallest self-replicating organisms, Mycoplasma pneumoniae. We combined strand-specific tiling arrays, complemented by transcriptome sequencing, with more than 252 spotted arrays. We detected 117 previously undescribed, mostly noncoding transcripts, 89 of them in antisense configuration to known genes. We identified 341 operons, of which 139 are polycistronic; almost half of the latter show decaying expression in a staircase-like manner. Under various conditions, operons could be divided into 447 smaller transcriptional units, resulting in many alternative transcripts. Frequent antisense transcripts, alternative transcripts, and multiple regulators per gene imply a highly dynamic transcriptome, more similar to that of eukaryotes than previously thought.

  18. Transcriptomic insights into human brain evolution: acceleration, neutrality, heterochrony.

    Science.gov (United States)

    Somel, Mehmet; Rohlfs, Rori; Liu, Xiling

    2014-12-01

    Primate brain transcriptome comparisons within the last 12 years have yielded interesting but contradictory observations on how the transcriptome evolves, and its adaptive role in human cognitive evolution. Since the human-chimpanzee common ancestor, the human prefrontal cortex transcriptome seems to have evolved more than that of the chimpanzee. But at the same time, most expression differences among species, especially those observed in adults, appear as consequences of neutral evolution at cis-regulatory sites. Adaptive expression changes in the human brain may be rare events involving timing shifts, or heterochrony, in specific neurodevelopmental processes. Disentangling adaptive and neutral expression changes, and associating these with human-specific features of the brain require improved methods, comparisons across more species, and further work on comparative development.

  19. Influence of Local Flow Field on Flow Accelerated Corrosion Downstream from an Orifice

    Science.gov (United States)

    Utanohara, Yoichi; Nagaya, Yukinori; Nakamura, Akira; Murase, Michio

    Flow accelerated corrosion (FAC) rate downstream from an orifice was measured in a high-temperature water test loop to evaluate the effects of flow field on FAC. Orifice flow was also measured using laser Doppler velocimetry (LDV) and simulated by steady RANS simulation and large eddy simulation (LES). The LDV measurements indicated the flow structure did not depend on the flow velocity in the range of Re = 2.3×104 to 1.2×105. Flow fields predicted by RANS and LES agreed well with LDV data. Measured FAC rate was higher downstream than upstream from the orifice and the maximum appeared at 2D (D: pipe diameter) downstream. The shape of the profile of the root mean square (RMS) wall shear stress predicted by LES had relatively good agreement with the shape of the profile of FAC rate. This result indicates that the effects of flow field on FAC can be evaluated using the calculated wall shear stress.

  20. Mercury exposure in terrestrial birds far downstream of an historical point source.

    Science.gov (United States)

    Jackson, Allyson K; Evers, David C; Folsom, Sarah B; Condon, Anne M; Diener, John; Goodrick, Lizzie F; McGann, Andrew J; Schmerfeld, John; Cristol, Daniel A

    2011-12-01

    Mercury (Hg) is a persistent environmental contaminant found in many freshwater and marine ecosystems. Historical Hg contamination in rivers can impact the surrounding terrestrial ecosystem, but there is little known about how far downstream this contamination persists. In 2009, we sampled terrestrial forest songbirds at five floodplain sites up to 137 km downstream of an historical source of Hg along the South and South Fork Shenandoah Rivers (Virginia, USA). We found that blood total Hg concentrations remained elevated over the entire sampling area and there was little evidence of decline with distance. While it is well known that Hg is a pervasive and long-lasting aquatic contaminant, it has only been recently recognized that it also biomagnifies effectively in floodplain forest food webs. This study extends the area of concern for terrestrial habitats near contaminated rivers for more than 100 km downstream from a waterborne Hg point source.

  1. Optimization of biopharmaceutical downstream processes supported by mechanistic models and artificial neural networks.

    Science.gov (United States)

    Pirrung, Silvia M; van der Wielen, Luuk A M; van Beckhoven, Ruud F W C; van de Sandt, Emile J A X; Eppink, Michel H M; Ottens, Marcel

    2017-01-05

    Downstream process development is a major area of importance within the field of bioengineering. During the design of such a downstream process, important decisions have to be made regarding the type of unit operations as well as their sequence and their operating conditions. Current computational approaches addressing these issues either show a high level of simplification or struggle with computational speed. Therefore, this article presents a new approach that combines detailed mechanistic models and speed-enhancing artificial neural networks. This approach was able to simultaneously optimize a process with three different chromatographic columns toward yield with a minimum purity of 99.9%. The addition of artificial neural networks greatly accelerated this optimization. Due to high computational speed, the approach is easily extendable to include more unit operations. Therefore, it can be of great help in the acceleration of downstream process development. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 2017.

  2. Transcriptomics of the bed bug (Cimex lectularius.

    Directory of Open Access Journals (Sweden)

    Xiaodong Bai

    Full Text Available BACKGROUND: Bed bugs (Cimex lectularius are blood-feeding insects poised to become one of the major pests in households throughout the United States. Resistance of C. lectularius to insecticides/pesticides is one factor thought to be involved in its sudden resurgence. Despite its high-impact status, scant knowledge exists at the genomic level for C. lectularius. Hence, we subjected the C. lectularius transcriptome to 454 pyrosequencing in order to identify potential genes involved in pesticide resistance. METHODOLOGY AND PRINCIPAL FINDINGS: Using 454 pyrosequencing, we obtained a total of 216,419 reads with 79,596,412 bp, which were assembled into 35,646 expressed sequence tags (3902 contigs and 31744 singletons. Nearly 85.9% of the C. lectularius sequences showed similarity to insect sequences, but 44.8% of the deduced proteins of C. lectularius did not show similarity with sequences in the GenBank non-redundant database. KEGG analysis revealed putative members of several detoxification pathways involved in pesticide resistance. Lamprin domains, Protein Kinase domains, Protein Tyrosine Kinase domains and cytochrome P450 domains were among the top Pfam domains predicted for the C. lectularius sequences. An initial assessment of putative defense genes, including a cytochrome P450 and a glutathione-S-transferase (GST, revealed high transcript levels for the cytochrome P450 (CYP9 in pesticide-exposed versus pesticide-susceptible C. lectularius populations. A significant number of single nucleotide polymorphisms (296 and microsatellite loci (370 were predicted in the C. lectularius sequences. Furthermore, 59 putative sequences of Wolbachia were retrieved from the database. CONCLUSIONS: To our knowledge this is the first study to elucidate the genetic makeup of C. lectularius. This pyrosequencing effort provides clues to the identification of potential detoxification genes involved in pesticide resistance of C. lectularius and lays the foundation for

  3. Transcriptomic signatures of ash (Fraxinus spp. phloem.

    Directory of Open Access Journals (Sweden)

    Xiaodong Bai

    Full Text Available 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

  4. Transcriptome analysis of encystation in Entamoeba invadens.

    Science.gov (United States)

    De Cádiz, Aleyla Escueta; Jeelani, Ghulam; Nakada-Tsukui, Kumiko; Caler, Elisabet; Nozaki, Tomoyoshi

    2013-01-01

    Encystation is an essential differentiation process for the completion of the life cycle of a group of intestinal protozoa including Entamoeba histolytica, the causative agent of intestinal and extraintestinal amebiasis. However, regulation of gene expression during encystation is poorly understood. To comprehensively understand the process at the molecular level, the transcriptomic profiles of E. invadens, which is a related reptilian species that causes an invasive disease similar to that of E. histolytica, was investigated during encystation. Using a custom-generated Affymetrix platform microarray, we performed time course (0.5, 2, 8, 24, 48, and 120 h) gene expression analysis of encysting E. invadens. ANOVA analysis revealed that a total of 1,528 genes showed ≥3 fold up-regulation at one or more time points, relative to the trophozoite stage. Of these modulated genes, 8% (116 genes) were up-regulated at the early time points (0.5, 2 and 8h), while 63% (962 genes) were up-regulated at the later time points (24, 48, and 120 h). Twenty nine percent (450 genes) are either up-regulated at 2 to 5 time points or constitutively up-regulated in both early and late stages. Among the up-regulated genes are the genes encoding transporters, cytoskeletal proteins, proteins involved in vesicular trafficking (small GTPases), Myb transcription factors, cysteine proteases, components of the proteasome, and enzymes for chitin biosynthesis. This study represents the first kinetic analysis of gene expression during differentiation from the invasive trophozoite to the dormant, infective cyst stage in Entamoeba. Functional analysis on individual genes and their encoded products that are modulated during encystation may lead to the discovery of targets for the development of new chemotherapeutics that interfere with stage conversion of the parasite.

  5. Analysis of the longitudinal dependence of the downstream fluence of large solar energetic proton events

    Science.gov (United States)

    Pacheco, Daniel; Sanahuja, Blai; Aran, Angels; Agueda, Neus; Jiggens, Piers

    2016-07-01

    Simulations of the solar energetic particle (SEP) intensity-time profiles are needed to estimate the radiation environment for interplanetary missions. At present, the physics-based models applied for such a purpose, and including a moving source of particles, are not able to model the portion of the SEP intensity enhancement occurring after the coronal/interplanetary shock crossing by the observer (a.k.a. the downstream region). This is the case, for example, of the shock-and-particle model used to build the SOLPENCO2 code. SOLPENCO2 provides the statistical modelling tool developed in the ESA/SEPEM project for interplanetary missions with synthetic SEP event simulations for virtual spacecraft located at heliocentric distances between 0.2 AU and 1.6 AU (http://dev.sepem.oma.be/). In this work we present an analysis of 168 individual SEP events observed at 1 AU from 1988 to 2013. We identify the solar eruptive phenomena associated with these SEP events, as well as the in-situ passage of interplanetary shocks. For each event, we quantify the amount of fluence accounted in the downstream region, i.e. after the passage of the shock, at the 11 SEPEM reference energy channels (i.e., from 5 to 300 MeV protons). First, from the subset of SEP events simultaneously detected by near Earth spacecraft (using SEPEM reference data) and by one of the STEREO spacecraft, we select those events for which the downstream region can be clearly determined. From the 8 selected multi-spacecraft events, we find that the western observations of each event have a minor downstream contribution than their eastern counterpart, and that the downstream-to-total fluence ratio of these events decreases as a function of the energy. Hence, there is a variation of the downstream fluence with the heliolongitude in SEP events. Based on this result, we study the variation of the downstream-to-total fluence ratios of the total set of individual events. We confirm the eastern-to-western decrease of the

  6. Factors Influencing the Disturbed Flow Patterns Downstream of Curved Atherosclerotic Arteries

    Institute of Scientific and Technical Information of China (English)

    Biyue Liu

    2008-01-01

    Pulsatile blood flows in curved atherosclerotic arteries are studied by com-puter simulations. Computations are carried out with various values of physiological parameters to examine the effects of flow parameters on the disturbed flow patterns downstream of a curved artery with a stenosis at the inner wall. The numerical re-sults indicate a strong dependence of flow pattern on the blood viscosity and inlet flow rate, while the influence of the inlet flow profile to the flow pattem in downstream is negligible.

  7. Cetuximab insufficiently inhibits glioma cell growth due to persistent EGFR downstream signaling

    DEFF Research Database (Denmark)

    Hasselbalch, Benedikte; Lassen, Ulrik; Poulsen, Hans S;

    2010-01-01

    Overexpression and/or amplification of the epidermal growth factor receptor (EGFR) is present in 35-45% of primary glioblastoma multiforme tumors and has been correlated with a poor prognosis. In this study, we investigated the effect of cetuximab and intracellular signaling pathways downstream...... of EGFR, important for cell survival and proliferation. We show insufficient EGFR downregulation and competition with endogenous EGFR ligands upon cetuximab treatment. Dose-response experiments showed inhibition of EGFR phosphorylation without affecting two of the prominent downstream signaling pathways...

  8. Extraction and purification methods in downstream processing of plant-based recombinant proteins.

    Science.gov (United States)

    Łojewska, Ewelina; Kowalczyk, Tomasz; Olejniczak, Szymon; Sakowicz, Tomasz

    2016-04-01

    During the last two decades, the production of recombinant proteins in plant systems has been receiving increased attention. Currently, proteins are considered as the most important biopharmaceuticals. However, high costs and problems with scaling up the purification and isolation processes make the production of plant-based recombinant proteins a challenging task. This paper presents a summary of the information regarding the downstream processing in plant systems and provides a comprehensible overview of its key steps, such as extraction and purification. To highlight the recent progress, mainly new developments in the downstream technology have been chosen. Furthermore, besides most popular techniques, alternative methods have been described.

  9. Recent hydrocarbon developments in Latin America: Key issues in the downstream oil sector

    Energy Technology Data Exchange (ETDEWEB)

    Wu, K.; Pezeshki, S.

    1995-03-01

    This report discusses the following: (1) An overview of major issues in the downstream oil sector, including oil demand and product export availability, the changing product consumption pattern, and refineries being due for major investment; (2) Recent upstream developments in the oil and gas sector in Argentina, Bolivia, Brazil, Chile, Colombia, Ecuador, Mexico, Peru, Trinidad and Tobago, and Venezuela; (3) Recent downstream developments in the oil and gas sector in Argentina, Chile, Colombia, Ecuador, Mexico, Peru, Cuba, and Venezuela; (4) Pipelines in Argentina, Bolivia, Brazil, Chile, and Mexico; and (5) Regional energy balance. 4 figs., 5 tabs.

  10. Transcriptomics resources of human tissues and organs

    DEFF Research Database (Denmark)

    Uhlén, Mathias; Hallström, Björn M.; Lindskog, Cecilia

    2016-01-01

    a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome......Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide...

  11. Transcriptome profiling of male gametophyte development in Nicotiana tabacum

    Directory of Open Access Journals (Sweden)

    Pavel Bokvaj

    2015-03-01

    Full Text Available Pollen, an extremely reduced bicellular or tricellular male reproductive structure of flowering plants, serves as a model for numerous studies covering wide range of developmental and physiological processes. The pollen development represents a fragile and vital phase of plant ontogenesis and pollen was among the first singular plant tissues thoroughly characterized at the transcriptomic level (Honys and Twell [5]. Arabidopsis pollen developmental transcriptome has been published over a decade ago (Honys and Twell, 2004 and transcriptomes of developing pollen of other species have followed (Rice, Deveshwar et al. [2]; Triticeae, Tran et al. [11]; upland cotton, Ma et al. [8]. However, the transcriptomic data describing the development of tobacco pollen, a bicellular model for cell biology studies, have been missing. Here we provide the transcriptomic data covering three stages (Tupý et al., 1983 of wild type tobacco (Nicotiana tabacum, cv. Samsun pollen development: uninucleate microspores (UNM, stage 1, early bicellular pollen (eBCP, stage 3 and late bicellular pollen (lBCP, stage 5 as a supplement to the mature pollen (MP, 4 h-pollen tube (PT4, 24 h-pollen tubes (PT24, leaf (LF and root (RT transcriptomic data presented in our previous studies (Hafidh et al., 2012a; Hafidh et al., 2012b. We characterized these transcriptomes to refine the knowledge base of male gametophyte-enriched genes as well as genes expressed preferentially at the individual stages of pollen development. Alongside updating the list of tissue-specific genes, we have investigated differentially expressed genes with respect to early expressed genes. Pollen tube growth and competition of pollen tubes in female pistil can be viewed as a race of the fittest. Accordingly, there is an apparent evolutionary trend among higher plants to store significant material reserves and nutrients during pollen maturation. This supply ensures that after pollen germination, the pollen tube

  12. Reservoir stratification affects methylmercury levels in river water, plankton, and fish downstream from Balbina hydroelectric dam, Amazonas, Brazil.

    Science.gov (United States)

    Kasper, Daniele; Forsberg, Bruce R; Amaral, João H F; Leitão, Rafael P; Py-Daniel, Sarah S; Bastos, Wanderley R; Malm, Olaf

    2014-01-21

    The river downstream from a dam can be more contaminated by mercury than the reservoir itself. However, it is not clear how far the contamination occurs downstream. We investigated the seasonal variation of methylmercury levels in the Balbina reservoir and how they correlated with the levels encountered downstream from the dam. Water, plankton, and fishes were collected upstream and at sites between 0.5 and 250 km downstream from the dam during four expeditions in 2011 and 2012. Variations in thermal stratification of the reservoir influenced the methylmercury levels in the reservoir and in the river downstream. Uniform depth distributions of methylmercury and oxygen encountered in the poorly stratified reservoir during the rainy season collections coincided with uniformly low methylmercury levels along the river downstream from the dam. During dry season collections, the reservoir was strongly stratified, and anoxic hypolimnion water with high methylmercury levels was exported downstream. Methylmercury levels declined gradually to 200 km downstream. In general, the methylmercury levels in plankton and fishes downstream from the dam were higher than those upstream. Higher methylmercury levels observed 200-250 km downstream from the dam during flooding season campaigns may reflect the greater inflow from tributaries and flooding of natural wetlands that occurred at this time.

  13. Feeding by whiteflies suppresses downstream jasmonic acid signaling by eliciting salicylic acid signaling.

    Science.gov (United States)

    Zhang, Peng-Jun; Li, Wei-Di; Huang, Fang; Zhang, Jin-Ming; Xu, Fang-Cheng; Lu, Yao-Bin

    2013-05-01

    Phloem-feeding whiteflies in the species complex Bemisia tabaci cause extensive crop damage worldwide. One of the reasons for their "success" is their ability to suppress the effectual jasmonic acid (JA) defenses of the host plant. However, little is understood about the mechanisms underlying whitefly suppression of JA-regulated defenses. Here, we showed that the expression of salicylic acid (SA)-responsive genes (EDS1 and PR1) in Arabidopsis thaliana was significantly enhanced during feeding by whitefly nymphs. Whereas upstream JA-responsive genes (LOX2 and OPR3) also were induced, the downstream JA-responsive gene (VSP1) was repressed, i.e., whiteflies only suppressed downstream JA signaling. Gene-expression analyses with various Arabidopsis mutants, including NahG, npr-1, ein2-1, and dde2-2, revealed that SA signaling plays a key role in the suppression of downstream JA defenses by whitefly feeding. Assays confirmed that SA activation enhanced whitefly performance by suppressing downstream JA defenses.

  14. Muskingum equation based downstream sediment flow simulation models for a river system

    Institute of Scientific and Technical Information of China (English)

    Briti Sundar Sil; Parthasarathi Choudhury

    2016-01-01

    Applications of sediment transport and water flow characteristics based sediment transport simulation models for a river system are presented in this study. An existing water–sediment model and a new sediment–water model are used to formulate the simulation models representing water and sediment movement in a river system. The sediment–water model parameters account for water flow characteristics embodying sediment transport properties of a section. The models are revised formulations of the multiple water inflows model describing water movement through a river system as given by the Muskingum principle. The models are applied to a river system in Mississippi River basin to estimate downstream sediment concentration, sediment discharge, and water discharge. River system and the river section parameters are estimated using a revised and the original multiple water inflows models by applying the genetic algorithm. The models estimate downstream sediment transport rates on the basis of upstream sediment/water flow rates to a system. Model performance is evaluated by using standard statistical criteria;downstream water discharge resulting from the original multiple water inflows model using the estimated river system parameters indicate that the revised models satisfactorily describe water movement through a river system. Results obtained in the study demonstrate the applicability of the sediment transport and water flow characteristics-based simulation models in predicting downstream sediment transport and water flow rates in a river system.

  15. SIMULATION AND DYNAMIC VISUALIZATION OF FLOW AND SEDIMENT MOTION DOWNSTREAM OF CUIJIAYING DAM

    Institute of Scientific and Technical Information of China (English)

    YU Ming-hui; XU Jin-jun; WAN Yuan-yang; DOU Shen-tang

    2006-01-01

    Based on a depth-averaged 2D numerical river model, the flow and sediment movement downstream of the Cuijiaying dam Hanjiang River(China) are investigated. A new technique is employed to achieve synchronous dynamic visualization of topography and velocity field. The calculating results can reflect the relationship between flow and corresponding topography.

  16. Water stress in global transboundary river basins : Significance of upstream water use on downstream stress

    NARCIS (Netherlands)

    Munia, H.; Guillaume, J. H A; Mirumachi, N.; Porkka, M.; Wada, Y.; Kummu, M.

    2016-01-01

    Growing population and water demand have increased pressure on water resources in various parts of the globe, including many transboundary river basins. While the impacts of upstream water use on downstream water availability have been analysed in many of these international river basins, this has n

  17. Biochemistry in an Industrial Context: Methods of Protein Purification and Downstream Processing.

    Science.gov (United States)

    Weathers, Pamela J.

    1988-01-01

    Explores a graduate level bioprocess engineering course in protein purification and downstream processing. Designed to provide students with hands-on training in the design and implementation of product processing for the biotechnology industry. Includes syllabus and plan of study. (MVL)

  18. Systems-wide analysis of BCR signalosomes and downstream phosphorylation and ubiquitylation

    DEFF Research Database (Denmark)

    Satpathy, Shankha; Wagner, Sebastian A; Beli, Petra;

    2015-01-01

    ) and to investigate the dynamics of downstream phosphorylation and ubiquitylation signaling. We identify most of the previously known components of BCR signaling, as well as many proteins that have not yet been implicated in this system. BCR activation leads to rapid tyrosine phosphorylation and ubiquitylation...

  19. In bed and downstream hot gas desulphurization during solid fuel gasification: A review

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Xiangmei; de Jong, Wiebren; Pal, Ranadeep; Verkooijen, Adrian H.M. [Faculty of Mechanical, Maritime and Materials Engineering, Process and Energy Department, Energy Technology Section, Delft University of Technology, Leeghwaterstraat 44, 2628 CA, Delft (Netherlands)

    2010-08-15

    Syngas produced by gasification process of biomass fuels is an environmental friendly alternative to conventional petrochemical fuels for the production of electricity, hydrogen, synthetic transportation biofuels and other chemicals. However, the advanced utilization of syngas is significantly limited due to the contaminants which can seriously deactivate the catalysts used for downstream reaction such as steam reforming methane, Fischer-Tropsch synthesis and corrosion of downstream equipments such as a gas turbine. Among the contaminants, sulphur compounds produced in the gasification process, which are mainly H{sub 2}S with small amounts of COS, CS{sub 2} and thiophenes depending on process conditions, must be removed. For biomass feedstock advances are required in the cleanup technologies and processes to upgrade the raw product gas with minimal impact on the overall process efficiency. Hot gas desulphurization (HGD) can improve the overall thermal efficiency due to the elimination of fuel gas cooling and associated heat exchangers. With this aim, the present review paper highlights currently developed methods used for desulphurization of hot gas produced from gasification process of solid fuels. The methods presented here are for both in situ and downstream sulphur capture. Also, the attention is paid to the regeneration of the used materials. In situ sulphur capture is mainly done by using calcium-based sorbents such as limestone and dolomite, whereas downstream sulphur capture is mainly focused on the use of regenerable single, mixed, and supported metal oxides. A comparison is indicated at the end to show the sulphur loading of various materials. (author)

  20. Hemodynamics analysis of patient-specific carotid bifurcation: a CFD model of downstream peripheral vascular impedance.

    Science.gov (United States)

    Dong, Jingliang; Wong, Kelvin K L; Tu, Jiyuan

    2013-04-01

    The study of cardiovascular models was presented in this paper based on medical image reconstruction and computational fluid dynamics. Our aim is to provide a reality platform for the purpose of flow analysis and virtual intervention outcome predication for vascular diseases. By connecting two porous mediums with transient permeability at the downstream of the carotid bifurcation branches, a downstream peripheral impedance model was developed, and the effect of the downstream vascular bed impedance can be taken into consideration. After verifying its accuracy with a healthy carotid bifurcation, this model was implemented in a diseased carotid bifurcation analysis. On the basis of time-averaged wall shear stress, oscillatory shear index, and the relative residence time, fractions of abnormal luminal surface were highlighted, and the atherosclerosis was assessed from a hemodynamic point of view. The effect of the atherosclerosis on the transient flow division between the two branches because of the existence of plaque was also analysed. This work demonstrated that the proposed downstream peripheral vascular impedance model can be used for computational modelling when the outlets boundary conditions are not available, and successfully presented the potential of using medical imaging and numerical simulation to provide existing clinical prerequisites for diagnosis and therapeutic treatment.

  1. The dynamics of entrepreneurship in ICT: case of mobile phones downstream services in Kenya

    NARCIS (Netherlands)

    R.N. Kanothi (Raphael)

    2009-01-01

    textabstractThe research paper explores the extent to which mobile phones downstream services, defined here as those provided using the existing connectivity, are generating opportunities for entrepreneurship development in Kenya. After identifying the services of mobile payphones, money transfer an

  2. 33 CFR 222.2 - Acquisition of lands downstream from spillways for hydrologic safety purposes.

    Science.gov (United States)

    2010-07-01

    ... hazards of spillway flow. In fact, debris may be transported to downstream areas that otherwise would not be adversely affected. Extreme erosion may result from high velocities and turbulence. Both debris... depth. (iii) Flood duration. (iv) Velocities. (v) Debris and erosion. (2) Determine the combinations...

  3. Effect of Pulsed Plasma Jets on the Recovering Boundary Layer Downstream of a Reflected Shock Interaction

    Science.gov (United States)

    Greene, Benton; Clemens, Noel; Magari, Patrick; Micka, Daniel; Ueckermann, Mattheus

    2015-11-01

    Shock-induced turbulent boundary layer separation can have many detrimental effects in supersonic inlets including flow distortion and instability, structural fatigue, poor pressure recovery, and unstart. The current study investigates the effect of pulsed plasma jets on the recovering boundary layer downstream of a reflected shock wave-boundary layer interaction. The effects of pitch and skew angle of the jet as well as the heating parameter and discharge time scale are tested using several pulsing frequencies. In addition, the effect of the plasma jets on the undisturbed boundary layer at 6 mm and 11 mm downstream of the jets is measured. A pitot-static pressure probe is used to measure the velocity profile of the boundary layer 35 mm downstream of the plasma jets, and the degree of boundary layer distortion is compared between the different models and run conditions. Additionally, the effect of each actuator configuration on the shape of the mean separated region is investigated using surface oil flow visualization. Previous studies with lower energy showed a weak effect on the downstream boundary layer. The current investigation will attempt to increase this effect using a higher-energy discharge. Funded by AFRL through and SBIR in collaboration with Creare, LLC.

  4. The Relative Frequency of Rossby Wave Train Triggering Mechanisms Associated with Downstream Development Over Europe

    Science.gov (United States)

    2014-06-01

    diabatic Rossby vortices. 14. SUBJECT TERMS Rossby wave train, downstream development, tropopause polar vortex, warm conveyor belt, diabatic Rossby...extratropical transition of tropical cyclones, and six (16%) by diabatic Rossby vortices. vi THIS PAGE INTENTIONALLY LEFT BLANK vii TABLE OF CONTENTS...9  3.  Diabatic Rossby Vortex .....................................................................12  4.  Extratropical

  5. MIIT Convened Work Meeting for Upstream and Downstream Cooperation Mechanism of Aluminum Material For Civilian Aircraft

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    On September 15,2015,the Department of Raw Material Industry and the Department of Equipment Industry of the Ministry of Industry and Information Technology(MIIT)jointly organized and convened the first work meeting for upstream and downstream cooperation mechanism of aluminum material for civilian aircraft in Shanghai.Entrusted by Vice

  6. Changes in biodiversity and ecosystem function downstream from mountaintop removal and valley fill coal mining

    Science.gov (United States)

    Mountaintop removal and valley fill coal mining has altered the physicochemical landscape of the Central Appalachian region in the U.S. Increased specific conductance and levels of component ions downstream from valley fill sites are toxic to aquatic life and can negatively impa...

  7. Streamflow gain-loss characteristics of Elkhead Creek downstream from Elkhead Reservoir near Craig, Colorado, 2009

    Science.gov (United States)

    Ruddy, Barbara C.

    2010-01-01

    The U.S. Geological Survey (USGS), in cooperation with the Colorado Water Conservation Board, the Upper Colorado River Endangered Fish Recovery Program (UCREFRP), Colorado Division of Water Resources, and City of Craig studied the gain-loss characteristics of Elkhead Creek downstream from Elkhead Reservoir to the confluence with the Yampa River during August through October 2009. Earlier qualitative interpretation of streamflow data downstream from the reservoir indicated that there could be a transit loss of nearly 10 percent. This potential loss could be a significant portion of the releases from Elkhead Reservoir requested by UCREFRP during late summer and early fall for improving critical habitat for endangered fish downstream in the Yampa River. Information on the gain-loss characteristics was needed for the effective management of the reservoir releases. In order to determine streamflow gain-loss characteristics for Elkhead Creek, eight measurement sets were made at four strategic instream sites and at one diversion from August to early October 2009. An additional measurement set was made after the study period during low-flow conditions in November 2009. Streamflow measurements were made using an Acoustic Doppler Velocimeter to provide high accuracy and consistency, especially at low flows. During this study, streamflow ranged from about 5 cubic feet per second up to more than 90 cubic feet per second with step increments in between. Measurements were made at least 24 hours after a change in reservoir release (streamflow) during steady-state conditions. The instantaneous streamflow measurements and the streamflow volume comparisons show the reach of Elkhead Creek immediately downstream from Elkhead Reservoir to the streamflow-gaging station 09246500, Elkhead Creek near Craig, CO, is neither a gaining nor losing reach. The instantaneous measurements immediately downstream from the dam and the combined measurements of Norvell ditch plus streamflow

  8. De novo assembly of Euphorbia fischeriana root transcriptome identifies prostratin pathway related genes

    Directory of Open Access Journals (Sweden)

    Barrero Roberto A

    2011-12-01

    Full Text Available Abstract Background Euphorbia fischeriana is an important medicinal plant found in Northeast China. The plant roots contain many medicinal compounds including 12-deoxyphorbol-13-acetate, commonly known as prostratin that is a phorbol ester from the tigliane diterpene series. Prostratin is a protein kinase C activator and is effective in the treatment of Human Immunodeficiency Virus (HIV by acting as a latent HIV activator. Latent HIV is currently the biggest limitation for viral eradication. The aim of this study was to sequence, assemble and annotate the E. fischeriana transcriptome to better understand the potential biochemical pathways leading to the synthesis of prostratin and other related diterpene compounds. Results In this study we conducted a high throughput RNA-seq approach to sequence the root transcriptome of E. fischeriana. We assembled 18,180 transcripts, of these the majority encoded protein-coding genes and only 17 transcripts corresponded to known RNA genes. Interestingly, we identified 5,956 protein-coding transcripts with high similarity (> = 75% to Ricinus communis, a close relative to E. fischeriana. We also evaluated the conservation of E. fischeriana genes against EST datasets from the Euphorbeacea family, which included R. communis, Hevea brasiliensis and Euphorbia esula. We identified a core set of 1,145 gene clusters conserved in all four species and 1,487 E. fischeriana paralogous genes. Furthermore, we screened E. fischeriana transcripts against an in-house reference database for genes implicated in the biosynthesis of upstream precursors to prostratin. This identified 24 and 9 candidate transcripts involved in the terpenoid and diterpenoid biosyntehsis pathways, respectively. The majority of the candidate genes in these pathways presented relatively low expression levels except for 1-hydroxy-2-methyl-2-(E-butenyl 4-diphosphate synthase (HDS and isopentenyl diphosphate/dimethylallyl diphosphate synthase (IDS, which

  9. Water Stress in Global Transboundary River Basins: Significance of Upstream Water Use on Downstream Stress

    Science.gov (United States)

    Munia, H.; Guillaume, J. H. A.; Mirumachi, N.; Porkka,M.; Wada, Yoshihide; Kummu, M.

    2016-01-01

    Growing population and water demand have increased pressure on water resources in various parts of the globe, including many transboundary river basins. While the impacts of upstream water use on downstream water availability have been analyzed in many of these international river basins, this has not been systematically done at the global scale using coherent and comparable datasets. In this study, we aim to assess the change in downstream water stress due to upstream water use in the world's transboundary river basins. Water stress was first calculated considering only local water use of each sub-basin based on country-basin mesh, then compared with the situation when upstream water use was subtracted from downstream water availability. Wefound that water stress was generally already high when considering only local water use, affecting 0.95-1.44 billion people or 33%-51% of the population in transboundary river basins. After accounting for upstream water use, stress level increased by at least 1 percentage-point for 30-65 sub-basins, affecting 0.29-1.13 billion people. Altogether 288 out of 298 middle-stream and downstream sub-basin areas experienced some change in stress level. Further, we assessed whether there is a link between increased water stress due to upstream water use and the number of conflictive and cooperative events in the transboundary river basins, as captured by two prominent databases. No direct relationship was found. This supports the argument that conflicts and cooperation events originate from a combination of different drivers, among which upstream-induced water stress may play a role. Our findings contribute to better understanding of upstream-downstream dynamics in water stress to help address water allocation problems.

  10. Development of an idealised downstream cyclone: Eulerian and Lagrangian perspective on the kinetic energy

    Directory of Open Access Journals (Sweden)

    Lukas Papritz

    2013-03-01

    Full Text Available In this idealised modelling study, the development of a downstream cyclone, which closely follows the life-cycle of a Shapiro-Keyser cyclone, is addressed from a quasi-geostrophic kinetic energy perspective. To this end a simulation of a dry, highly idealised, dispersive baroclinic wave, developing a primary and a downstream cyclone, is performed. Kinetic energy and processes contributing to its tendency – in particular baroclinic conversion and ageostrophic geopotential fluxes – are investigated in three dimensions both in an Eulerian and a Lagrangian framework from the genesis of the downstream cyclone as an upper-level kinetic energy centre, over frontal fracture to the fully developed cyclone showing the characteristic T-bone surface frontal structure, with a strong low-level jet along the bent-back front. Initially the downstream cyclone grows by the convergence of ageostrophic geopotential fluxes from the primary cyclone, but as vertical motions intensify this process is replaced by baroclinic conversion in the warm sector. We show that kinetic energy released in the warm sector is radiated away at all levels by ageostrophic geopotential fluxes: in the upper troposphere they are directed downstream, while in the lower troposphere they radiate kinetic energy to the rear of the cyclone. Thereby, vertical ageostrophic geopotential fluxes, their location and divergence, are identified to play a major role in the intensification of the cyclone in the lower troposphere and for the formation of the low-level jet. Low-level rearward ageostrophic geopotential fluxes converging along the bent-back front are shown to be a general characteristic of an eastward propagating baroclinic wave.

  11. Energy-saving scheme based on downstream packet scheduling in ethernet passive optical networks

    Science.gov (United States)

    Zhang, Lincong; Liu, Yejun; Guo, Lei; Gong, Xiaoxue

    2013-03-01

    With increasing network sizes, the energy consumption of Passive Optical Networks (PONs) has grown significantly. Therefore, it is important to design effective energy-saving schemes in PONs. Generally, energy-saving schemes have focused on sleeping the low-loaded Optical Network Units (ONUs), which tends to bring large packet delays. Further, the traditional ONU sleep modes are not capable of sleeping the transmitter and receiver independently, though they are not required to transmit or receive packets. Clearly, this approach contributes to wasted energy. Thus, in this paper, we propose an Energy-Saving scheme that is based on downstream Packet Scheduling (ESPS) in Ethernet PON (EPON). First, we design both an algorithm and a rule for downstream packet scheduling at the inter- and intra-ONU levels, respectively, to reduce the downstream packet delay. After that, we propose a hybrid sleep mode that contains not only ONU deep sleep mode but also independent sleep modes for the transmitter and the receiver. This ensures that the energy consumed by the ONUs is minimal. To realize the hybrid sleep mode, a modified GATE control message is designed that involves 10 time points for sleep processes. In ESPS, the 10 time points are calculated according to the allocated bandwidths in both the upstream and the downstream. The simulation results show that ESPS outperforms traditional Upstream Centric Scheduling (UCS) scheme in terms of energy consumption and the average delay for both real-time and non-real-time packets downstream. The simulation results also show that the average energy consumption of each ONU in larger-sized networks is less than that in smaller-sized networks; hence, our ESPS is better suited for larger-sized networks.

  12. Favorable fragmentation: river reservoirs can impede downstream expansion of riparian weeds.

    Science.gov (United States)

    Rood, Stewart B; Braatne, Jeffrey H; Goater, Lori A

    2010-09-01

    River valleys represent biologically rich corridors characterized by natural disturbances that create moist and barren sites suitable for colonization by native riparian plants, and also by weeds. Dams and reservoirs interrupt the longitudinal corridors and we hypothesized that this could restrict downstream weed expansion. To consider this "reservoir impediment" hypothesis we assessed the occurrences and abundances of weeds along a 315-km river valley corridor that commenced with an unimpounded reach of the Snake River and extended through Brownlee, Oxbow, and Hells Canyon reservoirs and dams, and downstream along the Snake River. Sampling along 206 belt transects with 3610 quadrats revealed 16 noxious and four invasive weed species. Ten weeds were upland plants, with Canada thistle (Cirsium arvense) restricted to the upstream reaches, where field morning glory (Convolvulus arvensis) was also more common. In contrast, St. John's wort (Hypericum perforatum) was more abundant below the dams, and medusahead wildrye (Taeniatherum caput-medusae) occurred primarily along the reservoirs. All seven riparian species were abundant in the upstream zones but sparse or absent below the dams. This pattern was observed for the facultative riparian species, poison hemlock (Conium maculatum) and perennial pepperweed (Lepidium latifolium), the obligate riparian, yellow nut sedge (Cyperus esculentus), the invasive perennial, reed canary grass (Phalaris arundinacea), and three invasive riparian trees, Russian olive (Elaeagnus angustifolia), false indigo (Amorpha fruticosa), and tamarisk (Tamarix spp.). The hydrophyte purple loosestrife (Lythrum salicaria) was also restricted to the upstream zone. These longitudinal patterns indicate that the reservoirs have impeded the downstream expansion of riparian weeds, and this may especially result from the repetitive draw-down and refilling of Brownlee Reservoir that imposes a lethal combination of drought and flood stress. The dams and

  13. Water stress in global transboundary river basins: significance of upstream water use on downstream stress

    Science.gov (United States)

    Munia, H.; Guillaume, J. H. A.; Mirumachi, N.; Porkka, M.; Wada, Y.; Kummu, M.

    2016-01-01

    Growing population and water demand have increased pressure on water resources in various parts of the globe, including many transboundary river basins. While the impacts of upstream water use on downstream water availability have been analysed in many of these international river basins, this has not been systematically done at the global scale using coherent and comparable datasets. In this study, we aim to assess the change in downstream water stress due to upstream water use in the world’s transboundary river basins. Water stress was first calculated considering only local water use of each sub-basin based on country-basin mesh, then compared with the situation when upstream water use was subtracted from downstream water availability. We found that water stress was generally already high when considering only local water use, affecting 0.95-1.44 billion people or 33%-51% of the population in transboundary river basins. After accounting for upstream water use, stress level increased by at least 1 percentage-point for 30-65 sub-basins, affecting 0.29-1.13 billion people. Altogether 288 out of 298 middle-stream and downstream sub-basin areas experienced some change in stress level. Further, we assessed whether there is a link between increased water stress due to upstream water use and the number of conflictive and cooperative events in the transboundary river basins, as captured by two prominent databases. No direct relationship was found. This supports the argument that conflicts and cooperation events originate from a combination of different drivers, among which upstream-induced water stress may play a role. Our findings contribute to better understanding of upstream-downstream dynamics in water stress to help address water allocation problems.

  14. Willingness of upstream and downstream resource managers to engage in compensation schemes for environmental services

    Directory of Open Access Journals (Sweden)

    Chapika Sangkapitux

    2009-04-01

    Full Text Available Providing compensation for agricultural conservation practices adopted by upstream farmers is still an alien concept in the Thai political context. The governance of common-pool natural resources, such as forest and water, has traditionally been under the control of powerful government line agencies, while the contribution of local communities to natural resource conservation have been hardly recognized by policy-makers. Drawing on a case study in Mae Sa watershed, Chiang Mai province, northern Thailand, this paper discusses the potential of developing compensation schemes in a socio-political context where upland farmers – mostly belonging to ethnic minority groups – tend to be considered a threat to the natural resource base rather than providers of environmental services. Based on data obtained from 371 households in the upstream communities and 151 households in the downstream communities of the watershed, upstream resource managers’ willingness to accept compensation for the conservation measures and downstream resource managers’ willingness to pay for water resource improvements were estimated through the use of choice experiments. Results from the study suggest that downstream resource managers would be willing to provide on average nearly 1% of their annual income for a substantial improvement of the quantity and quality of water resources, which could be achieved by compensating upstream farmers’ change of their agricultural systems towards more environment-friendly practices. Both willingness to pay of downstream respondents and willingness of upstream resource managers to accept compensation were positively correlated with age, education, participation in environmental conservation activities and previous experiences with droughts and/or erosion. The paper concludes that there is a clear potential for establishing compensation schemes for provision of environmental services in northern Thai watersheds. The important policy

  15. Transcriptome characterization of Ishige okamurae (Phaeophyceae) shows strong environmental acclimation

    Institute of Scientific and Technical Information of China (English)

    QU Jieqiong; WANG Xumin; CHI Shan; WU Shuangxiu; SUN Jing; LIU Cui; CHEN Shengping; YU Jun; LIU Tao

    2014-01-01

    Ishige okamurae, with leathery branched narrow fronds consisting of cylindrical hairs, is the typical species of the genus Ishige, which is considered as one of the most basal genera in the phylogeny of the Phaeophy-ceae. Apart from great public interest from the evolutionary respect, more attention has been brought on the abundant bioactive compounds in I. okamurae for therapeutic or economic considerations, such as di-phlorethohydroxycarmalol and ishigoside. Yet little is known about related key genes or metabolic pathways involved in I. okamurae, which calls upon us to carry out global analyses of transcriptome by next generation sequencing. Altogether, we obtained 78 583 assembled scaffolds with N50 of 1 709 nucleotides, and 25 357 unigenes with significant BLAST matches (E-value cutoff of 10-5). In terms of characterization of the tran-scriptome of I. okamurae, we focused on anti-stress metabolic pathways and synthetic routes of bioactive compounds in an attempt to obtain a better understanding of the interactive organism-environment regula-tory networks. Pathway-based analysis helped us to deepen our comprehension of the interaction between I. okamurae and its surroundings, with MAPK signal pathway as an example. Furthermore, we discovered a wide range of novel putative functional proteins that could be of wide application, such as Rab family, using sequence-based transcriptome. In conclusion, transcriptome characterization of I. okamurae (Phaeophy-ceae) shows strong environmental acclimation.

  16. Sex differences in the human peripheral blood transcriptome

    NARCIS (Netherlands)

    Jansen, R.; Batista, S.; Brooks, A.I.; Tischfield, J.A.; Willemsen, G.; Grootheest, G. van; Hottenga, J.J.; Milaneschi, Y.; Mbarek, H.; Madar, V.; Peyrot, W.J.; Vink, J.M.; Verweij, C.L.; Geus, E.J.C. de; Smit, J.H.; Wright, F.A.; Sullivan, P.F.; Boomsma, D.I.; Penninx, B.W.J.H.

    2014-01-01

    Background: Genomes of men and women differ in only a limited number of genes located on the sex chromosomes, whereas the transcriptome is far more sex-specific. Identification of sex-biased gene expression will contribute to understanding the molecular basis of sex-differences in complex traits and

  17. Transcriptomics and proteomics of drought tolerance in peanuts

    Science.gov (United States)

    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...

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

    Science.gov (United States)

    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.

  19. Transcriptome of the Antarctic brooding gastropod mollusc Margarella antarctica.

    Science.gov (United States)

    Clark, Melody S; Thorne, Michael A S

    2015-12-01

    454 RNA-Seq transcriptome data were generated from foot tissue of the Antarctic brooding gastropod mollusc Margarella antarctica. A total of 6195 contigs were assembled de novo, providing a useful resource for researchers with an interest in Antarctic marine species, phylogenetics and mollusc biology, especially shell production.

  20. Validation of noise models for single-cell transcriptomics

    NARCIS (Netherlands)

    Grün, Dominic; Kester, Lennart; van Oudenaarden, Alexander

    2014-01-01

    Single-cell transcriptomics has recently emerged as a powerful technology to explore gene expression heterogeneity among single cells. Here we identify two major sources of technical variability: sampling noise and global cell-to-cell variation in sequencing efficiency. We propose noise models to co

  1. Chloroplast microsatellite markers for Artocarpus (Moraceae) developed from transcriptome sequences

    Science.gov (United States)

    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...

  2. Bacillus anthracis genome organization in light of whole transcriptome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Jeffrey; Zhu, Wenhan; Passalacqua, Karla D.; Bergman, Nicholas; Borodovsky, Mark

    2010-03-22

    Emerging knowledge of whole prokaryotic transcriptomes could validate a number of theoretical concepts introduced in the early days of genomics. What are the rules connecting gene expression levels with sequence determinants such as quantitative scores of promoters and terminators? Are translation efficiency measures, e.g. codon adaptation index and RBS score related to gene expression? We used the whole transcriptome shotgun sequencing of a bacterial pathogen Bacillus anthracis to assess correlation of gene expression level with promoter, terminator and RBS scores, codon adaptation index, as well as with a new measure of gene translational efficiency, average translation speed. We compared computational predictions of operon topologies with the transcript borders inferred from RNA-Seq reads. Transcriptome mapping may also improve existing gene annotation. Upon assessment of accuracy of current annotation of protein-coding genes in the B. anthracis genome we have shown that the transcriptome data indicate existence of more than a hundred genes missing in the annotation though predicted by an ab initio gene finder. Interestingly, we observed that many pseudogenes possess not only a sequence with detectable coding potential but also promoters that maintain transcriptional activity.

  3. A quantitative transcriptome reference map of the normal human brain.

    Science.gov (United States)

    Caracausi, Maria; Vitale, Lorenza; Pelleri, Maria Chiara; Piovesan, Allison; Bruno, Samantha; Strippoli, Pierluigi

    2014-10-01

    We performed an innovative systematic meta-analysis of 60 gene expression profiles of whole normal human brain, to provide a quantitative transcriptome reference map of it, i.e. a reference typical value of expression for each of the 39,250 known, mapped and 26,026 uncharacterized (unmapped) transcripts. To this aim, we used the software named Transcriptome Mapper (TRAM), which is able to generate transcriptome maps based on gene expression data from multiple sources. We also analyzed differential expression by comparing the brain transcriptome with those derived from human foetal brain gene expression, from a pool of human tissues (except the brain) and from the two normal human brain regions cerebellum and cerebral cortex, which are two of the main regions severely affected when cognitive impairment occurs, as happens in the case of trisomy 21. Data were downloaded from microarray databases, processed and analyzed using TRAM software and validated in vitro by assaying gene expression through several magnitude orders by 'real-time' reverse transcription polymerase chain reaction (RT-PCR). The excellent agreement between in silico and experimental data suggested that our transcriptome maps may be a useful quantitative reference benchmark for gene expression studies related to the human brain. Furthermore, our analysis yielded biological insights about those genes which have an intrinsic over-/under-expression in the brain, in addition offering a basis for the regional analysis of gene expression. This could be useful for the study of chromosomal alterations associated to cognitive impairment, such as trisomy 21, the most common genetic cause of intellectual disability.

  4. The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development

    Directory of Open Access Journals (Sweden)

    Rafael D. Rosengarten

    2017-02-01

    Full Text Available Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs in D. discoideum. To characterize the antisense and long intergenic noncoding RNA (lncRNA transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq library preparation method that selectively depletes ribosomal RNAs (rRNAs. We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs, 621 lncRNAs, and 162 putative antisense RNAs (asRNAs. The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by which D. discoideum compensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development.

  5. Microfluidic single-cell whole-transcriptome sequencing.

    Science.gov (United States)

    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.

  6. Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome.

    Science.gov (United States)

    Azim, M Kamran; Khan, Ishtaiq A; Zhang, Yong

    2014-05-01

    We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80% of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37%) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member.

  7. Combining different mRNA capture methods to analyze the transcriptome: analysis of the Xenopus laevis transcriptome.

    Directory of Open Access Journals (Sweden)

    Michael D Blower

    Full Text Available mRNA sequencing (mRNA-seq is a commonly used technique to survey gene expression from organisms with fully sequenced genomes. Successful mRNA-seq requires purification of mRNA away from the much more abundant ribosomal RNA, which is typically accomplished by oligo-dT selection. However, mRNAs with short poly-A tails are captured poorly by oligo-dT based methods. We demonstrate that combining mRNA capture via oligo-dT with mRNA capture by the 5' 7-methyl guanosine cap provides a more complete view of the transcriptome and can be used to assay changes in mRNA poly-A tail length on a genome-wide scale. We also show that using mRNA-seq reads from both capture methods as input for de novo assemblers provides a more complete reconstruction of the transcriptome than either method used alone. We apply these methods of mRNA capture and de novo assembly to the transcriptome of Xenopus laevis, a well-studied frog that currently lacks a finished sequenced genome, to discover transcript sequences for thousands of mRNAs that are currently absent from public databases. The methods we describe here will be broadly applicable to many organisms and will provide insight into the transcriptomes of organisms with sequenced and unsequenced genomes.

  8. Integration of high-resolution methylome and transcriptome analyses to dissect epigenomic changes in childhood acute lymphoblastic leukemia.

    Science.gov (United States)

    Busche, Stephan; Ge, Bing; Vidal, Ramon; Spinella, Jean-François; Saillour, Virginie; Richer, Chantal; Healy, Jasmine; Chen, Shu-Huang; Droit, Arnaud; Sinnett, Daniel; Pastinen, Tomi

    2013-07-15

    B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic determinants underlying disease onset remain unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. Using the Illumina 450K array, we assessed DNA methylation in matched tumor-normal samples of 46 childhood patients with pre-B ALL, extending single CpG-site resolution analysis of the pre-B ALL methylome beyond CpG-islands (CGI). Unsupervised hierarchical clustering of CpG-site neighborhood, gene, or microRNA (miRNA) gene-associated methylation levels separated the tumor cohort according to major pre-B ALL subtypes, and methylation in CGIs, CGI shores, and in regions around the transcription start site was found to significantly correlate with transcript expression. Focusing on samples carrying the t(12;21) ETV6-RUNX1 fusion, we identified 119 subtype-specific high-confidence marker CpG-loci. Pathway analyses linked the CpG-loci-associated genes with hematopoiesis and cancer. Further integration with whole-transcriptome data showed the effects of methylation on expression of 17 potential drivers of leukemogenesis. Independent validation of array methylation and sequencing-derived transcript expression with Sequenom Epityper technology and real-time quantitative reverse transcriptase PCR, respectively, indicates more than 80% empirical accuracy of our genome-wide findings. In summary, genome-wide DNA methylation profiling enabled us to separate pre-B ALL according to major subtypes, to map epigenetic biomarkers specific for the t(12;21) subtype, and through a combined methylome and transcriptome approach to identify downstream effects on candidate drivers of leukemogenesis.

  9. Flow and mass transfer downstream of an orifice under flow accelerated corrosion conditions

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Wael H., E-mail: ahmedw@kfupm.edu.sa [Department of Mechanical Engineering, King Fahd University of Petroleum and Minerals (KFUPM), P.O. Box 874, Dhahran 31261 (Saudi Arabia); Bello, Mufatiu M.; El Nakla, Meamer; Al Sarkhi, Abdelsalam [Department of Mechanical Engineering, King Fahd University of Petroleum and Minerals (KFUPM), P.O. Box 874, Dhahran 31261 (Saudi Arabia)

    2012-11-15

    Highlights: Black-Right-Pointing-Pointer Mass transfer downstream of orifices was numerically and experimentally investigated. Black-Right-Pointing-Pointer The surface wear pattern is measured and used to validate the present numerical results. Black-Right-Pointing-Pointer The maximum mass transfer coefficient found to occur at approximately 2-3 pipe diameters downstream of the orifice. Black-Right-Pointing-Pointer The FAC wear rates were correlated with the turbulence kinetic energy and wall mass transfer in terms of Sherwood number. Black-Right-Pointing-Pointer The current study offered very useful information for FAC engineers for better preparation of nuclear plant inspection scope. - Abstract: Local flow parameters play an important role in characterizing flow accelerated corrosion (FAC) downstream of sudden area change in power plant piping systems. Accurate prediction of the highest FAC wear rate locations enables the mitigation of sudden and catastrophic failures, and the improvement of the plant capacity factor. The objective of the present study is to evaluate the effect of the local flow and mass transfer parameters on flow accelerated corrosion downstream of an orifice. In the present study, orifice to pipe diameter ratios of 0.25, 0.5 and 0.74 were investigated numerically by solving the continuity and momentum equations at Reynolds number of Re = 20,000. Laboratory experiments, using test sections made of hydrocal (CaSO{sub 4}{center_dot} Vulgar-Fraction-One-Half H{sub 2}O) were carried out in order to determine the surface wear pattern and validate the present numerical results. The numerical results were compared to the plants data as well as to the present experiments. The maximum mass transfer coefficient found to occur at approximately 2-3 pipe diameters downstream of the orifice. This location was also found to correspond to the location of elevated turbulent kinetic energy generated within the flow separation vortices downstream of the orifice

  10. Sediment Mobilization From Reservoirs Can Cause Short Term Oxygen Depletion In Downstream Receiving Waters

    Science.gov (United States)

    Anderson, C.; Schenk, L.; Bragg, H.; Singer, M.; Hume, N.

    2013-12-01

    Reservoir management can cause incidences of short-term sediment mobilization, e.g. during dam removal or drawdown for maintenance or habitat purposes. Much of the associated planning focuses on predicting, quantifying, and mitigating the physical impacts of sediment mobilization, transport, and deposition. Sediment pulses can cause multiple regulatory and management concerns, such as turbidity or suspended sediment concentrations that may exceed State standards, geomorphic change and effects on property or infrastructure, or wildlife impacts such as stress to fish via gill abrasion or burial of critical habitat. Water-quality issues associated with sediment mobilization, including nutrient and contaminant transport, are often given less attention, presumably because their effects are less immediate or because of resource constraints. Recent experience with large pulses of sediment from several western reservoirs involving dam removals and temporary drawdowns indicates that oxygen demand, leading to depletion of downstream dissolved oxygen (DO), can also be a significant short-term concern. During the October 2011 Condit Dam removal on the White Salmon River in Washington, DO in receiving waters about 4.5 km downstream of the dam dropped to less than 1 mg/L within 2 hours of the demolition; in response, salmonids were observed to be in distress, apparently gulping for air at the water surface. DO remained low for at least 24 hours in this reach, and dead fish were observed. In December 2012, during a drawdown designed to aid juvenile-salmonid migration through Fall Creek Reservoir in Oregon, DO dropped precipitously about 1.5 km downstream as turbidity peaked, and a muted DO decrease was also observed approximately 14 miles further downstream despite a large dilution from unaffected sources. Laboratory experiments and modeling using sediments from reservoirs proposed for removal on the Klamath River, California, demonstrated the likelihood for downstream DO

  11. Transcriptome analysis of monocyte-HIV interactions

    Directory of Open Access Journals (Sweden)

    Tran Huyen

    2010-06-01

    macrophages can contribute to sustained chronic immune activation during HIV infection, e.g. through the perturbation of cytokine and chemokine networks 141516. With the acknowledged notion of chronic immune activation as a paradoxical driving force of immune suppression 17, this pro-inflammatory macrophage phenotype during HIV infection may be a crucial parameter in disease progression. Yet other macrophage dysfunctions are associated with more peripheral HIV- or ART-associated disorders such as atherosclerosis 18, lipodystrophy 19, and metabolic syndrome during HIV infection and/or combination ART 2021. Monocytes, for their part, are much less permissive to infection with HIV, both in vitro 22 and in vivo, where estimates of infected circulating monocytes are consistently low 2324. Circulating monocytes represent the most accessible primary model for macrophage dysfunction during HIV infection, however, and are furthermore of sufficient importance to study in their own right. Infectious virus can be recovered from circulating monocytes, both in untreated patients 24 and in patients undergoing long-term successful combination ART 25. Additionally, the circulating monocyte pool as a whole does seem to be affected during HIV infection, despite the low frequency of actually infected monocytes. Transcriptome studies, in particular, show a form of hybrid phenotype exhibiting both increased and decreased pro-inflammatory features 2627. This modulation of the non-infected monocyte population could be due to the virus itself through mechanisms which do not require direct infection 28, or to other factors contributing to (aberrant immune activation occurring during HIV infection, such as perturbed cytokine networks 29 or other inflammatory stimulants 30. Several key factors in the described dysregulated processes have been identified 1831, but many molecular components remain elusive. Furthermore, other aspects of HIV and combination ART pathogenesis in which monocyte

  12. Measurements of energy spectra of fast electrons from PF-1000 in the upstream and downstream directions

    Energy Technology Data Exchange (ETDEWEB)

    Kwiatkowski, R.; Czaus, K.; Skladnik-Sadowska, E.; Malinowski, K.; Zebrowski, J. [The Andrzej Soltan Institute for Nuclear Studies (IPJ), 05-400 Otwock-Swierk (Poland); Sadowski, M.J. [The Andrzej Soltan Institute for Nuclear Studies (IPJ), 05-400 Otwock-Swierk (Poland); Karpinski, L.; Paduch, M.; Scholz, M. [Institute of Plasma Physics and Laser Microfusion (IPPLM), 01-497 Warsaw (Poland); Kubes, P. [Czech Technical University (CVUT), 166-27 Prague, (Czech Republic)

    2011-07-01

    The paper describes measurements of energy spectra of electrons emitted in the upstream direction along the symmetry-axis of the PF-1000 facility, operated with the deuterium filling at 21 kV, 290 kJ. The measurements were performed with a magnetic analyzer. The same analyzer was used to measure also electron beams emitted in along the symmetry-axis in the downstream direction. The recorded spectra showed that the electron-beams emitted in the upstream direction have energies in the range from about 40 keV to about 800 keV, while those in the downstream direction have energies in the range from about 60 keV to about 200 keV. These spectra confirm that in the PF (Plasma Focus) plasma column there appear strong local fields accelerating charged particles in different directions. This document is composed of a paper and a poster. (authors)

  13. PIV Measurements of flow downstream of polyurethane heart valve prosthesis for artificial heart: steady flow experiment

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J.K.; Sung, J.Y. [Seoul National University Graduate School, Seoul (Korea); Chang, J.K.; Yoo, J.Y.; Min, B.G. [Seoul National University, Seoul (Korea)

    1999-12-01

    Hemodynamic performance of a polyurethane heart valve prosthesis was evaluated in comparison with that of Bjork-Shiley Monostrut mechanical valve in steady flow representing the systolic peak flow phase. Pressure losses through the valves were obtained from the streamwise pressure distributions downstream of the valves. Unsteady and turbulent flow field distal to the heart valve prostheses were investigated using PIV(Particle Image Velocimetry) which can measure the full-field velocity instantaneously and noninvasively. By examining the velocity and Reynolds shear stress fields downstream of the polyurethane heart valve, it is known that there is a large recirculation region near the valve and high shear stress regions exist at the interface between strong axial jet flows along the wall and vortical flows in the central area. The possibilities of vascular complications, such as the thrombus formation and red blood cell damage, could be predicted from the overall view of the velocity and stress fields. (author). 22 refs., 9 figs., 1 tab.

  14. Electromagnetic field generation in the downstream of electrostatic shocks due to electron trapping

    CERN Document Server

    Stockem, A; Fonseca, R A; Silva, L O

    2014-01-01

    A new magnetic field generation mechanism in electrostatic shocks is found, which can produce fields with magnetic energy density as high as 0.01 of the kinetic energy density of the flows on time scales $ \\tilde \\, 10^4 \\, {\\omega}_{pe}^{-1}$. Electron trapping during the shock formation process creates a strong temperature anisotropy in the distribution function, giving rise to the pure Weibel instability. The generated magnetic field is well-confined to the downstream region of the electrostatic shock. The shock formation process is not modified and the features of the shock front responsible for ion acceleration, which are currently probed in laser-plasma laboratory experiments, are maintained. However, such a strong magnetic field determines the particle trajectories downstream and has the potential to modify the signatures of the collisionless shock.

  15. Effects of Flaming Gorge Dam hydropower operations on downstream flow, stage, and sediment transport

    Energy Technology Data Exchange (ETDEWEB)

    Yin, S.C.L.; Tomasko, D.; Cho, H.E.; Williams, G. [Argonne National Lab., IL (United States); McCoy, J.; Palmer, C. [USDOE Western Area Power Administration, Salt Lake City, UT (United States)

    1996-11-01

    Hydropower operations at Flaming Gorge Dam, located on the Green River in Utah, can produce rapid downstream changes in flow and stage. These changes can in turn affect sediment transport and ecologic resources below the dam. To evaluate these effects, four hydropower operational scenarios with varying degrees of hydropower-release fluctuations were examined. This study demonstrates that the combined use of river-flow routing, water-surface profile, and sediment-transport models can provide useful information for evaluating the potential impacts of hydropower-operations on ecological and other resources downstream of the dam. Study results show that flow fluctuations may or may not persist for a long distance, depending on the initial magnitude of fluctuation and the duration of hydropower peaking. Stage fluctuations depend not only on flow fluctuations but also on river channel characteristics, such as channel width and longitudinal slope.

  16. Reorganization of Coherent Structures Downstream a Circular Cylinder Located between Two Parallel Walls

    Directory of Open Access Journals (Sweden)

    F. Rehimi

    2011-01-01

    Full Text Available Experiments were performed at low Reynolds numbers in the range 75 Re 275 in the wake of a circular cylinder of dc diameter placed symmetrically between two parallel walls of H height. 2D2C particle image velocimetry (PIV was used to investigate the flow downstream the cylinder. In the unsteady flow regime downstream the cylinder, the detached primary vortices (Pi interact with walls generating secondary ones (Pi’ and modify the cylinder wake dynamic. The kinematical properties (advection velocity, circulation, rotation kinetic energy, etc. of the generated secondary vortices are studied and compared with the primary ones in order to show how the walls influence the von Kármán vortex street. The authors propose here a relation between the circulations and kinetic energies of primary and secondary vortices.

  17. The use of Reverse Micelles in Downstream Processing of Biotechnological Products

    CERN Document Server

    Lee, Kai Lun

    2011-01-01

    This paper aims to discuss the use of reverse micelles in downstream processing of biotechnological products. The interest in this technology is piqued firstly by various advantages of a liquid-liquid extraction process, among which are cost effectiveness, and ease of scaling up and implementing a continuous process for whole broth processing. The use of reverse micelles is thought to be among the most promising due to the high efficiency and selectivity being achieved in some systems. However, there are various issues that have impeded the widespread use of reverse micelles such as the identification and development of suitable surfactants and ligands; as well as difficulties in the back extraction process. These issues, as well as latest developments and applications of reverse micelles in downstream processing of biotechnological products will be discussed in this paper.

  18. Capture of white sturgeon larvae downstream of The Dalles Dam, Columbia River, Oregon and Washington, 2012

    Science.gov (United States)

    Parsley, Michael J.; Kofoot, Eric

    2013-01-01

    Wild-spawned white sturgeon (Acipenser transmontanus) larvae captured and reared in aquaculture facilities and subsequently released, are increasingly being used in sturgeon restoration programs in the Columbia River Basin. A reconnaissance study was conducted to determine where to deploy nets to capture white sturgeon larvae downstream of a known white sturgeon spawning area. As a result of the study, 103 white sturgeon larvae and 5 newly hatched free-swimming embryos were captured at 3 of 5 reconnaissance netting sites. The netting, conducted downstream of The Dalles Dam on the Columbia River during June 25–29, 2012, provided information for potentially implementing full-scale collection efforts of large numbers of larvae for rearing in aquaculture facilities and for subsequent release at a larger size in white sturgeon restoration programs.

  19. Turbulent jet flow generated downstream of a low temperature dielectric barrier atmospheric pressure plasma device

    Science.gov (United States)

    Whalley, Richard D.; Walsh, James L.

    2016-08-01

    Flowing low temperature atmospheric pressure plasma devices have been used in many technological applications ranging from energy efficient combustion through to wound healing and cancer therapy. The generation of the plasma causes a sudden onset of turbulence in the inhomogeneous axisymmetric jet flow downstream of the plasma plume. The mean turbulent velocity fields are shown to be self-similar and independent of the applied voltage used to generate the plasma. It is proposed that the production of turbulence is related to a combination of the small-amplitude plasma induced body forces and gas heating causing perturbations in the unstable shear layers at the jet exit which grow as they move downstream, creating turbulence.

  20. Circadian rhythms in healthy aging--effects downstream from the pacemaker

    Science.gov (United States)

    Monk, T. H.; Kupfer, D. J.

    2000-01-01

    Using both previously published findings and entirely new data, we present evidence in support of the argument that the circadian dysfunction of advancing age in the healthy human is primarily one of failing to transduce the circadian signal from the circadian timing system (CTS) to rhythms "downstream" from the pacemaker rather than one of failing to generate the circadian signal itself. Two downstream rhythms are considered: subjective alertness and objective performance. For subjective alertness, we show that in both normal nychthemeral (24 h routine, sleeping at night) and unmasking (36 h of constant wakeful bed rest) conditions, advancing age, especially in men, leads to flattening of subjective alertness rhythms, even when circadian temperature rhythms are relatively robust. For objective performance, an unmasking experiment involving manual dexterity, visual search, and visual vigilance tasks was used to demonstrate that the relationship between temperature and performance is strong in the young, but not in older subjects (and especially not in older men).

  1. Downstream management practices of transnational companies in institutionally vulnerable countries: Export and use of hazardous products

    DEFF Research Database (Denmark)

    Jørgensen, Michael Søgaard; Milanez, Bruno

    2017-01-01

    Analyses of social and environmental management in transnational product chains focus often upstream on suppliers in socially and institutionally vulnerable countries and these suppliers' hazardous processes. Furthermore focus is on transnational companies' responsibility when they source from...... and environmental management of a Danish pesticide company in vulnerable countries and especially in Brazil. The identified mechanisms are: the transnational company's on-going interpretation of the regulatory and ethical obligations for development and use of its hazardous products in vulnerable countries, path...... such suppliers. On the contrary, not much focus has been on transnational companies' downstream export of hazardous products to vulnerable countries and the product use in those countries. The article uses pesticides as case of hazardous products and identifies mechanisms in the downstream social...

  2. Beam Halo on the LHC TCDQ Diluter System and Thermal Load on the Downstream Superconducting Magnets

    CERN Document Server

    Goddard, B; Presland, A; Redaelli, S; Robert-Démolaize, G; Sarchiapone, L; Weiler, T; Weterings, W

    2006-01-01

    The moveable single-jawed graphite TCDQ diluter must be positioned very close to the circulating LHC beam in order to prevent damage to downstream components in the event of an unsynchronised beam abort. A two-jawed graphite TCS.IR6 collimator forms part of the TCDQ system. The requirement to place the jaws close to the beam means that the system can intercept a substantial beam halo load. Initial investigations indicated a worryingly high heat load on the Q4 coils. This paper presents the updated load cases, shielding and simulation geometry, and the results of simulations of the energy deposition in the TCDQ system and in the downstream superconducting Q4 magnet. The implications for the operation of the LHC are discussed.

  3. Re-modulated technology of WDM-PON employing different DQPSK downstream signals

    Science.gov (United States)

    Gao, Chao; Xin, Xiang-jun; Yu, Chong-xiu

    2012-11-01

    This paper proposes a kind of modulation architecture for wavelength-division-multiplexing passive optical network (WDMPON) employing optical differential quadrature phase shift keying (DQPSK) downstream signals and two different modulation formats of re-modulated upstream signals. At the optical line terminal (OLT), 10 Gbit/s signal is modulated with DQPSK. At the optical network unit (ONU), part of the downstream signal is re-modulated with on-off keying (OOK) or inverse-return-to-zero (IRZ). Simulation results show the impact on the system employing NRZ, RZ and carrier-suppressed return-to-zero (CSRZ). The analyses also reflect that the architecture can restrain chromatic dispersion and channel crosstalk, which makes it the best architecture of access network in the future.

  4. Turbulent jet flow generated downstream of a low temperature dielectric barrier atmospheric pressure plasma device.

    Science.gov (United States)

    Whalley, Richard D; Walsh, James L

    2016-08-26

    Flowing low temperature atmospheric pressure plasma devices have been used in many technological applications ranging from energy efficient combustion through to wound healing and cancer therapy. The generation of the plasma causes a sudden onset of turbulence in the inhomogeneous axisymmetric jet flow downstream of the plasma plume. The mean turbulent velocity fields are shown to be self-similar and independent of the applied voltage used to generate the plasma. It is proposed that the production of turbulence is related to a combination of the small-amplitude plasma induced body forces and gas heating causing perturbations in the unstable shear layers at the jet exit which grow as they move downstream, creating turbulence.

  5. Experimental Investigation of Two Interacting Thruster-Plumes Downstream of the Nozzles

    OpenAIRE

    Holz, André; Dettleff, Georg; Hannemann, Klaus; Ziegenhagen, Stefan

    2012-01-01

    The plume-plume interaction of two small cold gas thrusters is investigated under high vacuum conditions in the DLR high vacuum plume test facility STG-CT. In this paper we concentrate on the interaction downstream of the nozzles. After introducing the experimental equipment, characteristics of shock interaction are presented. Furthermore the appropriateness of the Penetration Knudsen Number for predicting the type of interaction also for thruster plumes is investigated.

  6. Coexistence of up- and downstream traffic waves on a ring road

    Science.gov (United States)

    van der Weele, K.; Kanellopoulos, G.

    2016-09-01

    It is an observational fact that density waves in vehicle traffic can move in either direction: small-amplitude waves travel in the same direction as the cars (downstream) whereas high-amplitude waves or "jams" travel in the opposite direction (upstream). We construct a model of ring road traffic to demonstrate how this comes about. Our model shows the spontaneous generation of these density waves, explains their stability properties, and pinpoints the precise density level at which the wave speed changes direction.

  7. Production of structured lipids: acyl migration during enzymatic interesterification and downstream processing

    DEFF Research Database (Denmark)

    Xu, Xuebing

    1997-01-01

    -2 position or sn-1,3 positions of glycerol backbone. These kinds of lipids are reported to be promising for both enteral and parenteral nutrition. However, acyl migration occurs in the reaction stage and downstream purification process. This side-reaction causes by-products which are harmful...... to the required products. In this paper, the reasons of acyl migration and factors affecting the acyl migration were reviewed and discussed. The possible solutions were also evaluated....

  8. Downstream approaches to phosphorus management in agricultural landscapes: regional applicability and use.

    Science.gov (United States)

    Kröger, R; Dunne, E J; Novak, J; King, K W; McLellan, E; Smith, D R; Strock, J; Boomer, K; Tomer, M; Noe, G B

    2013-01-01

    This review provides a critical overview of conservation practices that are aimed at improving water quality by retaining phosphorus (P) downstream of runoff genesis. The review is structured around specific downstream practices that are prevalent in various parts of the United States. Specific practices that we discuss include the use of controlled drainage, chemical treatment of waters and soils, receiving ditch management, and wetlands. The review also focuses on the specific hydrology and biogeochemistry associated with each of those practices. The practices are structured sequentially along flowpaths as you move through the landscape, from the edge-of-field, to adjacent aquatic systems, and ultimately to downstream P retention. Often practices are region specific based on geology, cropping practices, and specific P related problems and thus require a right practice, and right place mentality to management. Each practice has fundamental P transport and retention processes by systems that can be optimized by management with the goal of reducing downstream P loading after P has left agricultural fields. The management of P requires a system-wide assessment of the stability of P in different biogeochemical forms (particulate vs. dissolved, organic vs. inorganic), in different storage pools (soil, sediment, streams etc.), and under varying biogeochemical and hydrological conditions that act to convert P from one form to another and promote its retention in or transport out of different landscape components. There is significant potential of hierarchically placing practices in the agricultural landscape and enhancing the associated P mitigation. But an understanding is needed of short- and long-term P retention mechanisms within a certain practice and incorporating maintenance schedules if necessary to improve P retention times and minimize exceeding retention capacity.

  9. Drosophila Fascin is a novel downstream target of prostaglandin signaling during actin remodeling

    OpenAIRE

    Groen, Christopher M.; Spracklen, Andrew J.; Fagan, Tiffany N.; Tootle, Tina L.

    2012-01-01

    Although prostaglandins (PGs)—lipid signals produced downstream of cyclooxygenase (COX) enzymes—regulate actin cytoskeletal dynamics, their mechanisms of action are unknown. We previously established Drosophila oogenesis, in particular nurse cell dumping, as a new model to determine how PGs regulate actin remodeling. PGs, and thus the Drosophila COX-like enzyme Pxt, are required for both the parallel actin filament bundle formation and the cortical actin strengthening required for dumping. He...

  10. Downstream Regulatory Element Antagonist Modulator (DREAM), a target for anti-thrombotic agents.

    Science.gov (United States)

    Cho, Jaehyung

    2017-03-01

    Circulating platelets participate in the process of numerous diseases including thrombosis, inflammation, and cancer. Thus, it is of great importance to understand the underlying mechanisms mediating platelet activation under disease conditions. Emerging evidence indicates that despite the lack of a nucleus, platelets possess molecules that are involved in gene transcription in nucleated cells. This review will summarize downstream regulatory element antagonist modulator (DREAM), a transcriptional repressor, and highlight recent findings suggesting its novel non-transcriptional role in hemostasis and thrombosis.

  11. The study of glycerol-based fermentation and broth downstream by nanofiltration

    Directory of Open Access Journals (Sweden)

    Gryta Marek

    2014-12-01

    Full Text Available In this work, the glycerol fermentation was carried out using Citrobacter freundii bacteria. The influence of glycerol and metabolites concentrations, and the pH changes on the efficiency of 1,3-propanediol production, during batch and fed-batch processes, was presented. The nanofiltration was used for the separation of obtained post-fermentation solutions. The resulted 1,3-PD solutions were significantly desalted, which may facilitate further downstream processes during 1,3-PD production.

  12. Characterization of sequences downstream from transcriptional start site of Rhizobium meliloti nifHDK promoter

    Institute of Scientific and Technical Information of China (English)

    高云峰; 吴桐; 朱家璧; 俞冠翘; 沈善炯

    1997-01-01

    In free-living state, the nifHDK promoter P1 of Rhizobium meliloti is induced in response to mi-croaerobiosis and expressed to a high level, while the fixABCX promoter P2 is not. The sequences upstream from both P1 and P2 share extended homology (about 85% ), which are about 160 bp in length, but the sequences downstream of the respective transcriptional start site are different. When the downstream sequence (DS) of P2 was replaced by the corresponding fragment from+ 17 to + 61 of P1, the expression of P2 is greatly increased under free-living condi-tion by lowering the oxygen tension, and the activity of P2 promoter can also be significantly enhanced in E. coli by the NifA protein. The difference between the DS regions of P1 and P2 promoter resulted in different expressions of P1 and P2 promoter under free-living microaerobic condition and in E. coli. The expression of P2 does not depend on the downstream sequences from the promoter element during symbiosis. Primer extension experiments identified the

  13. MicroRNA-145 suppresses hepatocellular carcinoma by targeting IRS1 and its downstream Akt signaling

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yelin [Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou (China); Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou (China); Hu, Chen; Cheng, Jun [Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou (China); Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou (China); Chen, Binquan [Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou (China); Ke, Qinghong; Lv, Zhen; Wu, Jian [Department of Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou (China); Key Laboratory of Combined Multi-organ Transplantation, Ministry of Public Health, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou (China); Zhou, Yanfeng, E-mail: zyfhdj@yahoo.com [Department of Anesthesiology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou (China)

    2014-04-18

    Highlights: • MiR-145 expression is down-regulated in HCC tissues and inversely related with IRS1 levels. • MiR-145 directly targets IRS1 in HCC cells. • Restored expression of miR-145 suppressed HCC cell proliferation and growth. • MiR-145 induced IRS1 under-expression potentially reduced downstream AKT signaling. - Abstract: Accumulating evidences have proved that dysregulation of microRNAs (miRNAs) is involved in cancer initiation and progression. In this study, we showed that miRNA-145 level was significantly decreased in hepatocellular cancer (HCC) tissues and cell lines, and its low expression was inversely associated with the abundance of insulin receptor substrate 1 (IRS1), a key mediator in oncogenic insulin-like growth factor (IGF) signaling. We verified IRS1 as a direct target of miR-145 using Western blotting and luciferase reporter assay. Further, the restoration of miR-145 in HCC cell lines suppressed cancer cell growth, owing to down-regulated IRS1 expression and its downstream Akt/FOXO1 signaling. Our results demonstrated that miR-145 could inhibit HCC through targeting IRS1 and its downstream signaling, implicating the loss of miR-145 regulation may be a potential molecular mechanism causing aberrant oncogenic signaling in HCC.

  14. Detection, Validation, and Downstream Analysis of Allelic Variation in Gene Expression

    Science.gov (United States)

    Ciobanu, Daniel C.; Lu, Lu; Mozhui, Khyobeni; Wang, Xusheng; Jagalur, Manjunatha; Morris, John A.; Taylor, William L.; Dietz, Klaus; Simon, Perikles; Williams, Robert W.

    2010-01-01

    Common sequence variants within a gene often generate important differences in expression of corresponding mRNAs. This high level of local (allelic) control—or cis modulation—rivals that produced by gene targeting, but expression is titrated finely over a range of levels. We are interested in exploiting this allelic variation to study gene function and downstream consequences of differences in expression dosage. We have used several bioinformatics and molecular approaches to estimate error rates in the discovery of cis modulation and to analyze some of the biological and technical confounds that contribute to the variation in gene expression profiling. Our analysis of SNPs and alternative transcripts, combined with eQTL maps and selective gene resequencing, revealed that between 17 and 25% of apparent cis modulation is caused by SNPs that overlap probes rather than by genuine quantitative differences in mRNA levels. This estimate climbs to 40–50% when qualitative differences between isoform variants are included. We have developed an analytical approach to filter differences in expression and improve the yield of genuine cis-modulated transcripts to ∼80%. This improvement is important because the resulting variation can be successfully used to study downstream consequences of altered expression on higher-order phenotypes. Using a systems genetics approach we show that two validated cis-modulated genes, Stk25 and Rasd2, are likely to control expression of downstream targets and affect disease susceptibility. PMID:19884314

  15. Downstream hydraulic geometry relationships: Gathering reference reach-scale width values from LiDAR

    Science.gov (United States)

    Sofia, G.; Tarolli, P.; Cazorzi, F.; Dalla Fontana, G.

    2015-12-01

    This paper examines the ability of LiDAR topography to provide reach-scale width values for the analysis of downstream hydraulic geometry relationships along some streams in the Dolomites (northern Italy). Multiple reach-scale dimensions can provide representative geometries and statistics characterising the longitudinal variability in the channel, improving the understanding of geomorphic processes across networks. Starting from the minimum curvature derived from a LiDAR DTM, the proposed algorithm uses a statistical approach for the identification of the scale of analysis, and for the automatic characterisation of reach-scale bankfull widths. The downstream adjustment in channel morphology is then related to flow parameters (drainage area and stream power). With the correct planning of a LiDAR survey, uncertainties in the procedure are principally due to the resolution of the DTM. The outputs are in general comparable in quality to field survey measurements, and the procedure allows the quick comparison among different watersheds. The proposed automatic approach could improve knowledge about river systems with highly variable widths, and about systems in areas covered by vegetation or inaccessible to field surveys. With proven effectiveness, this research could offer an interesting starting point for the analysis of differences between watersheds, and to improve knowledge about downstream channel adjustment in relation, for example, to scale and landscape forcing (e.g. sediment transport, tectonics, lithology, climate, geomorphology, and anthropic pressure).

  16. Measurement of pulsatile turbulent flow downstream of polyurethane heart valve prosthesis using particle image velocimetry

    Energy Technology Data Exchange (ETDEWEB)

    Kim, J.K.; Sung, J.Y. [Graduate School, Seoul National University, Seoul (Korea); Chang, J.K.; Min, B.G.; Yoo, J.Y. [Seoul National University, Seoul (Korea)

    1998-11-01

    In-vitro flow characteristics downstream of a polyurethane artificial heart valve under a pulsatile flow condition were investigated using Particle Image Velocimetry (PIV). With a triggering system and a time-delay circuit the velocity field downstream of the valve was evaluated in conjunction with the opening behavior of a flexible valve leaflet during a cardiac cycle.. Reynolds shear stress distribution was calculated from the velocity fields at a peak systolic phase. Direct measurements of the wall shear stress by hot-film anemometry (HFA) were compared with the PIV data. The possibilities of vascular complications, such as the thrombus formation and red blood cell damage, could be estimated from the overall view of the instantaneous velocity and stress fields obtained. A correlation between the flow pattern downstream of the valve and the corresponding opening posture of the polyurethane valve membrane gives useful data necessary for the improved design of the frame structure and leaflet geometry of the valve. (author). 11 refs., 8 figs., 5 tabs.

  17. Assessing water deprivation at the sub-river basin scale in LCA integrating downstream cascade effects.

    Science.gov (United States)

    Loubet, Philippe; Roux, Philippe; Núñez, Montserrat; Belaud, Gilles; Bellon-Maurel, Véronique

    2013-12-17

    Physical water deprivation at the midpoint level is assessed in water-related LCIA methods using water scarcity indicators (e.g., withdrawal-to-availability and consumption-to-availability) at the river basin scale. Although these indicators represent a great step forward in the assessment of water-use-related impacts in LCA, significant challenges still remain in improving their accuracy and relevance. This paper presents a methodology that can be used to derive midpoint characterization factors for water deprivation taking into account downstream cascade effects within a single river basin. This effect is considered at a finer scale because a river basin must be split into different subunits. The proposed framework is based on a two-step approach. First, water scarcity is defined at the sub-river basin scale with the consumption-to-availability (CTA) ratio, and second, characterization factors for water deprivation (CFWD) are calculated, integrating the effects on downstream sub-river basins. The sub-river basin CTA and CFWD were computed based on runoff data, water consumption data and a water balance for two different river basins. The results show significant differences between the CFWD in a given river basin, depending on the upstream or downstream position. Finally, an illustrative example is presented, in which different land planning scenarios, taking into account additional water consumption in a city, are assessed. Our work demonstrates how crucial it is to localize the withdrawal and release positions within a river basin.

  18. Safety of snake antivenom immunoglobulins: efficacy of viral inactivation in a complete downstream process.

    Science.gov (United States)

    Caricati, C P; Oliveira-Nascimento, L; Yoshida, J T; Caricati, A T P; Raw, I; Stephano, M A

    2013-01-01

    Viral safety remains a challenge when processing a plasma-derived product. A variety of pathogens might be present in the starting material, which requires a downstream process capable of broad viral reduction. In this article, we used a wide panel of viruses to assess viral removal/inactivation of our downstream process for Snake Antivenom Immunoglobulin (SAI). First, we screened and excluded equine plasma that cross-reacted with any model virus, a procedure not published before for antivenoms. In addition, we evaluated for the first time the virucidal capacity of phenol applied to SAI products. Among the steps analyzed in the process, phenol addition was the most effective one, followed by heat, caprylic acid, and pepsin. All viruses were fully inactivated only by phenol treatment; heat, the second most effective step, did not inactivate the rotavirus and the adenovirus used. We therefore present a SAI downstream method that is cost-effective and eliminates viruses to the extent required by WHO for a safe product.

  19. Upstream to downstream: stormwater quality in Mayagüez, Puerto Rico.

    Science.gov (United States)

    Wengrove, Meagan E; Ballestero, Thomas P

    2012-08-01

    The focus of this research was upon consequences of urban stormwater runoff entering two streams in Mayagüez, Puerto Rico. Mayagüez is the largest urban area of the western side of the island of Puerto Rico and provides an excellent point of reference to monitor the affects of urban development on water quality in a tropical climate. The two monitored streams were Quebrada del Oro and Cano Majagual. The research hypothesis asks, "Does stormwater runoff from urban development measurably affect the water quality of downstream receiving water by raising the conductivity, temperature, and flow quantity characteristics during storm events in comparison to upstream water quality?" In essence, the results for Quebrada del Oro agreed with the hypothesis of this project, while Cano Majagual produced results different from the hypothesis primarily due to the absence of non-urbanized land use for both upstream and downstream sections as well as the buffering capacity of a large wetland just upstream of the downstream instrument location of Cano Majagual. Both streams showed signs of stream impairment according to the temperature criteria (32°C or 90°F) set by the Junta de Calidad Ambiental and the US Environmental Protection Agency. Dissolved oxygen levels of the streams were severely affected by water temperature and oxygen-consuming matter within these stream systems, making dissolved oxygen and temperature important water quality parameters for tropical climates.

  20. Downstream passage of fish larvae and eggs through a small-sized reservoir, Mucuri river, Brazil

    Directory of Open Access Journals (Sweden)

    Paulo S. Pompeu

    2011-12-01

    Full Text Available In South America, one important symptom of the failure of fish passages to sustain fish migratory recruitment is the inability of eggs and larvae to reach the nurseries. This is especially so when the breeding areas are located upstream of a reservoir, and the floodplain is downstream of the dam. Therefore, the transport of fish larvae and eggs across reservoir barriers is a key factor in the development of effective conservation strategies. In this paper, we evaluate the potential for migratory fish larvae and egg transportation across a small size reservoir in eastern Brazil. We sampled fish daily between 15th October 2002 and 15th February 2003 (spawning period in the Mucuri River, immediately upstream of the reservoir and downstream of the Santa Clara Power Plant dam. Our study was the first to indicate the possibility of successful larval passage through the reservoir of a hydroelectric reservoir and dam in South America, and showed that the passage of migratory fish larvae was associated significantly with residence time of water in the reservoir. The relatively short water residence time and elevated turbidity of the Santa Clara's reservoir waters during the rainy season certainly contributed to the successful passage, and can be considered as key factors for a priori evaluations of the feasibility of a downstream larval passage.

  1. Optimizing withdrawal from drinking water reservoirs to reduce downstream temperature pollution and reservoir hypoxia.

    Science.gov (United States)

    Weber, M; Rinke, K; Hipsey, M R; Boehrer, B

    2017-03-20

    Sustainable management of drinking water reservoirs requires balancing the demands of water supply whilst minimizing environmental impact. This study numerically simulates the effect of an improved withdrawal scheme designed to alleviate the temperature pollution downstream of a reservoir. The aim was to identify an optimal withdrawal strategy such that water of a desirable discharge temperature can be supplied downstream without leading to unacceptably low oxygen concentrations within the reservoir. First, we calibrated a one-dimensional numerical model for hydrodynamics and oxygen dynamics (GLM-AED2), verifying that the model reproduced water temperatures and hypolimnetic dissolved oxygen concentrations accurately over a 5 year period. Second, the model was extended to include an adaptive withdrawal functionality, allowing for a prescribed withdrawal temperature to be found, with the potential constraint of hypolimnetic oxygen concentration. Scenario simulations on epi-/metalimnetic withdrawal demonstrate that the model is able to autonomously determine the best withdrawal height depending on the thermal structure and the hypolimnetic oxygen concentration thereby optimizing the ability to supply a desirable discharge temperature to the downstream river during summer. This new withdrawal strategy also increased the hypolimnetic raw water volume to be used for drinking water supply, but reduced the dissolved oxygen concentrations in the deep and cold water layers (hypolimnion). Implications of the results for reservoir management are discussed and the numerical model is provided for operators as a simple and efficient tool for optimizing the withdrawal strategy within different reservoir contexts.

  2. On the electron temperature downstream of the solar wind termination shock

    Energy Technology Data Exchange (ETDEWEB)

    Chashei, I.V. [Lebedev Physical Institute, Moscow (Russian Federation); Fahr, H.J. [Bonn Univ. (Germany). Argelander Inst. fuer Astronomie

    2013-09-01

    In this paper we study the temperatures of electrons convected with the solar wind to large solar distances and finally transported over the solar wind termination shock. Nearly nothing, unless at high energies in the cosmic ray regime, is known about the thermodynamical behaviour of these distant electrons from in situ plasma observations. Hence it is tacitly assumed these electrons, due to their adiabatic behaviour and vanishing heat conduction or energization processes, have rapidly cooled off to very low temperatures once they eventually arrive at the solar wind termination shock (at about 100 AU). In this paper we show that such electrons, however, at their passage over the termination shock due to the shock-electric field action undergo an overadiabatic heating and therefore appear on the downstream side as a substantially heated plasma species. Looking quantitatively into this heating process we find that solar wind electrons achieve temperatures of the order of 2-4 x 10{sup 6} K downstream of the termination shock, depending on the upstream solar wind bulk velocity and the shock compression ratio. Hence these electrons therewith play an important dynamical role in structuring this shock and determining the downstream plasma flow properties. Furthermore, they present an additional ionization source for incoming neutral interstellar hydrogen and excite X-ray emission. They also behave similar to cosmic ray electrons and extend to some limited region upstream of the shock of the order of 0.1 AU by spatial diffusion and thereby also modify the upstream solar wind properties. (orig.)

  3. An integrated metabonomics and transcriptomics approach to understanding metabolic pathway disturbance induced by perfluorooctanoic acid.

    Science.gov (United States)

    Peng, Siyuan; Yan, Lijuan; Zhang, Jie; Wang, Zhanlin; Tian, Meiping; Shen, Heqing

    2013-12-01

    Perfluorooctanoic acid (PFOA) is one of the most representative perfluorinated compounds and liver is the major organ where PFOA is accumulated. Although the multiple toxicities had been reported, its toxicological profile remained unclear. In this study, a systems toxicology strategy integrating liquid chromatography/mass spectrometry-based metabonomics and transcriptomics analyses was applied for the first time to investigate the effects of PFOA on a representative Chinese normal human liver cell line L-02, with focusing on the metabolic disturbance. Fifteen potential biomarkers were identified on metabolic level and most observations were consistent with the altered levels of gene expression. Our results showed that PFOA induced the perturbations in various metabolic processes in L-02 cells, especially lipid metabolism-related pathways. The up-stream mitochondrial carnitine metabolism was proved to be influenced by PFOA treatment. The specific transformation from carnitine to acylcarnitines, which showed a dose-dependent effect, and the expression level of key genes involved in this pathway were observed to be altered correspondingly. Furthermore, the down-stream cholesterol biosynthesis was directly confirmed to be up-regulated by both increased cholesterol content and elevated expression level of key genes. The PFOA-induced lipid metabolism-related effects in L-02 cells started from the fatty acid catabolism in cytosol, fluctuated to the processes in mitochondria, extended to the cholesterol biosynthesis. Many other metabolic pathways like amino acid metabolism and tricarboxylic acid cycle might also be disturbed. The findings obtained from the systems biological research provide more details about metabolic disorders induced by PFOA in human liver.

  4. Transcriptomic analysis of the role of carboxylic acids in metabolite signaling in Arabidopsis leaves.

    Science.gov (United States)

    Finkemeier, Iris; König, Ann-Christine; Heard, William; Nunes-Nesi, Adriano; Pham, Phuong Anh; Leister, Dario; Fernie, Alisdair R; Sweetlove, Lee J

    2013-05-01

    The transcriptional response to metabolites is an important mechanism by which plants integrate information about cellular energy and nutrient status. Although some carboxylic acids have been implicated in the regulation of gene expression for select transcripts, it is unclear whether all carboxylic acids have the same effect, how many transcripts are affected, and how carboxylic acid signaling is integrated with other metabolite signals. In this study, we demonstrate that perturbations in cellular concentrations of citrate, and to a lesser extent malate, have a major impact on nucleus-encoded transcript abundance. Functional categories of transcripts that were targeted by both organic acids included photosynthesis, cell wall, biotic stress, and protein synthesis. Specific functional categories that were only regulated by citrate included tricarboxylic acid cycle, nitrogen metabolism, sulfur metabolism, and DNA synthesis. Further quantitative real-time polymerase chain reaction analysis of specific citrate-responsive transcripts demonstrated that the transcript response to citrate is time and concentration dependent and distinct from other organic acids and sugars. Feeding of isocitrate as well as the nonmetabolizable citrate analog tricarballylate revealed that the abundance of selected marker transcripts is responsive to citrate and not downstream metabolites. Interestingly, the transcriptome response to citrate feeding was most similar to those observed after biotic stress treatments and the gibberellin biosynthesis inhibitor paclobutrazol. Feeding of citrate to mutants with defects in plant hormone signaling pathways did not completely abolish the transcript response but hinted at a link with jasmonic acid and gibberellin signaling pathways. Our results suggest that changes in carboxylic acid abundances can be perceived and signaled in Arabidopsis (Arabidopsis thaliana) by as yet unknown signaling pathways.

  5. The inflammatory and normal transcriptome of mouse bladder detrusor and mucosa

    Directory of Open Access Journals (Sweden)

    Dyer David W

    2006-01-01

    Full Text Available Abstract Background An organ such as the bladder consists of complex, interacting set of tissues and cells. Inflammation has been implicated in every major disease of the bladder, including cancer, interstitial cystitis, and infection. However, scanty is the information about individual detrusor and urothelium transcriptomes in response to inflammation. Here, we used suppression subtractive hybridizations (SSH to determine bladder tissue- and disease-specific genes and transcriptional regulatory elements (TREs. Unique TREs and genes were assembled into putative networks. Results It was found that the control bladder mucosa presented regulatory elements driving genes such as myosin light chain phosphatase and calponin 1 that influence the smooth muscle phenotype. In the control detrusor network the Pax-3 TRE was significantly over-represented. During development, the Pax-3 transcription factor (TF maintains progenitor cells in an undifferentiated state whereas, during inflammation, Pax-3 was suppressed and genes involved in neuronal development (synapsin I were up-regulated. Therefore, during inflammation, an increased maturation of neural progenitor cells in the muscle may underlie detrusor instability. NF-κB was specifically over-represented in the inflamed mucosa regulatory network. When the inflamed detrusor was compared to control, two major pathways were found, one encoding synapsin I, a neuron-specific phosphoprotein, and the other an important apoptotic protein, siva. In response to LPS-induced inflammation, the liver X receptor was over-represented in both mucosa and detrusor regulatory networks confirming a role for this nuclear receptor in LPS-induced gene expression. Conclusion A new approach for understanding bladder muscle-urothelium interaction was developed by assembling SSH, real time PCR, and TRE analysis results into regulatory networks. Interestingly, some of the TREs and their downstream transcripts originally involved in

  6. Transcriptomic analysis of the effects of a fish oil enriched diet on murine brains.

    Directory of Open Access Journals (Sweden)

    Rasha Hammamieh

    Full Text Available The health benefits of fish oil enriched with high omega-3 polyunsaturated fatty acids (n-3 PUFA are widely documented. Fish oil as dietary supplements, however, show moderate clinical efficacy, highlighting an immediate scope of systematic in vitro feedback. Our transcriptomic study was designed to investigate the genomic shift of murine brains fed on fish oil enriched diets. A customized fish oil enriched diet (FD and standard lab diet (SD were separately administered to two randomly chosen populations of C57BL/6J mice from their weaning age until late adolescence. Statistical analysis mined 1,142 genes of interest (GOI differentially altered in the hemibrains collected from the FD- and SD-fed mice at the age of five months. The majority of identified GOI (∼ 40% encodes proteins located in the plasma membrane, suggesting that fish oil primarily facilitated the membrane-oriented biofunctions. FD potentially augmented the nervous system's development and functions by selectively stimulating the Src-mediated calcium-induced growth cascade and the downstream PI3K-AKT-PKC pathways. FD reduced the amyloidal burden, attenuated oxidative stress, and assisted in somatostatin activation-the signatures of attenuation of Alzheimer's disease, Parkinson's disease, and affective disorder. FD induced elevation of FKBP5 and suppression of BDNF, which are often linked with the improvement of anxiety disorder, depression, and post-traumatic stress disorder. Hence we anticipate efficacy of FD in treating illnesses such as depression that are typically triggered by the hypoactivities of dopaminergic, adrenergic, cholinergic, and GABAergic networks. Contrastingly, FD's efficacy could be compromised in treating illnesses such as bipolar disorder and schizophrenia, which are triggered by hyperactivities of the same set of neuromodulators. A more comprehensive investigation is recommended to elucidate the implications of fish oil on disease pathomechanisms, and the

  7. Complex biallelic IGH rearrangements in IgM-expressing Z-138 cell line : Involvement of downstream immunoglobulin class switch recombination

    NARCIS (Netherlands)

    Guikema, JEJ; Fenton, JAL; de Boer, C; Kleiverda, K; Brink, AATP; Raap, AK; Estrov, Z; Schuuring, E; Kluin, PM

    2005-01-01

    Chromosomal translocations involving the immunoglobulin (Ig) receptor loci usually disrupt and silence these loci. On the basis of observations in follicular lymphoma (FL) with downstream Ig heavy chain (IGH) class switch recombination (CSR), we hypothesized that downstream CSR-mediated chromosomal

  8. Elucidation of a downstream boundary of the 3' IgH regulatory region.

    Science.gov (United States)

    Manis, John P; Michaelson, Jennifer S; Birshtein, Barbara K; Alt, Frederick W

    2003-01-01

    Class switch recombination (CSR) changes the immunoglobulin heavy chain (IgH) constant region gene (C(H)) in B cells from IgM to IgG, IgA, or IgE, without modifying the variable region gene segment. This process requires transcription through switch (S) regions located upstream of the C(H) genes targeted for CSR, a process that relies on the activity of an uncharacterized regulatory region at the 3' end of the C(H) locus (3' IgH RR) that has been implicated via the effects of pgk-neo cassettes inserted into the locus. The 30kb region just downstream of the most 3' C(H) gene (Ca) contains four known enhancer elements including HS3a, HS1,2, HS3b, and HS4. Replacement of either of the proximal two enhancer elements (HS3a or HS1,2) with a pgk-neo gene cassette disrupted germline transcription of and CSR to most C(H) genes. However, replacement of either of the enhancers with a loxP sequence had no effect on CSR indicating that these elements are not critical for CSR. Insertion of a pgk-neo cassette at various sites within the C(H) locus inhibited CSR to upstream, but not downstream C(H) genes, supporting the notion that the pgk-neo cassette insertion into the locus short-circuits the ability of the 3' RR to facilitate CSR of dependent C(H) genes upstream of the insertion. These analyses also indicated that the key elements of the 3' IgH RR were downstream from HS1,2. In this study, we have sought to localize the 3' IgH RR by defining its 3' boundary. For this purpose, a pgk-neo gene cassette was targeted 2kb downstream of the HS4 element in ES cells that had normal ability to undergo CSR. We then employed Rag-2 deficient blastocyst complementation to generate chimeric mice that harbored B cells homozygous for this mutation. Such chimeras exhibited normal reconstitution of the splenic compartment and had normal serum immunoglobulin levels. Upon in vitro activation, transcription from the pgk-neo cassette was induced in B cells, however, CSR to all measured IgH isotypes

  9. What is the primary driver of downstream connectivity: runoff generation, storage or conveyance?

    Science.gov (United States)

    Ali, G.; Elliott, J.; Lobb, D.; Yarotski, J.

    2013-12-01

    Understanding how headwater streams are connected to downstream areas through the generation and delivery of stream discharge is critical for process conceptualization and hydrological modelling. Several factors have been shown to influence downstream connectivity (DC), notably the location of runoff-generating areas, the mitigating effect of surface depressional storage areas on the delivery of runoff to streams, and the effectiveness of diffuse and concentrated flow paths as runoff conveyance features. Limited efforts have been made to rank these factors in order of importance. Here we aimed to identify the relative influence of runoff generation, storage and conveyance factors on DC in an agricultural Prairie watershed. The 75 km2 South Tobacco Creek Watershed (STCW, south-central Manitoba, Canada) is drained by a 20 km-long creek that drops nearly 200 m in elevation over its course; it is characterized by highly seasonal dynamics such as sheet flow on frozen ground in spring, intermittent flow in summer, and significant surface and subsurface flow events in fall. Hourly discharge records were obtained for seven pairs of upstream-downstream gauging stations within the STCW: for each pair, the magnitude of DC was estimated using cross-correlation values of the two discharge timeseries, while the timing of DC was characterized using cross-correlation lags (in hours or days) to assess the delay of peak flows between upstream and downstream stations. LiDAR data was also used to extract topographic information on: i) the location of runoff-generating areas (i.e., upper-, mid-, low- slope and riparian areas), ii) the area and depth of surface depressional storage basins, and iii) the total length of flow conveyance features (defined streams, all flow paths) in the incremental catchment area between upstream and downstream gauging stations. The computed discharge cross-correlation values indicate that the magnitude of DC is highest in spring, followed by fall then

  10. Rhythmic Degradation Explains and Unifies Circadian Transcriptome and Proteome Data

    Directory of Open Access Journals (Sweden)

    Sarah Lück

    2014-10-01

    Full Text Available The rich mammalian cellular circadian output affects thousands of genes in many cell types and has been the subject of genome-wide transcriptome and proteome studies. The results have been enigmatic because transcript peak abundances do not always follow the peaks of gene-expression activity in time. We posited that circadian degradation of mRNAs and proteins plays a pivotal role in setting their peak times. To establish guiding principles, we derived a theoretical framework that fully describes the amplitudes and phases of biomolecules with circadian half-lives. We were able to explain the circadian transcriptome and proteome studies with the same unifying theory, including cases in which transcripts or proteins appeared before the onset of increased production rates. Furthermore, we estimate that 30% of the circadian transcripts in mouse liver and Drosophila heads are affected by rhythmic posttranscriptional regulation.

  11. Transcriptome dynamics of the microRNA inhibition response

    DEFF Research Database (Denmark)

    Wen, Jiayu; Leucci, Elenora; Vendramin, Roberto

    2015-01-01

    We report a high-resolution time series study of transcriptome dynamics following antimiR-mediated inhibition of miR-9 in a Hodgkin lymphoma cell-line-the first such dynamic study of the microRNA inhibition response-revealing both general and specific aspects of the physiological response. We show...... validate the key observations with independent time series qPCR and we experimentally validate key predicted miR-9 targets. Methodologically, we developed sensitive functional data analytic predictive methods to analyse the weak response inherent in microRNA inhibition experiments. The methods...... of this study will be applicable to similar high-resolution time series transcriptome analyses and provides the context for more accurate experimental design and interpretation of future microRNA inhibition studies....

  12. Transcriptome profiling of Curcuma longa L. cv. Suvarna

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    Ambika Sahoo

    2016-12-01

    Full Text Available Turmeric is an economically valued crop, because of its utility in the food, pharmaceutical industries and Ayurvedic medicine, attracts the attention in many areas of research work. In the present study, we executed resequencing through transcriptome assembly of the turmeric cultivar Suvarna (CL_Suv_10. Resequencing of Suvarna variety has generated 5 Gbases raw data with 75 bp paired-end sequence. The raw data has been submitted to SRA database of NCBI with accession number SRR4042181. Reads were assembled using Cufflinks-2.2.1 tool which ended up with 42994 numbers of transcripts. The length of transcripts ranged from 83 to15565, with a N50 value 1216 and median transcript length 773. The transcripts were annotated through number of databases. For the first time transcriptome profiling of cultivar Suvarna has been done, which could help towards identification of single nucleotide polymorphisms (SNPs between Suvarna and other turmeric cultivars for its authentic identification.

  13. Transcriptome and genome size analysis of the venus flytrap

    DEFF Research Database (Denmark)

    Jensen, Michael Krogh; Vogt, Josef Korbinian; Bressendorff, Simon;

    2015-01-01

    The insectivorous Venus flytrap (Dionaea muscipula) is renowned from Darwin's studies of plant carnivory and the origins of species. To provide tools to analyze the evolution and functional genomics of D. muscipula, we sequenced a normalized cDNA library synthesized from mRNA isolated from D....... muscipula flowers and traps. Using the Oases transcriptome assembler 79,165,657 quality trimmed reads were assembled into 80,806 cDNA contigs, with an average length of 679 bp and an N50 length of 1,051 bp. A total of 17,047 unique proteins were identified, and assigned to Gene Ontology (GO) and classified......, using a single copy sequence PCR-based method, we estimated that the genome size of D. muscipula is approx. 3 Gb. Our genome size estimate and transcriptome analyses will contribute to future research on this fascinating, monotypic species and its heterotrophic adaptations....

  14. The developmental dynamics of the maize leaf transcriptome.

    Science.gov (United States)

    Li, Pinghua; Ponnala, Lalit; Gandotra, Neeru; Wang, Lin; Si, Yaqing; Tausta, S Lori; Kebrom, Tesfamichael H; Provart, Nicholas; Patel, Rohan; Myers, Christopher R; Reidel, Edwin J; Turgeon, Robert; Liu, Peng; Sun, Qi; Nelson, Timothy; Brutnell, Thomas P

    2010-12-01

    We have analyzed the maize leaf transcriptome using Illumina sequencing. We mapped more than 120 million reads to define gene structure and alternative splicing events and to quantify transcript abundance along a leaf developmental gradient and in mature bundle sheath and mesophyll cells. We detected differential mRNA processing events for most maize genes. We found that 64% and 21% of genes were differentially expressed along the developmental gradient and between bundle sheath and mesophyll cells, respectively. We implemented Gbrowse, an electronic fluorescent pictograph browser, and created a two-cell biochemical pathway viewer to visualize datasets. Cluster analysis of the data revealed a dynamic transcriptome, with transcripts for primary cell wall and basic cellular metabolism at the leaf base transitioning to transcripts for secondary cell wall biosynthesis and C(4) photosynthetic development toward the tip. This dataset will serve as the foundation for a systems biology approach to the understanding of photosynthetic development.

  15. Transcriptome analysis of the Asian honey bee Apis cerana cerana.

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    Zi Long Wang

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

  16. Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii

    Science.gov (United States)

    Puigvert, Marina; Guarischi-Sousa, Rodrigo; Zuluaga, Paola; Coll, Núria S.; Macho, Alberto P.; Setubal, João C.; Valls, Marc

    2017-01-01

    Bacterial wilt of potatoes—also called brown rot—is a devastating disease caused by the vascular pathogen Ralstonia solanacearum that leads to significant yield loss. As in other plant-pathogen interactions, the first contacts established between the bacterium and the plant largely condition the disease outcome. Here, we studied the transcriptome of R. solanacearum UY031 early after infection in two accessions of the wild potato Solanum commersonii showing contrasting resistance to bacterial wilt. Total RNAs obtained from asymptomatic infected roots were deep sequenced and for 4,609 out of the 4,778 annotated genes in strain UY031 were recovered. Only 2 genes were differentially-expressed between the resistant and the susceptible plant accessions, suggesting that the bacterial component plays a minor role in the establishment of disease. On the contrary, 422 genes were differentially expressed (DE) in planta compared to growth on a synthetic rich medium. Only 73 of these genes had been previously identified as DE in a transcriptome of R. solanacearum extracted from infected tomato xylem vessels. Virulence determinants such as the Type Three Secretion System (T3SS) and its effector proteins, motility structures, and reactive oxygen species (ROS) detoxifying enzymes were induced during infection of S. commersonii. On the contrary, metabolic activities were mostly repressed during early root colonization, with the notable exception of nitrogen metabolism, sulfate reduction and phosphate uptake. Several of the R. solanacearum genes identified as significantly up-regulated during infection had not been previously described as virulence factors. This is the first report describing the R. solanacearum transcriptome directly obtained from infected tissue and also the first to analyze bacterial gene expression in the roots, where plant infection takes place. We also demonstrate that the bacterial transcriptome in planta can be studied when pathogen numbers are low by

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

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    Ninthujah Kanageswaran

    Full Text Available 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.

  18. Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome

    Science.gov (United States)

    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

  19. Deciphering the Developmental Dynamics of the Mouse Liver Transcriptome.

    Directory of Open Access Journals (Sweden)

    Sumedha S Gunewardena

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

  20. Transcriptomics resources of human tissues and organs

    OpenAIRE

    Uhlén, Mathias; Hallström, Björn M; Lindskog, Cecilia; Mardinoglu, Adil; Pontén, Fredrik; Nielsen, Jens

    2016-01-01

    Abstract Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large‐scale transcriptomics studies have analyzed the expression of protein‐coding genes across tissues. These datasets provide a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue‐restricted manner. Here...

  1. SoyXpress: A database for exploring the soybean transcriptome

    Directory of Open Access Journals (Sweden)

    Cheng Kei

    2008-08-01

    Full Text Available Abstract Background Experiments using whole transcriptome microarrays produce massive amounts of data. To gain a comprehensive understanding of this gene expression data it needs to be integrated with other available information such as gene function and metabolic pathways. Bioinformatics tools are essential to handle, organize and interpret the results. To date, no database provides whole transcriptome analysis capabilities integrated with terms describing biological functions for soybean (Glycine max (L Merr.. To this end we have developed SoyXpress, a relational database with a suite of web interfaces to allow users to easily retrieve data and results of the microarray experiment with cross-referenced annotations of expressed sequence tags (EST and hyperlinks to external public databases. This environment makes it possible to explore differences in gene expression, if any, between for instance transgenic and non-transgenic soybean cultivars and to interpret the results based on gene functional annotations to determine any changes that could potentially alter biological processes. Results SoyXpress is a database designed for exploring the soybean transcriptome. Currently SoyXpress houses 380,095 soybean Expressed Sequence Tags (EST, linked with metabolic pathways, Gene Ontology terms, SwissProt identifiers and Affymetrix gene expression data. Array data is presently available from an experiment profiling global gene expression of three conventional and two genetically engineered soybean cultivars. The microarray data is linked with the sequence data, for maximum knowledge extraction. SoyXpress is implemented in MySQL and uses a Perl CGI interface. Conclusion SoyXpress is designed for the purpose of exploring potential transcriptome differences in different plant genotypes, including genetically modified crops. Soybean EST sequences, microarray and pathway data as well as searchable and browsable gene ontology are integrated and presented. Soy

  2. Sequencing the transcriptome of milk production: milk trumps mammary tissue

    OpenAIRE

    Lemay, Danielle G; Hovey, Russell C.; Hartono, Stella R; Hinde, Katie; Smilowitz, Jennifer T.; Ventimiglia, Frank; Schmidt, Kimberli A; Lee, Joyce WS; Islas-Trejo, Alma; Silva, Pedro Ivo; Korf, Ian; Medrano, Juan F.; Barry, Peter A.; German, J. Bruce

    2013-01-01

    Abstract Background Studies of normal human mammary gland development and function have mostly relied on cell culture, limited surgical specimens, and rodent models. Although RNA extracted from human milk has been used to assay the mammary transcriptome non-invasively, this assay has not been adequately validated in primates. Thus, the objectives of the current study were to assess the suitability of lactating rhesus macaques as a model for lactating ...

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

    Directory of Open Access Journals (Sweden)

    Candice A Stafford-Banks

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

  4. Comparing de novo assemblers for 454 transcriptome data

    Directory of Open Access Journals (Sweden)

    Blaxter Mark L

    2010-10-01

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

  5. Elephant Transcriptome Provides Insights into the Evolution of Eutherian Placentation

    OpenAIRE

    Hou, Zhuo-Cheng; Sterner, Kirstin N.; Romero, Roberto; Than, Nandor Gabor; Gonzalez, Juan M.; Weckle, Amy; Xing, Jun; Benirschke, Kurt; Goodman, Morris; Wildman, Derek E.

    2012-01-01

    The chorioallantoic placenta connects mother and fetus in eutherian pregnancies. In order to understand the evolution of the placenta and provide further understanding of placenta biology, we sequenced the transcriptome of a term placenta of an African elephant (Loxodonta africana) and compared these data with RNA sequence and microarray data from other eutherian placentas including human, mouse, and cow. We characterized the composition of 55,910 expressed sequence tag (i.e., cDNA) contigs u...

  6. Transcriptomic Profiles Differentiate Normal Rectal Epithelium and Adenocarcinoma

    OpenAIRE

    2015-01-01

    Adenocarcinoma is a histologic diagnosis based on subjective findings. Transcriptional profiles have been used to differentiate normal tissue from disease and could provide a means of identifying malignancy. The goal of this study was to generate and test transcriptomic profiles that differentiate normal from adenocarcinomatous rectum. Comparisons were made between cDNA microarrays derived from normal epithelium and rectal adenocarcinoma. Results were filtered according to standard deviation ...

  7. Targeting Master Regulators of the Breast Cancer Metastasis Transcriptome

    Science.gov (United States)

    2014-07-01

    rigorous state -of-the- art bioinformatic analysis, and functional models using isogenic human breast cancer cells with varying metastatic potential, we will...A, Ergun B, Erbersdobler A, Jung K, Stephan C. RECK overexpression decreases invasive potential in prostate cancer cells. Prostate 2012; 72: 948–954...Breast Cancer Metastasis Transcriptome PRINCIPAL INVESTIGATOR: Timothy A. Chan MD, PhD CONTRACTING ORGANIZATION: Sloan-Kettering Institute

  8. Transcriptomic analysis of barley plant responses to cold stress

    OpenAIRE

    Wu, Jing

    2010-01-01

    Previous molecular and genomic studies have shown that several group genes in Arabidopsis with various functions are induced by cold stresses, and that various transcription factors are involved in the regulation of stress-inducible genes which contribute to an increase in cold tolerance. Here, we present the results of transcriptome analysis indicating the existence of genes of potential importance to cold stress and multiple low-temperature regulatory pathways in addition to the cold respon...

  9. De novo transcriptome assembly of mangosteen (Garcinia mangostana L.) fruit.

    Science.gov (United States)

    Matra, Deden Derajat; Kozaki, Toshinori; Ishii, Kazuo; Poerwanto, Roedhy; Inoue, Eiichi

    2016-12-01

    Garcinia mangostana L. (Mangosteen), of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.

  10. De novo transcriptome assembly of two contrasting pumpkin cultivars

    Directory of Open Access Journals (Sweden)

    Aliki Xanthopoulou

    2016-03-01

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

  11. Human transcriptome array for high-throughput clinical studies.

    Science.gov (United States)

    Xu, Weihong; Seok, Junhee; Mindrinos, Michael N; Schweitzer, Anthony C; Jiang, Hui; Wilhelmy, Julie; Clark, Tyson A; Kapur, Karen; Xing, Yi; Faham, Malek; Storey, John D; Moldawer, Lyle L; Maier, Ronald V; Tompkins, Ronald G; Wong, Wing Hung; Davis, Ronald W; Xiao, Wenzhong

    2011-03-01

    A 6.9 million-feature oligonucleotide array of the human transcriptome [Glue Grant human transcriptome (GG-H array)] has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing as well as detection of coding SNPs and noncoding transcripts. The performance of the array was examined and compared with mRNA sequencing (RNA-Seq) results over multiple independent replicates of liver and muscle samples. Compared with RNA-Seq of 46 million uniquely mappable reads per replicate, the GG-H array is highly reproducible in estimating gene and exon abundance. Although both platforms detect similar expression changes at the gene level, the GG-H array is more sensitive at the exon level. Deeper sequencing is required to adequately cover low-abundance transcripts. The array has been implemented in a multicenter clinical program and has generated high-quality, reproducible data. Considering the clinical trial requirements of cost, sample availability, and throughput, the GG-H array has a wide range of applications. An emerging approach for large-scale clinical genomic studies is to first use RNA-Seq to the sufficient depth for the discovery of transcriptome elements relevant to the disease process followed by high-throughput and reliable screening of these elements on thousands of patient samples using custom-designed arrays.

  12. Genome-wide transcriptome analysis of 150 cell samples†

    Science.gov (United States)

    Russom, Aman; Xiao, Wenzhong; Wilhelmy, Julie; Wang, Shenglong; Heath, Joe Don; Kurn, Nurith; Tompkins, Ronald G.; Davis, Ronald W.; Toner, Mehmet

    2013-01-01

    A major challenge in molecular biology is interrogating the human transcriptome on a genome wide scale when only a limited amount of biological sample is available for analysis. Current methodologies using microarray technologies for simultaneously monitoring mRNA transcription levels require nanogram amounts of total RNA. To overcome the sample size limitation of current technologies, we have developed a method to probe the global gene expression in biological samples as small as 150 cells, or the equivalent of approximately 300 pg total RNA. The new method employs microfluidic devices for the purification of total RNA from mammalian cells and ultra-sensitive whole transcriptome amplification techniques. We verified that the RNA integrity is preserved through the isolation process, accomplished highly reproducible whole transcriptome analysis, and established high correlation between repeated isolations of 150 cells and the same cell culture sample. We validated the technology by demonstrating that the combined microfluidic and amplification protocol is capable of identifying biological pathways perturbed by stimulation, which are consistent with the information recognized in bulk-isolated samples. PMID:20023796

  13. Genome-wide transcriptome analysis of 150 cell samples.

    Science.gov (United States)

    Irimia, Daniel; Mindrinos, Michael; Russom, Aman; Xiao, Wenzhong; Wilhelmy, Julie; Wang, Shenglong; Heath, Joe Don; Kurn, Nurith; Tompkins, Ronald G; Davis, Ronald W; Toner, Mehmet

    2009-01-01

    A major challenge in molecular biology is interrogating the human transcriptome on a genome wide scale when only a limited amount of biological sample is available for analysis. Current methodologies using microarray technologies for simultaneously monitoring mRNA transcription levels require nanogram amounts of total RNA. To overcome the sample size limitation of current technologies, we have developed a method to probe the global gene expression in biological samples as small as 150 cells, or the equivalent of approximately 300 pg total RNA. The new method employs microfluidic devices for the purification of total RNA from mammalian cells and ultra-sensitive whole transcriptome amplification techniques. We verified that the RNA integrity is preserved through the isolation process, accomplished highly reproducible whole transcriptome analysis, and established high correlation between repeated isolations of 150 cells and the same cell culture sample. We validated the technology by demonstrating that the combined microfluidic and amplification protocol is capable of identifying biological pathways perturbed by stimulation, which are consistent with the information recognized in bulk-isolated samples.

  14. Blood transcriptome based biomarkers for human circadian phase

    Science.gov (United States)

    Laing, Emma E; Möller-Levet, Carla S; Poh, Norman; Santhi, Nayantara; Archer, Simon N; Dijk, Derk-Jan

    2017-01-01

    Diagnosis and treatment of circadian rhythm sleep-wake disorders both require assessment of circadian phase of the brain’s circadian pacemaker. The gold-standard univariate method is based on collection of a 24-hr time series of plasma melatonin, a suprachiasmatic nucleus-driven pineal hormone. We developed and validated a multivariate whole-blood mRNA-based predictor of melatonin phase which requires few samples. Transcriptome data were collected under normal, sleep-deprivation and abnormal sleep-timing conditions to assess robustness of the predictor. Partial least square regression (PLSR), applied to the transcriptome, identified a set of 100 biomarkers primarily related to glucocorticoid signaling and immune function. Validation showed that PLSR-based predictors outperform published blood-derived circadian phase predictors. When given one sample as input, the R2 of predicted vs observed phase was 0.74, whereas for two samples taken 12 hr apart, R2 was 0.90. This blood transcriptome-based model enables assessment of circadian phase from a few samples. DOI: http://dx.doi.org/10.7554/eLife.20214.001 PMID:28218891

  15. Transcriptomics resources of human tissues and organs.

    Science.gov (United States)

    Uhlén, Mathias; Hallström, Björn M; Lindskog, Cecilia; Mardinoglu, Adil; Pontén, Fredrik; Nielsen, Jens

    2016-04-04

    Quantifying the differential expression of genes in various human organs, tissues, and cell types is vital to understand human physiology and disease. Recently, several large-scale transcriptomics studies have analyzed the expression of protein-coding genes across tissues. These datasets provide a framework for defining the molecular constituents of the human body as well as for generating comprehensive lists of proteins expressed across tissues or in a tissue-restricted manner. Here, we review publicly available human transcriptome resources and discuss body-wide data from independent genome-wide transcriptome analyses of different tissues. Gene expression measurements from these independent datasets, generated using samples from fresh frozen surgical specimens and postmortem tissues, are consistent. Overall, the different genome-wide analyses support a distribution in which many proteins are found in all tissues and relatively few in a tissue-restricted manner. Moreover, we discuss the applications of publicly available omics data for building genome-scale metabolic models, used for analyzing cell and tissue functions both in physiological and in disease contexts.

  16. De novo transcriptome assembly of mangosteen (Garcinia mangostana L. fruit

    Directory of Open Access Journals (Sweden)

    Deden Derajat Matra

    2016-12-01

    Full Text Available Garcinia mangostana L. (Mangosteen, of the family Clusiaceae, is one of the economically important tropical fruits in Indonesia. In the present study, we performed de novo transcriptomic analysis of Garcinia mangostana L. through RNA-Seq technology. We obtained the raw data from 12 libraries through Ion Proton System. Clean reads of 191,735,809 were obtained from 307,634,890 raw reads. The raw data obtained in this study can be accessible in DDBJ database with accession number of DRA005014 with bioproject accession number of PRJDB5091. We obtained 268,851 transcripts as well as 155,850 unigenes, having N50 value of 555 and 433 bp, respectively. Transcript/unigene length ranged from 201 to 5916 bp. The unigenes were annotated with two main databases from NCBI and UniProtKB, respectively having annotated-sequences of 73,287 and 73,107, respectively. These transcriptomic data will be beneficial for studying transcriptome of Garcinia mangostana L.

  17. Transcriptome Analysis of Enterococcus faecalis in Response to Alkaline Stress

    Directory of Open Access Journals (Sweden)

    Ran eshujun

    2015-08-01

    Full Text Available E. faecalis is the most commonly isolated species from endodontic failure root canals; its persistence in treated root canals has been attributed to its ability to resist high pH stress. The goal of this study was to characterize the E. faecalis transcriptome and to identify candidate genes for response and resistance to alkaline stress using Illumina HiSeq 2000 sequencing.We found that E. faecalis could survive and form biofilms in a pH 10 environment and that alkaline stress had a great impact on the transcription of many genes in the E. faecalis genome. The transcriptome sequencing results revealed that 613 genes were differentially expressed (DEGs for E. faecalis grown in pH 10 medium; 211 genes were found to be differentially up-regulated and 402 genes differentially down-regulated. Many of the down-regulated genes found are involved in cell energy production and metabolism and carbohydrate and amino acid metabolism, and the up-regulated genes are mostly related to nucleotide transport and metabolism. The results presented here reveal that cultivation of E. faecalis in alkaline stress has a profound impact on its transcriptome. The observed regulation of genes and pathways revealed that E. faecalis reduced its carbohydrate and amino acid metabolism and increased nucleotide synthesis to adapt and grow in alkaline stress. A number of the regulated genes may be useful candidates for the development of new therapeutic approaches for the treatment of E. faecalis infections.

  18. TBro: visualization and management of de novo transcriptomes

    Science.gov (United States)

    Ankenbrand, Markus J.; Weber, Lorenz; Becker, Dirk; Förster, Frank; Bemm, Felix

    2016-01-01

    RNA sequencing (RNA-seq) has become a powerful tool to understand molecular mechanisms and/or developmental programs. It provides a fast, reliable and cost-effective method to access sets of expressed elements in a qualitative and quantitative manner. Especially for non-model organisms and in absence of a reference genome, RNA-seq data is used to reconstruct and quantify transcriptomes at the same time. Even SNPs, InDels, and alternative splicing events are predicted directly from the data without having a reference genome at hand. A key challenge, especially for non-computational personnal, is the management of the resulting datasets, consisting of different data types and formats. Here, we present TBro, a flexible de novo transcriptome browser, tackling this challenge. TBro aggregates sequences, their annotation, expression levels as well as differential testing results. It provides an easy-to-use interface to mine the aggregated data and generate publication-ready visualizations. Additionally, it supports users with an intuitive cart system, that helps collecting and analysing biological meaningful sets of transcripts. TBro’s modular architecture allows easy extension of its functionalities in the future. Especially, the integration of new data types such as proteomic quantifications or array-based gene expression data is straightforward. Thus, TBro is a fully featured yet flexible transcriptome browser that supports approaching complex biological questions and enhances collaboration of numerous researchers. Database URL: tbro.carnivorom.com PMID:28025338

  19. Insights into transcriptomes of big and low sagebrush.

    Directory of Open Access Journals (Sweden)

    Mark D Huynh

    Full Text Available We report the sequencing and assembly of three transcriptomes from Big (Artemisia tridentata ssp. wyomingensis and A. tridentata ssp. tridentata and Low (A. arbuscula ssp. arbuscula sagebrush. The sequence reads are available in the Sequence Read Archive of NCBI. We demonstrate the utilities of these transcriptomes for gene discovery and phylogenomic analysis. An assembly of 61,883 transcripts followed by transcript identification by the program TRAPID revealed 16 transcripts directly related to terpene synthases, proteins critical to the production of multiple secondary metabolites in sagebrush. A putative terpene synthase was identified in two of our sagebrush samples. Using paralogs with synonymous mutations we reconstructed an evolutionary time line of ancient genome duplications. By applying a constant mutation rate to the data we estimate that these three ancient duplications occurred about 18, 34 and 60 million years ago. These transcriptomes offer a foundation for future studies of sagebrush, including inferences in chemical defense and the identification of species and subspecies of sagebrush for restoration and preservation of the threatened sage-grouse.

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

    Science.gov (United States)

    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.

  1. Transcriptome kinetics of circulating neutrophils during human experimental endotoxemia.

    Directory of Open Access Journals (Sweden)

    Stan de Kleijn

    Full Text Available Polymorphonuclear cells (neutrophils play an important role in the systemic inflammatory response syndrome and the development of sepsis. These cells are essential for the defense against microorganisms, but may also cause tissue damage. Therefore, neutrophil numbers and activity are considered to be tightly regulated. Previous studies have investigated gene transcription during experimental endotoxemia in whole blood and peripheral blood mononuclear cells. However, the gene transcription response of the circulating pool of neutrophils to systemic inflammatory stimulation in vivo is currently unclear. We examined neutrophil gene transcription kinetics in healthy human subjects (n = 4 administered a single dose of endotoxin (LPS, 2 ng/kg iv. In addition, freshly isolated neutrophils were stimulated ex vivo with LPS, TNFα, G-CSF and GM-CSF to identify stimulus-specific gene transcription responses. Whole transcriptome microarray analysis of circulating neutrophils at 2, 4 and 6 hours after LPS infusion revealed activation of inflammatory networks which are involved in signaling of TNFα and IL-1α and IL-1β. The transcriptome profile of inflammatory activated neutrophils in vivo reflects extended survival and regulation of inflammatory responses. These changes in neutrophil transcriptome suggest a combination of early activation of circulating neutrophils by TNFα and G-CSF and a mobilization of young neutrophils from the bone marrow.

  2. The Healthy Infant Nasal Transcriptome: A Benchmark Study

    Science.gov (United States)

    Chu, Chin-Yi; Qiu, Xing; Wang, Lu; Bhattacharya, Soumyaroop; Lofthus, Gerry; Corbett, Anthony; Holden-Wiltse, Jeanne; Grier, Alex; Tesini, Brenda; Gill, Steven R.; Falsey, Ann R.; Caserta, Mary T.; Walsh, Edward E.; Mariani, Thomas J.

    2016-01-01

    Responses by resident cells are likely to play a key role in determining the severity of respiratory disease. However, sampling of the airways poses a significant challenge, particularly in infants and children. Here, we report a reliable method for obtaining nasal epithelial cell RNA from infants for genome-wide transcriptomic analysis, and describe baseline expression characteristics in an asymptomatic cohort. Nasal epithelial cells were collected by brushing of the inferior turbinates, and gene expression was interrogated by RNA-seq analysis. Reliable recovery of RNA occurred in the absence of adverse events. We observed high expression of epithelial cell markers and similarity to the transcriptome for intrapulmonary airway epithelial cells. We identified genes displaying low and high expression variability, both inherently, and in response to environmental exposures. The greatest gene expression differences in this asymptomatic cohort were associated with the presence of known pathogenic viruses and/or bacteria. Robust bacteria-associated gene expression patterns were significantly associated with the presence of Moraxella. In summary, we have developed a reliable method for interrogating the infant airway transcriptome by sampling the nasal epithelium. Our data demonstrates both the fidelity and feasibility of our methodology, and describes normal gene expression and variation within a healthy infant cohort. PMID:27658638

  3. De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2015-12-01

    Full Text Available Sour cherry (Prunus cerasus in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170. De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing.

  4. Nuclear RNA sequencing of the mouse erythroid cell transcriptome.

    Directory of Open Access Journals (Sweden)

    Jennifer A Mitchell

    Full Text Available In addition to protein coding genes a substantial proportion of mammalian genomes are transcribed. However, most transcriptome studies investigate steady-state mRNA levels, ignoring a considerable fraction of the transcribed genome. In addition, steady-state mRNA levels are influenced by both transcriptional and posttranscriptional mechanisms, and thus do not provide a clear picture of transcriptional output. Here, using deep sequencing of nuclear RNAs (nucRNA-Seq in parallel with chromatin immunoprecipitation sequencing (ChIP-Seq of active RNA polymerase II, we compared the nuclear transcriptome of mouse anemic spleen erythroid cells with polymerase occupancy on a genome-wide scale. We demonstrate that unspliced transcripts quantified by nucRNA-seq correlate with primary transcript frequencies measured by RNA FISH, but differ from steady-state mRNA levels measured by poly(A-enriched RNA-seq. Highly expressed protein coding genes showed good correlation between RNAPII occupancy and transcriptional output; however, genome-wide we observed a poor correlation between transcriptional output and RNAPII association. This poor correlation is due to intergenic regions associated with RNAPII which correspond with transcription factor bound regulatory regions and a group of stable, nuclear-retained long non-coding transcripts. In conclusion, sequencing the nuclear transcriptome provides an opportunity to investigate the transcriptional landscape in a given cell type through quantification of unspliced primary transcripts and the identification of nuclear-retained long non-coding RNAs.

  5. Integrated transcriptomic and proteomic evaluation of gentamicin nephrotoxicity in rats

    Energy Technology Data Exchange (ETDEWEB)

    Com, Emmanuelle, E-mail: emmanuelle.com@univ-rennes1.fr [sanofi-aventis R and D, Disposition Safety and Animal Research, Vitry-sur-Seine (France); INSERM U625, Proteomics Core Facility Biogenouest, Rennes (France); Boitier, Eric; Marchandeau, Jean-Pierre [sanofi-aventis R and D, Disposition Safety and Animal Research, Vitry-sur-Seine (France); Brandenburg, Arnd [Genedata AG, Basel (Switzerland); Schroeder, Susanne [Nycomed GmbH, Barsbüttel (Germany); Hoffmann, Dana; Mally, Angela [University of Würzburg, Department of Toxicology, University of Würzburg, Würzburg (Germany); Gautier, Jean-Charles [sanofi-aventis R and D, Disposition Safety and Animal Research, Vitry-sur-Seine (France)

    2012-01-01

    Gentamicin is an aminoglycoside antibiotic, which induces renal tubular necrosis in rats. In the context of the European InnoMed PredTox project, transcriptomic and proteomic studies were performed to provide new insights into the molecular mechanisms of gentamicin-induced nephrotoxicity. Male Wistar rats were treated with 25 and 75 mg/kg/day subcutaneously for 1, 3 and 14 days. Histopathology observations showed mild tubular degeneration/necrosis and regeneration and moderate mononuclear cell infiltrate after long-term treatment. Transcriptomic data indicated a strong treatment-related gene expression modulation in kidney and blood cells at the high dose after 14 days of treatment, with the regulation of 463 and 3241 genes, respectively. Of note, the induction of NF-kappa B pathway via the p38 MAPK cascade in the kidney, together with the activation of T-cell receptor signaling in blood cells were suggestive of inflammatory processes in relation with the recruitment of mononuclear cells in the kidney. Proteomic results showed a regulation of 163 proteins in kidney at the high dose after 14 days of treatment. These protein modulations were suggestive of a mitochondrial dysfunction with impairment of cellular energy production, induction of oxidative stress, an effect on protein biosynthesis and on cellular assembly and organization. Proteomic results also provided clues for potential nephrotoxicity biomarkers such as AGAT and PRBP4 which were strongly modulated in the kidney. Transcriptomic and proteomic data turned out to be complementary and their integration gave a more comprehensive insight into the putative mode of nephrotoxicity of gentamicin which was in accordance with histopathological findings. -- Highlights: ► Gentamicin induces renal tubular necrosis in rats. ► The mechanisms of gentamicin nephrotoxicity remain still elusive. ► Transcriptomic and proteomic analyses were performed to study this toxicity in rats. ► Transcriptomic and proteomic

  6. TRAF5 is a downstream target of MAVS in antiviral innate immune signaling.

    Directory of Open Access Journals (Sweden)

    Eric D Tang

    Full Text Available The recognition of nucleic acids by the innate immune system during viral infection results in the production of type I interferons and the activation of antiviral immune responses. The RNA helicases RIG-I and MDA-5 recognize distinct types of cytosolic RNA species and signal through the mitochondrial protein MAVS to stimulate the phosphorylation and activation of the transcription factors IRF3 and IRF7, thereby inducing type I interferon expression. Alternatively, the activation of NF-kappaB leads to proinflammatory cytokine production. The function of MAVS is dependent on both its C-terminal transmembrane (TM domain and N-terminal caspase recruitment domain (CARD. The TM domain mediates MAVS dimerization in response to viral RNA, allowing the CARD to bind to and activate the downstream effector TRAF3. Notably, dimerization of the MAVS CARD alone is sufficient to activate IRF3, IRF7, and NF-kappaB. However, TRAF3-deficient cells display only a partial reduction in interferon production in response to RNA virus infection and are not defective in NF-kappaB activation. Here we find that the related ubiquitin ligase TRAF5 is a downstream target of MAVS that mediates both IRF3 and NF-kappaB activation. The TM domain of MAVS allows it to dimerize and thereby associate with TRAF5 and induce its ubiquitination in a CARD-dependent manner. Also, NEMO is recruited to the dimerized MAVS CARD domain in a TRAF3 and TRAF5-dependent manner. Thus, our findings reveal a possible function for TRAF5 in mediating the activation of IRF3 and NF-kappaB downstream of MAVS through the recruitment of NEMO. TRAF5 may be a key molecule in the innate response against viral infection.

  7. Isotopic Composition of Inorganic Mercury and Methylmercury Downstream of a Historical Gold Mining Region.

    Science.gov (United States)

    Donovan, Patrick M; Blum, Joel D; Singer, Michael Bliss; Marvin-DiPasquale, Mark; Tsui, Martin T K

    2016-02-16

    We measured total mercury (THg) and monomethyl mercury (MMHg) concentrations and mercury (Hg) isotopic compositions in sediment and aquatic organisms from the Yuba River (California, USA) to identify Hg sources and biogeochemical transformations downstream of a historical gold mining region. Sediment THg concentrations and δ(202)Hg decreased from the upper Yuba Fan to the lower Yuba Fan and the Feather River. These results are consistent with the release of Hg during gold mining followed by downstream mixing and dilution. The Hg isotopic composition of Yuba Fan sediment (δ(202)Hg = -0.38 ± 0.17‰ and Δ(199)Hg = 0.04 ± 0.03‰; mean ± 1 SD, n = 7) provides a fingerprint of inorganic Hg (IHg) that could be methylated locally or after transport downstream. The isotopic composition of MMHg in the Yuba River food web was estimated using biota with a range of %MMHg (the percent of THg present as MMHg) and compared to IHg in sediment, algae, and the food web. The estimated δ(202)Hg of MMHg prior to photodegradation (-1.29 to -1.07‰) was lower than that of IHg and we suggest this is due to mass-dependent fractionation (MDF) of up to -0.9‰ between IHg and MMHg. This result is in contrast to net positive MDF (+0.4 to +0.8‰) previously observed in lakes, estuaries, coastal oceans, and forests. We hypothesize that this unique relationship could be due to differences in the extent or pathway of biotic MMHg degradation in stream environments.

  8. Interaction of circular cylinder wake with a short asymmetrically located downstream plate

    Science.gov (United States)

    Yucel, S. B.; Cetiner, O.; Unal, M. F.

    2010-07-01

    This study reveals the interaction patterns of separated shear layers from a circular cylinder with a short downstream plate and their reflection on the frequency and the formation length of the vortices from the cylinder as a function of plate location relative to the cylinder. The effect of horizontal ( G/D) and vertical ( Z/D) distances between the cylinder and the plate on the near wake is studied via Digital Particle Image Velocimetry (DPIV) in a water channel for Reynolds numbers of 200, 400 and 750, based on the cylinder diameter D. It is shown that the interaction of wake with the plate of length D can be categorized depending on the horizontal and the vertical distances between the cylinder and the plate. For the vertical distance range of Z/D ≤ 0.7, there is a critical horizontal spacing before which the shear layers from the cylinder are inhibited to form vortices in front of the plate. Resulting elongated recirculation region between the plate and the cylinder suggests modification of the absolutely unstable near wake of free circular cylinder in favor of convective instability. Z/D = 0.9 provides a passage from Z/D ≤ 0.7 to ≥1.1 and is associated with a dominant effect on the near-wake characteristics of interaction of shear layers from the cylinder with those from the downstream plate. For Z/D ≥ 1.1, there is again, yet a smaller critical horizontal spacing after which vortices interact with decreased downstream plate interference. In this vertical separation distance range, a gap flow between the plate and the cylinder plays a determining role on the formation length and St number of vortices for small horizontal spacing values.

  9. Isotopic composition of inorganic mercury and methylmercury downstream of a historical gold mining region

    Science.gov (United States)

    Donovan, Patrick M.; Blum, Joel D.; Singer, Michael B.; Marvin-DiPasquale, Mark C.; Tsui, Martin T.K.

    2016-01-01

    We measured total mercury (THg) and monomethyl mercury (MMHg) concentrations and mercury (Hg) isotopic compositions in sediment and aquatic organisms from the Yuba River (California, USA) to identify Hg sources and biogeochemical transformations downstream of a historical gold mining region. Sediment THg concentrations and δ202Hg decreased from the upper Yuba Fan to the lower Yuba Fan and the Feather River. These results are consistent with the release of Hg during gold mining followed by downstream mixing and dilution. The Hg isotopic composition of Yuba Fan sediment (δ202Hg = −0.38 ± 0.17‰ and Δ199Hg = 0.04 ± 0.03‰; mean ± 1 SD, n = 7) provides a fingerprint of inorganic Hg (IHg) that could be methylated locally or after transport downstream. The isotopic composition of MMHg in the Yuba River food web was estimated using biota with a range of %MMHg (the percent of THg present as MMHg) and compared to IHg in sediment, algae, and the food web. The estimated δ202Hg of MMHg prior to photodegradation (−1.29 to −1.07‰) was lower than that of IHg and we suggest this is due to mass-dependent fractionation (MDF) of up to −0.9‰ between IHg and MMHg. This result is in contrast to net positive MDF (+0.4 to +0.8‰) previously observed in lakes, estuaries, coastal oceans, and forests. We hypothesize that this unique relationship could be due to differences in the extent or pathway of biotic MMHg degradation in stream environments.

  10. On the electron temperature downstream of the solar wind termination shock

    Directory of Open Access Journals (Sweden)

    I. V. Chashei

    2013-07-01

    Full Text Available In this paper we study the temperatures of electrons convected with the solar wind to large solar distances and finally transported over the solar wind termination shock. Nearly nothing, unless at high energies in the cosmic ray regime, is known about the thermodynamical behaviour of these distant electrons from in~situ plasma observations. Hence it is tacitly assumed these electrons, due to their adiabatic behaviour and vanishing heat conduction or energization processes, have rapidly cooled off to very low temperatures once they eventually arrive at the solar wind termination shock (at about 100 AU. In this paper we show that such electrons, however, at their passage over the termination shock due to the shock–electric field action undergo an over-adiabatic heating and therefore appear on the downstream side as a substantially heated plasma species. Looking quantitatively into this heating process we find that solar wind electrons achieve temperatures of the order of 2–4 × 106 K downstream of the termination shock, depending on the upstream solar wind bulk velocity and the shock compression ratio. Hence these electrons therewith play an important dynamical role in structuring this shock and determining the downstream plasma flow properties. Furthermore, they present an additional ionization source for incoming neutral interstellar hydrogen and excite X-ray emission. They also behave similar to cosmic ray electrons and extend to some limited region upstream of the shock of the order of 0.1 AU by spatial diffusion and thereby also modify the upstream solar wind properties.

  11. Water discharge changes of the Changjiang River downstream Datong during dry season

    Institute of Scientific and Technical Information of China (English)

    CHENXiqing; WANGXiaoli; ZHANGErfeng

    2003-01-01

    Based on hydrometric data and extensive investigations on water-extracting projects, this paper presents a preliminary study on water discharge changes between Datong and Xuliujing during dry season. The natural hydrological processes and human factors that influence the water discharge are analyzed with the help of GIS method. The investigations indicate that the water-extracting projects downstream from Datong to Xuliujing had amounted to 64 in number by the end of 2000,with a water-extracting capacity up to 4,626 m3/s averaged in a tidal cycle. The water extraction from the Changjiang River has become the most important factor influencing the water discharge downstream Datong during dry season. The potential magnitude in water discharge changes are estimated based on historical records of water extraction and a water balance model. The computational results were calibrated with the actual data. The future trend in changes of water discharge into the sea during dry season was discussed by taking into consideration of newly built hydro-engineering projects. The water extraction downstream Datong in dry season before 2000 had a great influence on discharges into the sea in the extremely dry year like 1978-1979. It produced a net decrease of more than 490 m3/s in monthly mean discharges from the Changjiang into the sea. It is expected that the water extraction will continually increase in the coming decades, especially in dry years, when the net decrease in monthly mean water discharge will increase to more than 1000 m3/s and will give a far-reaching effect on the changes of water discharge from the Changjiang into the sea.

  12. Modelling landslide-generated tsunami: from landslide propagation to downstream flood in dam context

    Science.gov (United States)

    Franz, Martin; Podladchikov, Yury; Humair, Florian; Matasci, Battista; Jaboyedoff, Michel

    2015-04-01

    Alpine regions have a high density of dammed lakes, either natural or anthropogenic. Those are frequently surrounded by steep slopes and thus, are potentially affected by mass wasting processes. The penetration of landsliding material in the water body may lead to impulse waves that could overtop the dam and, in the worst case scenario, breach or break the latter. The possible resulting outburst flood is a serious threat for populated places, commonly concentrated downstream in the valleys. In order to assess the risk resulting from the succession of all phenomenon, a numerical model able to handle all of them is required. Although specific models of flooding simulation or wave propagation are efficient, there is currently no fully achieved model capable to integrate all the above-mentioned processes at the same time. In order to address this, we propose a new model capable to handle these difficult combinations and which is suitable for risk assessment in dam contexts. Our model is based on both the shallow water equations and viscous flow equations. The first ones are stabilised by the Lax-Friedrichs scheme and compute the wave propagation and the downstream flow, i.e. the wet state. The viscous flow equations are used for the dry state and to propagate the landslide body. The transition from one state to the other is ruled by a threshold based on the Reynolds number. First, in order to test the capacity of our model to endure critical situations, we conducted numerical sandbox tests such as Riemann problems, dam break, and landslide tsunami-related ones in 2 dimensions. In a second time, the model is applied on a real case study: the Oeschinen Lake (Switzerland). This naturally dammed lake is specifically selected since it is potentially affected by all above-mentioned phenomenon, including landsliding, wave generation, wave propagation in the water body and on the shore as well as the downstream flooding. Results show that the municipality of Kandersteg

  13. Flow interaction between a streamwise oscillating cylinder and a downstream stationary cylinder

    Science.gov (United States)

    Xu, S. J.; Gan, L.; Zhou, Y.

    2016-11-01

    In this paper, we present some experimental results about the physical effects of a cylinder's streamwise oscillation motion on a downstream one in a tandem arrangement. The upstream cylinder undergoes a controlled simple harmonic oscillation at amplitudes A/ d = 0.2-0.8, where d is the cylinder diameter, and the frequency ratio of f_e/f_s = 0-3.0, where f_e is the cylinder oscillation frequency and f_s is the natural frequency of vortex shedding from a single stationary cylinder. Under these conditions, the vortex shedding is locked to the controlled oscillation motion. Flow visualisation using the planar laser-induced fluorescence and qualitative measurements using hot-wire anemometry reveal three distinct flow regimes behind the downstream cylinder. For f_e/f_s > (f_e/f_s)_c, where (f_e/f_s)_c is a critical frequency ratio which depends on A/ d and Reynolds number Re, a so-called SA-mode occurs. The upstream oscillating cylinder generates binary vortices symmetrically arranged about the centreline, each containing a pair of counter-rotating vortices, and the downstream cylinder sheds vortices alternately at 0.5f_e. For 0.7-1.0 < f_e/f_s < (f_e/f_s)_c a complex vortex street that consists of two outer rows of vortices generated by the oscillating cylinder and two inner rows of vortices shed from the downstream stationary cylinder, which is referred to as AA-mode. For 0.3-0.6 < f_e/f_s< 0.8-1.0, one single staggered vortex street (A-mode) is observed. It is also found that, when f_e/f_s is near unity, the streamwise interaction of the two cylinders gives rise to the most energetic wake in the cross-stream direction, in terms of its maximum width, and the wake is AA-mode-like. The effects of other parameters such as the spacing between the two cylinders, Re and A/ d on the flow pattern are also discussed in details. The observations are further compared to the stationary tandem cylinder cases.

  14. Double scouring by turbulent jets downstream of a submerged sluice gate

    CERN Document Server

    Bove, I; Gutiérreza, N; Gutiérreza, V; Sarasúa, L G

    2013-01-01

    In this work we study the scour produced by a jet downstream of a submerged sluice gate on a sediment bed of non-cohesive particles. The experiments were performed for various values of sill heights and {\\deg}uid depths. New regimes were observed in which two holes are simultaneously developed. We identify the origins of the two holes and show that they are produced by different scouring mechanisms. The dependence of the position of the holes with the approach {\\deg}uid depth and the gate opening were studied and expressed in terms of adequate non-dimensional numbers.

  15. European downstream oil industry safety performance. Statistical summary of reported incidents - 2012

    Energy Technology Data Exchange (ETDEWEB)

    Burton, A. [Awaken Consulting, Shropshire, Herefordshire (United Kingdom); Den Haan, K.H.

    2013-08-15

    In this nineteenth annual report on European downstream oil industry safety performance, 2012 statistics are presented on work-related personal injuries for the industry's own employees and contractors. Data were received from 38 CONCAWE Member Companies representing approximately 98% of the European refining capacity. Trends over the last nineteen years are also highlighted and the data are compared to similar statistics from related industries. This report also presents the fourth year of results for Process Safety Performance Indicators from CONCAWE members.

  16. European downstream oil industry safety performance. Statistical summary of reported incidents - 2011

    Energy Technology Data Exchange (ETDEWEB)

    Burton, A. [Awaken Consulting, Shropshire, Herefordshire (United Kingdom); Den Haan, K.H.

    2012-07-15

    In this eighteenth annual report on European downstream oil industry safety performance, 2011 statistics are presented on work-related personal injuries for the industry's own employees and contractors. Data were received from 34 CONCAWE Member Companies representing approximately 96% of the European refining capacity. Trends over the last eighteen years are also highlighted and the data are compared to similar statistics from related industries. This report also presents the third year of results for Process Safety Performance Indicators from CONCAWE members.

  17. ASYMPTOTIC ANALYSIS OF DOWNSTREAM EIGENVALUES FOR STATIONARY PERTURBATION OF COUETTE-POISEUILLE FLOW

    Institute of Scientific and Technical Information of China (English)

    Song Jin-bao; Wei En-bo; Tian Ji-wei

    2003-01-01

    Two-dimensional viscous flow in a straight channel was studied. The steady Navier-Stokes equations were linearized on the assumption of small disurbance from the Couette-Poiseuille flow, leading to an eigenvalue equation resembling the Orr-Sommerfeld equation. The eigenvalues determine the rate of decay for the stationary perturbation. Asymptotic forms of the downstream eigenvalues were derived in the limiting cases of small and large Reynolds number, for the flow with a general mass flux per unit width, and thus the work of Wilson (1969) and Stocker and Duck (1995) was generalized. The asymptotic results are in agreement with numerical ones presented by Song and Chen (1995).

  18. Heavy Solar Wind Ion Dynamics at and Downstream from the Bow Shock

    Science.gov (United States)

    Dougherty, Virginia M.

    1997-01-01

    This is a contract under the NASA Supporting Research and Technology Program for the analysis and interpretation of the scientific data from the Plasma Composition Experiment on the International Sun Earth Explorer 1 (ISEE-1) spacecraft and the Fast Plasma Experiment on the ISEE-1 and -2 spacecraft. These combined data sets will be used in a comprehensive study of the heavy solar wind ion dynamics at and downstream from the Earth's bow shock. The report summarizes activities during the above period and outlines expected activities during the forthcoming quarter.

  19. Natural gas engineering and safety challenges downstream process, analysis, utilization and safety

    CERN Document Server

    Nasr, GG

    2014-01-01

    Provides a critical and extensive compilation of the downstream processes of natural gas that involve the principle of gas processing , transmission and distribution, gas flow and network analysis, instrumentation and measurement systems and its utilisation Enriches understanding of the business and management aspects of natural gas as well as highlighting some of the recent research and innovations in the field Covers the needs of practising engineers from different disciplines, who may include project managers, planning and design engineers - the book is also suitable for the demands of u

  20. Estimating Subcatchment Runoff Coefficients using Weather Radar and a Downstream Runoff Sensor

    DEFF Research Database (Denmark)

    Ahm, Malte; Thorndahl, Søren Liedtke; Rasmussen, Michael R.;

    2013-01-01

    This paper presents a method for estimating runoff coefficients of urban drainage subcatchments based on a combination of high resolution weather radar data and flow measurements from a downstream runoff sensor. By utilising the spatial variability of the precipitation it is possible to estimate...... the runoff coefficients of the separate subcatchments. The method is demonstrated through a case study of an urban drainage catchment (678 ha) located in the city of Aarhus, Denmark. The study has proven that it is possible to use corresponding measurements of the relative rainfall distribution over...

  1. A Case Study on the Role of Water Vapor from Southwest China in Downstream Heavy Rainfall

    Institute of Scientific and Technical Information of China (English)

    PAN Yang; YU Rucong; LI Jian; XU Youping

    2008-01-01

    Based on the observation data analysis and numerical simulation, the development of an eastward- moving vortex generated in Southwest China during the period 25-27 June 2003 is studied. The water vapor budget analysis indicates that water vapor in the lower troposphere over Southwest China is transported downstream to the Yangtze and Huaihe River valleys by the southwesterly winds south of the vortex center. A potential vorticity (PV) budget analysis reveals that a positive feedback between latent heat release and low-level positive vorticity plays a vital role in the sudden development and eastward movement of the vortex. Numerical simulations are consistent with these results.

  2. Characterization of adult transcriptomes from the omnivorous lady beetle Coleomegilla maculata fed pollen or insect Egg Diet

    Science.gov (United States)

    32 reference transcriptome sequences described herein are filed with the National Center for Biotechnology Information (NCBI), GenBank Bioproject PRJNA236444. Transcriptome Shotgun Assembly (TSA) will also be submitted when upload instructions are received from gb-admin....

  3. Detection of driver protein complexes in breast cancer metastasis by large-scale transcriptome-interactome integration.

    Science.gov (United States)

    Garcia, Maxime; Finetti, Pascal; Bertucci, Francois; Birnbaum, Daniel; Bidaut, Ghislain

    2014-01-01

    With the development of high-throughput gene expression profiling technologies came the opportunity to define genomic signatures predicting clinical condition or cancer patient outcome. However, such signatures show dependency on training set, lack of generalization, and instability, partly due to microarray data topology. Additional issues for analyzing tumor gene expression are that subtle molecular perturbations in driver genes leading to cancer and metastasis (masked in typical differential expression analysis) may provoke expression changes of greater amplitude in downstream genes (easily detected). In this chapter, we are describing an interactome-based algorithm, Interactome-Transcriptome Integration (ITI) that is used to find a generalizable signature for prediction of breast cancer relapse by superimposition of a large-scale protein-protein interaction data (human interactome) over several gene expression datasets. ITI extracts regions in the interactome whose expression is discriminating for predicting relapse-free survival in cancer and allow detection of subnetworks that constitutes a generalizable and stable genomic signature. In this chapter, we describe the practical aspects of running the full ITI pipeline (subnetwork detection and classification) on six microarray datasets.

  4. Exploration of FoxM1 and downstream related target molecule expression in cervical cancer tissue

    Institute of Scientific and Technical Information of China (English)

    Yi-Chong Yuan; QiongYang

    2016-01-01

    Objective:To study the expression of FoxM1 and downstream related target molecules in cervical cancer tissue.Methods:Cervical cancer tissue and normal cervical tissue were collected to detect the expression of FoxM1, proliferation-related genes (CDK6 and CDK8) and angiogenesis-related genes (VEGFA, VEGFB and VEGFC); Hela cells were cultured and transfected with FoxM1 siRNA, and then expression of CDK6, CDK8, VEGFA, VEGFB and VEGFC were detected.Results:mRNA contents of FoxM1, CDK6, CDK8, VEGFA, VEGFB and VEGFC in cervical cancer tissue were significantly higher than those in normal cervical tissue; mRNA content of FoxM1 was positively correlated with mRNA contents of CDK6, CDK8, VEGFA, VEGFB and VEGFC; mRNA contents of CDK6, CDK8, VEGFA, VEGFB and VEGFC of FoxM1-siRNA group were significantly lower than those of negative control-siRNA group.Conclusion:FoxM1 expression abnormally increases in cervical cancer tissue, and its downstream target genes include CDK6, CDK8, VEGFA, VEGFB and VEGFC.

  5. RIGID GIGAPOROUS CHROMATOGRAPHIC MEDIA AND THEIR POTENTIAL IMPACT ON DOWNSTREAM PROCESSING

    Institute of Scientific and Technical Information of China (English)

    Tingyue Gu; Weiqing Zhou; Guanghui Ma; Zhiguo Su

    2005-01-01

    More and more biomolecules are being produced by the biotechnology industry for applications ranging from medicine and food to engineering materials. Liquid chromatography plays a center-stage role in a typical downstream process producing biomolecules such as recombinant proteins. Rigid gigaporous media are porous particles possessing large transecting through-pores with a pore-to-particle diameter ratio of dpore/dparticle> 0.01. They allow convective flow in the large through-pores, while the smaller diffusion-pores (typically several hundred angstroms in size) supply the needed surface areas. Because of the transecting gigapores, a portion of the mobile phase flows through the pores in addition to fluid flow in the interstitial spaces between the particles in a packed-bed column. This considerably lowers the operating column pressure drop. This lower pressure drop makes axial-direction scale-up of chromatographic columns possible to avoid pancake columns that invariably degrade separation resolution. The large gigapores also make the binding sites on the diffusion pore surfaces more accessible, thus increasing the loading capacity of large protein molecules that can be hindered sterically if only diffusion pores are present. This work discusses the development of rigid gigaporous media and their potential impact on the design of multi-stage downstream process from the angle of multi-scale analysis.

  6. Proteomics analysis of cellular imatinib targets and their candidate downstream effectors.

    Science.gov (United States)

    Breitkopf, Susanne B; Oppermann, Felix S; Keri, Gyorgy; Grammel, Markus; Daub, Henrik

    2010-11-05

    Inhibition of deregulated protein kinases by small molecule drugs has evolved into a major therapeutic strategy for the treatment of human malignancies. Knowledge about direct cellular targets of kinase-selective drugs and the identification of druggable downstream mediators of oncogenic signaling are relevant for both initial therapy selection and the nomination of alternative targets in case molecular resistance emerges. To address these issues, we performed a proof-of-concept proteomics study designed to monitor drug effects on the pharmacologically tractable subproteome isolated by affinity purification with immobilized, nonselective kinase inhibitors. We applied this strategy to chronic myeloid leukemia cells that express the transforming Bcr-Abl fusion kinase. We used SILAC to measure how cellular treatment with the Bcr-Abl inhibitor imatinib affects protein binding to a generic kinase inhibitor resin and further quantified site-specific phosphorylations on resin-retained proteins. Our integrated approach indicated additional imatinib target candidates, such as flavine adenine dinucleotide synthetase, as well as repressed phosphorylation events on downstream effectors not yet implicated in imatinib-regulated signaling. These included activity-regulating phosphorylations on the kinases Btk, Fer, and focal adhesion kinase, which may qualify them as alternative target candidates in Bcr-Abl-driven oncogenesis. Our approach is rather generic and may have various applications in kinase drug discovery.

  7. Discovery and characterization of novel vascular and hematopoietic genes downstream of etsrp in zebrafish.

    Directory of Open Access Journals (Sweden)

    Gustavo A Gomez

    Full Text Available The transcription factor Etsrp is required for vasculogenesis and primitive myelopoiesis in zebrafish. When ectopically expressed, etsrp is sufficient to induce the expression of many vascular and myeloid genes in zebrafish. The mammalian homolog of etsrp, ER71/Etv2, is also essential for vascular and hematopoietic development. To identify genes downstream of etsrp, gain-of-function experiments were performed for etsrp in zebrafish embryos followed by transcription profile analysis by microarray. Subsequent in vivo expression studies resulted in the identification of fourteen genes with blood and/or vascular expression, six of these being completely novel. Regulation of these genes by etsrp was confirmed by ectopic induction in etsrp overexpressing embryos and decreased expression in etsrp deficient embryos. Additional functional analysis of two newly discovered genes, hapln1b and sh3gl3, demonstrates their importance in embryonic vascular development. The results described here identify a group of genes downstream of etsrp likely to be critical for vascular and/or myeloid development.

  8. Bmx is a downstream Rap1 effector in VEGF-induced endothelial cell activation.

    Science.gov (United States)

    Stoletov, Konstantin V; Terman, Bruce I

    2004-07-16

    We had previously shown that Rap1 mediates certain of the signaling pathways involved in VEGF-induced endothelial cell migration, although the downstream Rap1 effectors are not known. Towards the goal of identifying those effectors, we utilized a commercially available antibody array filter to identify proteins that either directly interact with Rap1 or interact indirectly through a multi-protein complex. The protocol identified 10 possible Rap1-interacting proteins, including the Bmx non-receptor tyrosine kinase. The conclusion that VEGF treatment leads to a Rap1/Bmx complex was confirmed by an experiment in which cell lysates from VEGF and control cells were immunoprecipitated with Bmx antibodies and Western blotting was done using anti-Rap1 antibodies. VEGF treatment led to the recruitment of Bmx to the CAS scaffolding protein, and inhibition of the Bmx kinase blocked VEGF-induced cell migration. Formation of a Rap1/Bmx complex was not observed in cells transfected with an expression vector for a dominant-negative Rap1, indicating that Bmx is a downstream Rap1 effector in VEGF-induced endothelial cell activation.

  9. Effect of boundary conditions on downstream vorticity from counter-rotating swirlers

    Institute of Scientific and Technical Information of China (English)

    Huo Weiye; Lin Yuzhen; Zhang Chi; Sung Chih-Jen

    2015-01-01

    Particle image velocimetry (PIV) is utilized to measure the non-reacting flow field in a reflow combustor with multiple and single swirlers. The velocity field, vortex structure and total vorticity levels are experimentally obtained using two different boundary conditions, representing a single confined swirler and multiple swirlers in an annular combustor. The influence of the bound-ary conditions on the flow field at several locations downstream of the swirlers is experimentally investigated, showing that the central vortex in the multi-swirler case is more concentrated than in the single-swirler case. The vorticity of the central vortex and average cross-sectional vorticity are relatively low at the swirler outlet in both cases. Both of these statistics gradually increase to the maximum values near 20 mm downstream of the swirler outlet, and subsequently decrease. It is also found that the central vortex in the multi-swirler case is consistently greater than the sin-gle-swirler case. These results demonstrate the critical influence of boundary conditions on flow characteristic of swirling flow, providing insight into the difference of the experiments on test-bed combustor and the full-scale annular combustors.

  10. Evaluating lignocellulosic biomass, its derivatives, and downstream products with Raman spectroscopy.

    Science.gov (United States)

    Lupoi, Jason S; Gjersing, Erica; Davis, Mark F

    2015-01-01

    The creation of fuels, chemicals, and materials from plants can aid in replacing products fabricated from non-renewable energy sources. Before using biomass in downstream applications, it must be characterized to assess chemical traits, such as cellulose, lignin, or lignin monomer content, or the sugars released following an acid or enzymatic hydrolysis. The measurement of these traits allows researchers to gage the recalcitrance of the plants and develop efficient deconstruction strategies to maximize yields. Standard methods for assessing biomass phenotypes often have experimental protocols that limit their use for screening sizeable numbers of plant species. Raman spectroscopy, a non-destructive, non-invasive vibrational spectroscopy technique, is capable of providing qualitative, structural information and quantitative measurements. Applications of Raman spectroscopy have aided in alleviating the constraints of standard methods by coupling spectral data with multivariate analysis to construct models capable of predicting analytes. Hydrolysis and fermentation products, such as glucose and ethanol, can be quantified off-, at-, or on-line. Raman imaging has enabled researchers to develop a visual understanding of reactions, such as different pretreatment strategies, in real-time, while also providing integral chemical information. This review provides an overview of what Raman spectroscopy is, and how it has been applied to the analysis of whole lignocellulosic biomass, its derivatives, and downstream process monitoring.

  11. Expected signal for the TBID and the ionization chambers downstream of the CNGS target station

    CERN Document Server

    Sarchiapone, L; Gschwendtner, E; Lorenzo-Sentis, M

    2006-01-01

    Downstream of the carbon graphite target of the CNGS (CERN Neutrinos to Gran Sasso) facility at CERN a secondary emission monitor called TBID (Target Beam Instrumentation Downstream) is installed to measure the multiplicities and the left/right as well as up/down asymmetries of secondary particles from the target. Calculations show that the titanium windows used to close off the TBID vacuum tank might not withstand the highest beam intensities with small spot sizes expected at CNGS, in case the proton beam accidentally misses the 4-5 mm diameter target rods. Therefore it has been suggested to place two ionisation chambers as a backup for the TBID, located left and right of the TBID monitor. Monte Carlo simulations with the particle transport code FLUKA were performed firstly to obtain the fluence of charged particles in the region of interest and secondly to estimate the induced radioactivity (background signal) in this area. This allows to assess the actual signal/noise situation and thus to determine the op...

  12. Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.

    Science.gov (United States)

    Franzén, Oscar; Ermel, Raili; Cohain, Ariella; Akers, Nicholas K; Di Narzo, Antonio; Talukdar, Husain A; Foroughi-Asl, Hassan; Giambartolomei, Claudia; Fullard, John F; Sukhavasi, Katyayani; Köks, Sulev; Gan, Li-Ming; Giannarelli, Chiara; Kovacic, Jason C; Betsholtz, Christer; Losic, Bojan; Michoel, Tom; Hao, Ke; Roussos, Panos; Skogsberg, Josefin; Ruusalepp, Arno; Schadt, Eric E; Björkegren, Johan L M

    2016-08-19

    Genome-wide association studies (GWAS) have identified hundreds of cardiometabolic disease (CMD) risk loci. However, they contribute little to genetic variance, and most downstream gene-regulatory mechanisms are unknown. We genotyped and RNA-sequenced vascular and metabolic tissues from 600 coronary artery disease patients in the Stockholm-Tartu Atherosclerosis Reverse Networks Engineering Task study (STARNET). Gene expression traits associated with CMD risk single-nucleotide polymorphism (SNPs) identified by GWAS were more extensively found in STARNET than in tissue- and disease-unspecific gene-tissue expression studies, indicating sharing of downstream cis-/trans-gene regulation across tissues and CMDs. In contrast, the regulatory effects of other GWAS risk SNPs were tissue-specific; abdominal fat emerged as an important gene-regulatory site for blood lipids, such as for the low-density lipoprotein cholesterol and coronary artery disease risk gene PCSK9 STARNET provides insights into gene-regulatory mechanisms for CMD risk loci, facilitating their translation into opportunities for diagnosis, therapy, and prevention.

  13. Charge-exchange Induced Modulation of the Heliosheath Ion Distribution Downstream of the Termination Shock

    Science.gov (United States)

    Fahr, H. J.; Fichtner, H.; Scherer, K.

    2015-12-01

    We consider the evolution of the solar wind ion distribution function alongthe plasma flow downstream from the termination shock induced by chargeexchange processes with cold interstellar H-atoms. We start from a kineticphase space transport equation valid in the bulk frame of the plasma flowthat takes into account convective changes, cooling processes, energydiffusion and ion injection, and describes solar wind and pick-up ionsas a co-moving, isotropic, joint ion population. From this kinetic transportequation one can ascend to an equation for the pressure moment of the iondistribution function, a so-called pressure transport equation, describingthe evolution of the ion pressure in the comoving rest frame. Assuming thatthe local ion distribution can be represented by an adequate kappa functionwith a kappa parameter that varies with the streamline coordinate, weobtain an ordinary differential equation for kappa as function of thestreamline coordinate s. With this result then we gain the heliosheath iondistribution function downstream of the termination shock. The latter thencan be used to predict the Voyager-2 measured moments of the distributionfunction like ion density and ion temperature, and it can also be used topredict spectral fluxes of ENA`s originating from these ions and registeredby IBEX-Hi and IBEX-Lo.We especially analyse the solar wind ion temperature decreasemeasured by Voyager-2 between the years 2008 to 2011 and try to explain itas a charge-exchange induced cooling of the ion distribution function duringthe associated ion convection period.

  14. Downstream plasma transport and metal ionization in a high-powered pulsed-plasma magnetron

    Energy Technology Data Exchange (ETDEWEB)

    Meng, Liang; Szott, Matthew M.; McLain, Jake T.; Ruzic, David N. [Center for Plasma-Materials Interactions, Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); Yu, He [Center for Plasma-Materials Interactions, Department of Nuclear, Plasma, and Radiological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 (United States); State Key Laboratory of Electronic Thin Films and Integrated Devices, School of Optoelectronic Information, University of Electronic Science and Technology of China, Chengdu 610054 (China)

    2014-06-14

    Downstream plasma transport and ionization processes in a high-powered pulsed-plasma magnetron were studied. The temporal evolution and spatial distribution of electron density (n{sub e}) and temperature (T{sub e}) were characterized with a 3D scanning triple Langmuir probe. Plasma expanded from the racetrack region into the downstream region, where a high n{sub e} peak was formed some time into the pulse-off period. The expansion speed and directionality towards the substrate increased with a stronger magnetic field (B), largely as a consequence of a larger potential drop in the bulk plasma region during a relatively slower sheath formation. The fraction of Cu ions in the deposition flux was measured on the substrate using a gridded energy analyzer. It increased with higher pulse voltage. With increased B field from 200 to 800 Gauss above racetrack, n{sub e} increased but the Cu ion fraction decreased from 42% to 16%. A comprehensive model was built, including the diffusion of as-sputtered Cu flux, the Cu ionization in the entire plasma region using the mapped n{sub e} and T{sub e} data, and ion extraction efficiency based on the measured plasma potential (V{sub p}) distribution. The calculations matched the measurements and indicated the main causes of lower Cu ion fractions in stronger B fields to be the lower T{sub e} and inefficient ion extraction in a larger pre-sheath potential.

  15. Channel erosion in a rapidly urbanizing region of Tijuana, Mexico: Enlargement downstream of channel hardpoints

    Science.gov (United States)

    Taniguchi, Kristine; Biggs, Trent; Langendoen, Eddy; Castillo, Carlos; Gudiño, Napoleon; Yuan, Yongping; Liden, Douglas

    2016-04-01

    Urban-induced erosion in Tijuana, Mexico, has led to excessive sediment deposition in the Tijuana Estuary in the United States. Urban areas in developing countries, in contrast to developed countries, are characterized by much lower proportions of vegetation and impervious surfaces due to limited access to urban services such as road paving and landscaping, and larger proportions of exposed soils. In developing countries, traditional watershed scale variables such as impervious surfaces may not be good predictors of channel enlargement. In this research, we surveyed the stream channel network of an erodible tributary of the Tijuana River Watershed, Los Laureles Canyon, at 125 locations, including repeat surveys from 2008. Structure from Motion (SfM) and 3D photo-reconstruction techniques were used to create digital terrain models of stream reaches upstream and downstream of channel hardpoints. Channels are unstable downstream of hardpoints, with incision up to 2 meters and widening up to 12 meters. Coordinated channelization is essential to avoid piece-meal approaches that lead to channel degradation. Watershed impervious area is not a good predictor of channel erosion due to the overriding importance of hardpoints and likely to the high sediment supply from the unpaved roads which prevents channel erosion throughout the stream network.

  16. Delineation of downstream signalling components during acrosome reaction mediated by heat solubilized human zona pellucida

    Directory of Open Access Journals (Sweden)

    Talwar Pankaj

    2010-01-01

    Full Text Available Abstract Background Human egg is enveloped by a glycoproteinaceous matrix, zona pellucida (ZP, responsible for binding of the human spermatozoa to the egg and induction of acrosomal exocytosis in the spermatozoon bound to ZP. In the present manuscript, attempts have been made to delineate the downstream signalling components employed by human ZP to induce acrosome reaction. Methods Heat-solubilized human ZP (SIZP was used to study the induction of acrosome reaction in capacitated human spermatozoa using tetramethylrhodamine isothiocyanate conjugated Pisum sativum agglutinin (TRITC-PSA in absence or presence of various pharmacological inhibitors. In addition, intracellular calcium ([Ca2+]i levels in sperm using Fluo-3 acetoxymethyl ester as fluorescent probe were also estimated in response to SIZP. Results SIZP induces acrosomal exocytosis in capacitated human sperm in a dose dependent manner accompanied by an increase in [Ca2+]i. Human SIZP mediated induction of acrosome reaction depends on extracellular Ca2+ and involves activation of Gi protein-coupled receptor, tyrosine kinase, protein kinases A & C and phosphoinositide 3 (PI3- kinase. In addition, T-type voltage operated calcium channels and GABA-A receptor associated chloride (Cl- channels play an important role in SIZP mediated induction of acrosome reaction. Conclusions Results described in the present study provide a comprehensive account of the various downstream signalling components associated with human ZP mediated acrosome reaction.

  17. Heavy metals in sediments of Ganga River: up- and downstream urban influences

    Science.gov (United States)

    Pandey, Jitendra; Singh, Rachna

    2015-09-01

    Bottom sediment in a river often acts as a sink and indicator of changes in water column and magnitude of anthropogenic influences through air and watersheds. Heavy metal concentration in sediments of Ganga River was studied along a 37-km stretch to assess whether there is a significant difference between sites situated upstream and downstream of Varanasi urban core. Metal concentration increased consistently along the study gradient, indicating the influence of urban sources. Concentration in the river sediment was found highest for Fe followed by Mn, Zn, Cr, Cu, Ni, Pb, and Cd. Mann-Kendall trend analysis showed marked seasonality in the concentration with values being highest in summer and lowest in rainy season. Enrichment factor revealed severe enrichment of Cd and Pb at downstream sites, and principal component analysis segregated sites into four distinct groups indicating source relationships. Concentrations of Cd, Pb, Ni, Cu, and Cr did exceed WHO standards. The study has relevance designing control measures and action plans for reducing sediment contamination in anthropogenic impacted rivers.

  18. A Versatile Control Scheme For Dynamic Voltage Restorer To Limit Downstream Fault Currents

    Directory of Open Access Journals (Sweden)

    A.Nagendra

    2014-12-01

    Full Text Available The Dynamic Voltage Restorer (DVR is a custom power device utilized to counteract voltage sags. It injects controlled three-phase ac voltages in series with the supply voltage, subsequent to voltage sag, to enhance voltage quality by adjusting the voltage magnitude, wave shape, and phase angle. The DVR is conventionally bypassed during a downstream fault to prevent potential adverse impacts on the fault and to protect the DVR components against the fault current. This paper proposes an augmented control strategy for the DVR that provides:1 voltage-sag compensation under balanced and unbalanced conditions and 2 a fault current interruption (FCI function. This paper introduces and evaluates an auxiliary control strategy for downstream fault current interruption in a radial distribution line by means of a dynamic voltage restorer (DVR. The proposed controller supplements the voltage-sag compensation control of the DVR. It does not require phaselocked loop and independently controls the magnitude and phase angle of the injected voltage for each phase. Fast least error squares digital filters are used to estimate the magnitude and phase of the measured voltages and effectively reduce the impacts of noise, harmonics, and disturbances on the estimated phasor parameters, and this enables effective fault current interrupting even under arcing fault conditions. The performance of the DVR for fault current interruption is analyzed by using MATLAB/SIMULINK software.

  19. Physiological and endocrine changes in Atlantic salmon smolts during hatchery rearing, downstream migration and ocean entry

    Science.gov (United States)

    McCormick, Stephen D.; Sheehan, Timothy F.; Björnsson, Björn Thrandur; Lipsky, Christine; Kocik, John F.; Regish, Amy M.; O'Dea, Michael F.

    2013-01-01

    Billions of hatchery salmon smolts are released annually in an attempt to mitigate anthropogenic impacts on freshwater habitats, often with limited success. Mortality of wild and hatchery fish is high during downstream and early ocean migration. To understand changes that occur during migration, we examined physiological and endocrine changes in Atlantic salmon (Salmo salar) smolts during hatchery rearing, downstream migration, and early ocean entry in two successive years. Gill Na+/K+-ATPase activity increased in the hatchery during spring, increased further after river release, and was slightly lower after recapture in the ocean. Plasma growth hormone levels increased in the hatchery, were higher in the river, and increased further in the ocean. Plasma IGF-I remained relatively constant in the hatchery, increased in the river, then decreased in the ocean. Plasma thyroid hormones were variable in the hatchery, but increased in both river- and ocean-captured smolts. Naturally reared fish had lower condition factor, gill NKA activity, and plasma thyroxine than hatchery fish in the river but were similar in the ocean. This novel data set provides a vital first step in understanding the role and norms of endocrine function in smolts and the metrics of successful marine entry.

  20. Novel Strategies for Upstream and Downstream Processing of Tannin Acyl Hydrolase

    Directory of Open Access Journals (Sweden)

    Luis V. Rodríguez-Durán

    2011-01-01

    Full Text Available Tannin acyl hydrolase also referred as tannase is an enzyme with important applications in several science and technology fields. Due to its hydrolytic and synthetic properties, tannase could be used to reduce the negative effects of tannins in beverages, food, feed, and tannery effluents, for the production of gallic acid from tannin-rich materials, the elucidation of tannin structure, and the synthesis of gallic acid esters in nonaqueous media. However, industrial applications of tannase are still very limited due to its high production cost. Thus, there is a growing interest in the production, recovery, and purification of this enzyme. Recently, there have been published a number of papers on the improvement of upstream and downstream processing of the enzyme. These papers dealt with the search for new tannase producing microorganisms, the application of novel fermentation systems, optimization of culture conditions, the production of the enzyme by recombinant microorganism, and the design of efficient protocols for tannase recovery and purification. The present work reviews the state of the art of basic and biotechnological aspects of tannin acyl hydrolase, focusing on the recent advances in the upstream and downstream processing of the enzyme.

  1. Highly resolved numerical simulation of combustion downstream of a rocket engine igniter

    Science.gov (United States)

    Buttay, R.; Gomet, L.; Lehnasch, G.; Mura, A.

    2017-02-01

    We study ignition processes in the turbulent reactive flow established downstream of highly under-expanded coflowing jets. The corresponding configuration is typical of a rocket engine igniter, and to the best knowledge of the authors, this study is the first that documents highly resolved numerical simulations of such a reactive flowfield. Considering the discharge of axisymmetric coaxial under-expanded jets, various morphologies are expected, depending on the value of the nozzle pressure ratio, a key parameter used to classify them. The present computations are conducted with a value of this ratio set to fifteen. The simulations are performed with the massively parallel CREAMS solver on a grid featuring approximately 440,000,000 computational nodes. In the main zone of interest, the level of spatial resolution is D/74, with D the central inlet stream diameter. The computational results reveal the complex topology of the compressible flowfield. The obtained results also bring new and useful insights into the development of ignition processes. In particular, ignition is found to take place rather far downstream of the shock barrel, a conclusion that contrasts with early computational studies conducted within the unsteady RANS computational framework. Consideration of detailed chemistry confirms the essential role of hydroperoxyl radicals, while the analysis of the Takeno index reveals the predominance of a non-premixed combustion mode.

  2. A Siltation Simulation and Desiltation Measurement Study Downstream of the Suzhou Creek Sluice, China

    Institute of Scientific and Technical Information of China (English)

    季永兴; 杨绯; 张汉云; 卢永金

    2013-01-01

    The Suzhou Creek Sluice is currently the largest underwater plain gate in the world, with a single span of 100 m. It is located in a tidal estuary at the junction of the Huangpu River and Suzhou Creek in Shanghai, China. In this study, physical and 2D vertical mathematical models were used to investigate and distinguish the mechanism of siltation downstream of an underwater plain gate from that of other gates types. According to quantitative data obtained by site investigation and the application of the physical hydrodynamic models, it was found that the characteristics of the tidal estuary as well as the fact that the sluice span is equal to the creek width are the major reasons contributing to siltation. A possible desiltation treatment system is proposed for the underwater plain gate. The system includes selection of a suitable location that allows the determination of a reasonable top elevation of the sluice floor, reserving sufficient space under the gate to accommodate siltation, setting up a mechanical desiltation system, and flushing silt along with overflow over the top of the gate. Furthermore, on-site hydraulic silt flushing experiments and a topography survey were conducted. These results showed that the measurement system is effective, and by maintaining this scheduled operation once a month, the downstream riverbed has been maintained in a good condition.

  3. An update on USGS studies of the Summitville Mine and its downstream environmental effects

    Science.gov (United States)

    Plumlee, Geoffrey S.; Edelmann, Patrick R.

    1995-01-01

    The Summitville gold mine, located at ~3800 meters (11,500 ft) elevation in the San Juan Mountains of southwestern Colorado, was the focus of extensive public attention in 1992 and 1993 for environmental problems stemming from recent open-pit mining activities. Summitville catalyzed national debates about the environmental effects of modern mining activities, and became the focus of arguments for proposed revisions to the 1872 Mining Law governing mining activities on public lands. In early 1993, the State of Colorado, U.S. Environmental Protection Agency (EPA), U.S. Geological Survey (USGS), U.S. Fish and Wildlife Service (USFWS), Colorado State University, San Luis Valley agencies, downstream water users, private companies, and individuals began a multi-disciplinary research program to provide needed scientific information on Summitville's environmental problems and downstream environmental effects. Detailed results of this multi-agency effort were presented, along with legal and policy issues, at the Summitville Forum in January, 1995, at Colorado State University, Fort Collins, Colorado.

  4. The remote effect of the Tibetan Plateau on downstream flow in early summer

    Science.gov (United States)

    Wang, Yafei; Xu, Xiangde; Lupo, Anthony R.; Li, Pingyun; Yin, Zhicong

    2011-10-01

    By using numerical experiments and observational data, this study examined the uplifting and thermal effects of the Tibetan Plateau (TP) on downstream airflow in early summer. Our principal finding is that the uplifting effect of the TP in an Atmospheric General Climate Model (AGCM), including air made warmer than its surroundings climatologically by the huge topography, results mainly in a local response in the atmosphere, i.e., a large ridge north of the TP in the troposphere in June. There was no Rossby wave response to the uplifting effect. However, simulations and statistical analyses strongly suggested that the anomalous TP atmospheric heating associated with global climate warming tends to excite a Rossby wave originating from the TP via Lake Baikal and continuing to move through the Okhotsk Sea to downstream areas. The appearance of the Rossby wave coincides with the positive phase of the eastern part of a normal stationary wave originating in the Caspian Sea traveling via the Okhotsk Sea to the sea area east of Japan that often occurs in June. Thus the TP atmospheric heating acts as an additional wave source in relaying and enhancing the eastern part of the normal wave propagation. Its path usually lies beyond 40°N latitude, which is where the westerly jet stream takes over the role of waveguide.

  5. A model of mudflow propagation downstream from the Grohovo landslide near the city of Rijeka (Croatia)

    Science.gov (United States)

    Žic, E.; Arbanas, Ž.; Bićanić, N.; Ožanić, N.

    2014-11-01

    Mudflows regularly generate significant human and property losses. Analyzing mudflows is important to assess the risks and to delimit vulnerable areas where mitigation measures are required. In recent decades, modeling of the propagation stage has been largely performed within the framework of continuum mechanics, and a number of new and sophisticated computational models have been developed. Most of the available approaches treat the heterogeneous and multiphase moving mass as a single-phase continuum. The smoothed particle hydrodynamics model (SPH model) adopted here considers, in two phases, a granular skeleton with voids filled with either water or mud. The SPH depth integrated numerical model (Pastor et al., 2009a) used for the present simulations is a 2-D model capable of predicting the runout distance, flow velocity, deposition pattern and the final volume of mudflows. It is based on mathematical and rheological models. In this study, the main characteristics of mudflow processes that have emerged in the past in the area downstream of the Grohovo landslide are examined, and the more relevant parameters and attributes describing the mudflow are presented. Principal equations that form the basis of the SPH depth integrated model are reviewed and applied to analyze the Grohovo landslide and the propagation of the mudflow wave downstream of the landslide. Based on the SPH method, the runout distance, quantities of the deposited materials and the velocity of mudflow progression which occurred in the past at the observed area are analysed and qualitatively compared to the recorded consequences of the actual event.

  6. Effect of boundary conditions on downstream vorticity from counter-rotating swirlers

    Directory of Open Access Journals (Sweden)

    Huo Weiye

    2015-02-01

    Full Text Available Particle image velocimetry (PIV is utilized to measure the non-reacting flow field in a reflow combustor with multiple and single swirlers. The velocity field, vortex structure and total vorticity levels are experimentally obtained using two different boundary conditions, representing a single confined swirler and multiple swirlers in an annular combustor. The influence of the boundary conditions on the flow field at several locations downstream of the swirlers is experimentally investigated, showing that the central vortex in the multi-swirler case is more concentrated than in the single-swirler case. The vorticity of the central vortex and average cross-sectional vorticity are relatively low at the swirler outlet in both cases. Both of these statistics gradually increase to the maximum values near 20 mm downstream of the swirler outlet, and subsequently decrease. It is also found that the central vortex in the multi-swirler case is consistently greater than the single-swirler case. These results demonstrate the critical influence of boundary conditions on flow characteristic of swirling flow, providing insight into the difference of the experiments on test-bed combustor and the full-scale annular combustors.

  7. First-Year Downstream Sediment Budget Following the Marmot Dam Removal from the Sandy River, Oregon

    Science.gov (United States)

    Podolak, C. J.; Wilcock, P. R.; Pittman, A.

    2008-12-01

    The October 2007 removal of the Marmot Dam, from the Sandy River, OR, provides an opportunity to assess the impact of increased sediment flux on a river channel. The Sandy River drains the west flank of Mt Hood and typically carries a large load of sand and gravel. The 14-meter-tall dam impounded over 750,000 m3 of sediment, only a small amount of which was removed during the decommissioning. Using a one- dimensional modeling approach, it was assessed that the river could transport the accumulated sediment without large adverse impacts downstream of the dam (Cui et al, 2008 - abstract submitted). In order to observe the actual changes to the river due to the dam removal and to test the modeled predictions, a significant monitoring effort has be in place on the Sandy River including bedload and suspended load measurements, discharge measurements, high-fidelity topographic surveys, repeat photography, multiple airborne LIDAR flights, long profile surveys, as well as mapping and characterizing the grain sizes throughout several reaches downstream of the dam. A key step in the quest to describe and predict the spatial distribution of the sediment throughout the downstream reach is to first account for all the sediment (both stored in the reservoir and supplied from upstream). Here, we examine the transport and deposition downstream of the dam through a 2-fraction sediment budget approach using the former dam as the upstream limit of the reach and choosing a the mouth of a bedrock gorge 7 km below the dam site as the downstream limit. Suspended sediment and bedload measurements taken by the USGS just below the dam site (Major et al, 2008 - abstract submitted) are combined with suspended sediment and bedload measurements collected just below the mouth of the gorge and the annual hydrograph to define the sediment fluxes into and out of the reach. Repeat surveys in the reach below the dam (Wallick et al, 2008 - abstract submitted) provide the measure of change in storage

  8. Unsteady turbulence interaction in a tip leakage flow downstream of a simulated axial compressor rotor

    Science.gov (United States)

    Ma, Ruolong

    The unsteady behavior of a tip leakage flow downstream of a simulated axial compressor rotor has been studied. The Virginia Tech low speed linear cascade wind tunnel was adapted to model the unsteady tip leakage flow produced by a rotor operating in the vortical wakes of a set of stator vanes. The cascade, consisting of 8 GE rotor B blades, has adjustable tip gap, inlet angle of 65.1°, turning angle of 11.8° and solidity of 1.076. The cascade Reynolds number, based on blade chord, was 393,000. A moving end wall was used to simulate the relative motion between rotor and casing, and vortex generators attached to the moving end wall were used to produce an idealized periodic unsteady vortical inflow similar to that shed by the junction of a row of inlet guide vanes. Measurements of the vortical inflow to the cascade produced by the generators and of the mean blade loading at the mid span are presented. The periodic and aperiodic behavior of the tip leakage flow downstream of the cascade, produced by this vortical disturbance, is also presented using phase and time averaged 3-component turbulence and pressure fluctuation measurements. These measurements are made for tip gap from 0.83% to 3.3% chord and streamwise locations from 0.772% to 1.117% blade spacing axially downstream of the cascade. The phase averaged inflow measurements reveal that the inflow produced by the vortex generators consists of a pair asymmetric counter-rotating vortices embedded in a thin (4.6% chord) endwall boundary layer. The vortices extend some 7.4% chord from the end wall. Their strength is about two orders smaller than the typical circulation of the tip leakage vortices produced by the cascade. Phase averaged single point three component hot-wire measurements downstream of the cascade reveal that the vortical inflow is, however, capable of producing significant large scale fluctuations in the size, strength, structure and position of the tip leakage vortex. These effects increase in

  9. Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish

    NARCIS (Netherlands)

    Palstra, A.P.; Beltran, S.; Burgerhout, E.; Brittijn, S.A.; Magnoni, L.J.; Henkel, C.V.; Jansen, A.; Thillart, G.E.E.J.M.; Spaink, H.P.; Planas, J.V.

    2013-01-01

    Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of swimming

  10. Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis

    NARCIS (Netherlands)

    Nicolas, Pierre; Maeder, Ulrike; Dervyn, Etienne; Rochat, Tatiana; Leduc, Aurelie; Pigeonneau, Nathalie; Bidnenko, Elena; Marchadier, Elodie; Hoebeke, Mark; Aymerich, Stephane; Becher, Doerte; Bisicchia, Paola; Botella, Eric; Delumeau, Olivier; Doherty, Geoff; Denham, Emma L.; Fogg, Mark J.; Fromion, Vincent; Goelzer, Anne; Hansen, Annette; Haertig, Elisabeth; Harwood, Colin R.; Homuth, Georg; Jarmer, Hanne; Jules, Matthieu; Klipp, Edda; Le Chat, Ludovic; Lecointe, Francois; Lewis, Peter; Liebermeister, Wolfram; March, Anika; Mars, Ruben A. T.; Nannapaneni, Priyanka; Noone, David; Pohl, Susanne; Rinn, Bernd; Ruegheimer, Frank; Sappa, Praveen K.; Samson, Franck; Schaffer, Marc; Schwikowski, Benno; Steil, Leif; Stuelke, Joerg; Wiegert, Thomas; Devine, Kevin M.; Wilkinson, Anthony J.; van Dijl, Jan Maarten; Hecker, Michael; Voelker, Uwe; Bessieres, Philippe; Noirot, Philippe

    2012-01-01

    Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional

  11. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

    DEFF Research Database (Denmark)

    Nicolas, Pierre; Mäder, Ulrike; Dervyn, Etienne

    2012-01-01

    Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutritional...

  12. Defining diversity, specialization, and gene specificity in transcriptomes through information theory

    Science.gov (United States)

    Martínez, Octavio; Reyes-Valdés, M. Humberto

    2008-01-01

    The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from mRNA libraries or by measuring light signals in DNA microarrays. In any case, it is difficult to completely comprehend the global changes that occur in the transcriptome, given that thousands of gene expression measurements are involved. We propose an approach to define and estimate the diversity and specialization of transcriptomes and gene specificity. We define transcriptome diversity as the Shannon entropy of its frequency distribution. Gene specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either housekeeping or highly specific genes and clarifying the meaning of these concepts in the literature. Tissue specialization is measured by average gene specificity. We introduce the formulae using a simple example and show their application in two datasets of gene expression in human tissues. Visualization of the positions of transcriptomes in a system of diversity and specialization coordinates makes it possible to understand at a glance their interrelations, summarizing in a powerful way which transcriptomes are richer in diversity of expressed genes, or which are relatively more specialized. The framework presented enlightens the relation among transcriptomes, allowing a better understanding of their changes through the development of the organism or in response to environmental stimuli. PMID:18606989

  13. Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse

    Directory of Open Access Journals (Sweden)

    Lauren L. Kordonowy

    2016-10-01

    Full Text Available Rodents of the genus Peromyscus have become increasingly utilized models for investigations into adaptive biology. This genus is particularly powerful for research linking genetics with adaptive physiology or behaviors, and recent research has capitalized on the unique opportunities afforded by the ecological diversity of these rodents. Well characterized genomic and transcriptomic data is intrinsic to explorations of the genetic architecture responsible for ecological adaptations. Therefore, this study characterizes the transcriptome of three male reproductive tissues (testes, epididymis and vas deferens of Peromyscus eremicus (Cactus mouse, a desert specialist. The transcriptome assembly process was optimized in order to produce a high quality and substantially complete annotated transcriptome. This composite transcriptome was generated to characterize the expressed transcripts in the male reproductive tract of P. eremicus, which will serve as a crucial resource for future research investigating our hypothesis that the male Cactus mouse possesses an adaptive reproductive phenotype to mitigate water-loss from ejaculate. This study reports genes under positive selection in the male Cactus mouse reproductive transcriptome relative to transcriptomes from Peromyscus maniculatus (deer mouse and Mus musculus. Thus, this study expands upon existing genetic research in this species, and we provide a high quality transcriptome to enable further explorations of our proposed hypothesis for male Cactus mouse reproductive adaptations to minimize seminal fluid loss.

  14. COUPLING EFFECT BETWEEN RELIABILITY OF BEDDING LAYER AND STABILITY OF DOWNSTREAM CONCRETE SLAB OF OVERFLOW EARTH-ROCK COFFERDAM

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The protection of downstream concrete slab is a key issue for the stability of overflow earth-rock cofferdam. The coupling effect between bedding layer and concrete slab was taken into account when the stability of downstream concrete slab was researched. The characteristics of overflow and seepage over the downstream concrete slab were investigated when floodwater passes over the cofferdam. Firstly a limit equation of seepage failure for the bedding layer was derived with the consideration of geometric and mechanical factors, and a reliability model was established and numerically simulated. Then based on the reliability calculation for the bedding layer, the coupling effect between bedding layer and downstream concrete slab was analyzed. Under the most unfavorable pressure condition for the concrete slab, its instability criterion was put forward, which offers a structural design tool of downstream concrete slab for overflow earth-rock cofferdam. Compared with model tests, it shows that the model of reliability calculation of bedding layer and the stability analysis of downstream concrete slab are effective.

  15. Construction of coffee transcriptome networks based on gene annotation semantics.

    Science.gov (United States)

    Castillo, Luis F; Galeano, Narmer; Isaza, Gustavo A; Gaitán, Alvaro

    2012-07-24

    Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models. When thousands of gene models are being described in an organism genome, construction and visualization of gene networks impose novel challenges in the understanding of complex expression patterns and the generation of new knowledge in genomics research. In order to take advantage of accumulated text data after conventional gene sequence analysis, this work applied semantics in combination with visualization tools to build transcriptome networks from a set of coffee gene annotations. A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST) and Interproscan, were filtered out by coverage, identity, length of the query, and e-values. Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF) using Ruby scripts and Methontology to find associations between concepts. Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations. A large gene network connecting transcripts by way of relational concepts was created where detailed connections remain to be validated for biological significance based on current biochemical and genetics frameworks. Besides reusing text information in the generation of gene connections and for data mining purposes, this tool development opens the possibility to visualize complex and abundant transcriptome data, and triggers the formulation of new hypotheses in metabolic pathways analysis.

  16. Using next generation transcriptome sequencing to predict an ectomycorrhizal metablome.

    Energy Technology Data Exchange (ETDEWEB)

    Larsen, P. E.; Sreedasyam, A.; Trivedi, G; Podila, G. K.; Cseke, L. J.; Collart, F. R. (Biosciences Division); (On Assignment, Scientific Staffing); (Univ. of Alabama at Huntsville)

    2011-05-13

    Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides) roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.

  17. Comparative transcriptomic analysis of developing cotton cotyledons and embryo axis.

    Directory of Open Access Journals (Sweden)

    Xiaoming Jiao

    Full Text Available BACKGROUND: As a by product of higher value cotton fibre, cotton seed has been increasingly recognised to have excellent potential as a source of additional food, feed, biofuel stock and even a renewable platform for the production of many diverse biological molecules for agriculture and industrial enterprises. The large size difference between cotyledon and embryo axis that make up a cotton seed results in the under-representation of embryo axis gene transcript levels in whole seed embryo samples. Therefore, the determination of gene transcript levels in the cotyledons and embryo axes separately should lead to a better understanding of metabolism in these two developmentally diverse tissues. RESULTS: A comparative study of transcriptome changes between cotton developing cotyledon and embryo axis has been carried out. 17,384 unigenes (20.74% of all the unigenes were differentially expressed in the two adjacent embryo tissues, and among them, 7,727 unigenes (44.45% were down-regulated and 9,657 unigenes (55.55% were up-regulated in cotyledon. CONCLUSIONS: Our study has provided a comprehensive dataset that documents the dynamics of the transcriptome at the mid-maturity of cotton seed development and in discrete seed tissues, including embryo axis and cotyledon tissues. The results showed that cotton seed is subject to many transcriptome variations in these two tissue types and the differential gene expression between cotton embryo axis and cotyledon uncovered in our study should provide an important starting point for understanding how gene activity is coordinated during seed development to make a seed. Further, the identification of genes involved in rapid metabolite accumulation stage of seed development will extend our understanding of the complex molecular and cellular events in these developmental processes and provide a foundation for future studies on the metabolism, embryo differentiation of cotton and other dicot oilseed crops.

  18. Using next generation transcriptome sequencing to predict an ectomycorrhizal metabolome

    Directory of Open Access Journals (Sweden)

    Cseke Leland J

    2011-05-01

    Full Text Available Abstract Background Mycorrhizae, symbiotic interactions between soil fungi and tree roots, are ubiquitous in terrestrial ecosystems. The fungi contribute phosphorous, nitrogen and mobilized nutrients from organic matter in the soil and in return the fungus receives photosynthetically-derived carbohydrates. This union of plant and fungal metabolisms is the mycorrhizal metabolome. Understanding this symbiotic relationship at a molecular level provides important contributions to the understanding of forest ecosystems and global carbon cycling. Results We generated next generation short-read transcriptomic sequencing data from fully-formed ectomycorrhizae between Laccaria bicolor and aspen (Populus tremuloides roots. The transcriptomic data was used to identify statistically significantly expressed gene models using a bootstrap-style approach, and these expressed genes were mapped to specific metabolic pathways. Integration of expressed genes that code for metabolic enzymes and the set of expressed membrane transporters generates a predictive model of the ectomycorrhizal metabolome. The generated model of mycorrhizal metabolome predicts that the specific compounds glycine, glutamate, and allantoin are synthesized by L. bicolor and that these compounds or their metabolites may be used for the benefit of aspen in exchange for the photosynthetically-derived sugars fructose and glucose. Conclusions The analysis illustrates an approach to generate testable biological hypotheses to investigate the complex molecular interactions that drive ectomycorrhizal symbiosis. These models are consistent with experimental environmental data and provide insight into the molecular exchange processes for organisms in this complex ecosystem. The method used here for predicting metabolomic models of mycorrhizal systems from deep RNA sequencing data can be generalized and is broadly applicable to transcriptomic data derived from complex systems.

  19. Transcriptomic analysis of flower development in wintersweet (Chimonanthus praecox.

    Directory of Open Access Journals (Sweden)

    Daofeng Liu

    Full Text Available Wintersweet (Chimonanthus praecox is familiar as a garden plant and woody ornamental flower. On account of its unique flowering time and strong fragrance, it has a high ornamental and economic value. Despite a long history of human cultivation, our understanding of wintersweet genetics and molecular biology remains scant, reflecting a lack of basic genomic and transcriptomic data. In this study, we assembled three cDNA libraries, from three successive stages in flower development, designated as the flower bud with displayed petal, open flower and senescing flower stages. Using the Illumina RNA-Seq method, we obtained 21,412,928, 26,950,404, 24,912,954 qualified Illumina reads, respectively, for the three successive stages. The pooled reads from all three libraries were then assembled into 106,995 transcripts, 51,793 of which were annotated in the NCBI non-redundant protein database. Of these annotated sequences, 32,649 and 21,893 transcripts were assigned to gene ontology categories and clusters of orthologous groups, respectively. We could map 15,587 transcripts onto 312 pathways using the Kyoto Encyclopedia of Genes and Genomes pathway database. Based on these transcriptomic data, we obtained a large number of candidate genes that were differentially expressed at the open flower and senescing flower stages. An analysis of differentially expressed genes involved in plant hormone signal transduction pathways indicated that although flower opening and senescence may be independent of the ethylene signaling pathway in wintersweet, salicylic acid may be involved in the regulation of flower senescence. We also succeeded in isolating key genes of floral scent biosynthesis and proposed a biosynthetic pathway for monoterpenes and sesquiterpenes in wintersweet flowers, based on the annotated sequences. This comprehensive transcriptomic analysis presents fundamental information on the genes and pathways which are involved in flower development in

  20. Preadult life history variation determines adult transcriptome expression.

    Science.gov (United States)

    Etges, William J; de Oliveira, Cássia; Rajpurohit, Subhash; Gibbs, Allen G

    2016-02-01

    Preadult determinants of adult fitness and behaviour have been documented in a variety of organisms with complex life cycles, but little is known about expression patterns of genes underlying these adult traits. We explored the effects of differences in egg-to-adult development time on adult transcriptome and cuticular hydrocarbon variation in order to understand the nature of the genetic correlation between preadult development time and premating isolation between populations of Drosophila mojavensis reared in different host cactus environments. Transcriptome variation was analysed separately in flies reared on each host and revealed that hundreds of genes in adults were differentially expressed (FDR P pitaya agria cactus, longer preadult development times caused increased expression of genes in adults enriched for ribosome production, protein metabolism, chromatin remodelling and regulation of alternate splicing and transcription. Baja California flies reared on organ pipe cactus showed fewer differentially expressed genes in adults due to longer preadult development time, but these were enriched for ATP synthesis and the TCA cycle. Mainland flies reared on organ pipe cactus with shorter development times showed increased transcription of genes enriched for mitochondria and energy production, protein synthesis and glucose metabolism: adults with longer development times had increased expression of genes enriched for adult life span, cuticle proteins and ion binding, although most differentially expressed genes were unannotated. Differences due to population, sex, mating status and their interactions were also assessed. Adult cuticular hydrocarbon profiles also showed shifts due to egg-to-adult development time and were influenced by population and mating status. These results help to explain why preadult life history variation determines subsequent expression of the adult transcriptome along with traits involved with reproductive isolation and revealed previously

  1. Probing the Xenopus laevis inner ear transcriptome for biological function

    Directory of Open Access Journals (Sweden)

    Powers TuShun R

    2012-06-01

    Full Text Available Abstract Background The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus Xenopus is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Results Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization. Conclusions We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the Xenopus inner ear transcriptome

  2. Transcriptome dynamics of transgene amplification in Chinese hamster ovary cells.

    Science.gov (United States)

    Vishwanathan, Nandita; Le, Huong; Jacob, Nitya M; Tsao, Yung-Shyeng; Ng, Sze-Wai; Loo, Bernard; Liu, Zhong; Kantardjieff, Anne; Hu, Wei-Shou

    2014-03-01

    Dihydrofolate reductase (DHFR) system is used to amplify the product gene to multiple copies in Chinese Hamster Ovary (CHO) cells for generating cell lines which produce the recombinant protein at high levels. The physiological changes accompanying the transformation of the non-protein secreting host cells to a high producing cell line is not well characterized. We performed transcriptome analysis on CHO cells undergoing the selection and amplification processes. A host CHO cell line was transfected with a vector containing genes encoding the mouse DHFR (mDHFR) and a recombinant human IgG (hIgG). Clones were isolated following selection and subcloned following amplification. Control cells were transfected with a control plasmid which did not have the hIgG genes. Although methotrexate (MTX) amplification increased the transcript level of the mDHFR gene significantly, its effect on both hIgG heavy and light chain genes was more modest. The subclones appeared to retain the transcriptome signatures of their parental clones, however, their productivity varied among those derived from the same clone. The transcript levels of hIgG transgenes of all subclones fall in a narrower range than the product titer, alluding to the role of many functional attributes, other than transgene transcript, on productivity. We cross examined functional class enrichment during selection and amplification as well as between high and low producers and discerned common features among them. We hypothesize that the role of amplification is not merely increasing transcript levels, but also enriching survivors which have developed the cellular machinery for secreting proteins, leading to an increased frequency of isolating high-producing clones. We put forward the possibility of assembling a hyper-productivity gene set through comparative transcriptome analysis of a wide range of samples.

  3. A first insight into Pycnoporus sanguineus BAFC 2126 transcriptome.

    Directory of Open Access Journals (Sweden)

    Cristian O Rohr

    Full Text Available Fungi of the genus Pycnoporus are white-rot basidiomycetes widely studied because of their ability to synthesize high added-value compounds and enzymes of industrial interest. Here we report the sequencing, assembly and analysis of the transcriptome of Pycnoporus sanguineus BAFC 2126 grown at stationary phase, in media supplemented with copper sulfate. Using the 454 pyrosequencing platform we obtained a total of 226,336 reads (88,779,843 bases that were filtered and de novo assembled to generate a reference transcriptome of 7,303 transcripts. Putative functions were assigned for 4,732 transcripts by searching similarities of six-frame translated sequences against a customized protein database and by the presence of conserved protein domains. Through the analysis of translated sequences we identified transcripts encoding 178 putative carbohydrate active enzymes, including representatives of 15 families with roles in lignocellulose degradation. Furthermore, we found many transcripts encoding enzymes related to lignin hydrolysis and modification, including laccases and peroxidases, as well as GMC oxidoreductases, copper radical oxidases and other enzymes involved in the generation of extracellular hydrogen peroxide and iron homeostasis. Finally, we identified the transcripts encoding all of the enzymes involved in terpenoid backbone biosynthesis pathway, various terpene synthases related to the biosynthesis of sesquiterpenoids and triterpenoids precursors, and also cytochrome P450 monooxygenases, glutathione S-transferases and epoxide hydrolases with potential functions in the biodegradation of xenobiotics and the enantioselective biosynthesis of biologically active drugs. To our knowledge this is the first report of a transcriptome of genus Pycnoporus and a resource for future molecular studies in P. sanguineus.

  4. Single-cell Transcriptome Study as Big Data

    Institute of Scientific and Technical Information of China (English)

    Pingjian Yu; Wei Lin

    2016-01-01

    The rapid growth of single-cell RNA-seq studies (scRNA-seq) demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing (NGS)-based studies, we propose a workflow that accounts for the unique characteris-tics of scRNA-seq data and primary objectives of single-cell studies.

  5. Massively parallel sequencing and analysis of the Necator americanus transcriptome.

    Directory of Open Access Journals (Sweden)

    Cinzia Cantacessi

    Full Text Available BACKGROUND: The blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide. In order to elucidate fundamental molecular biological aspects of this hookworm, the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses. METHODOLOGY/PRINCIPAL FINDINGS: A total of 19,997 contigs were assembled from the sequence data; 6,771 of these contigs had known orthologues in the free-living nematode Caenorhabditis elegans, and most of them encoded proteins with WD40 repeats (10.6%, proteinase inhibitors (7.8% or calcium-binding EF-hand proteins (6.7%. Bioinformatic analyses inferred that the C. elegans homologues are involved mainly in biological pathways linked to ribosome biogenesis (70%, oxidative phosphorylation (63% and/or proteases (60%; most of these molecules were predicted to be involved in more than one biological pathway. Comparative analyses of the transcriptomes of N. americanus and the canine hookworm, Ancylostoma caninum, revealed qualitative and quantitative differences. For instance, proteinase inhibitors were inferred to be highly represented in the former species, whereas SCP/Tpx-1/Ag5/PR-1/Sc7 proteins ( = SCP/TAPS or Ancylostoma-secreted proteins were predominant in the latter. In N. americanus, essential molecules were predicted using a combination of orthology mapping and functional data available for C. elegans. Further analyses allowed the prioritization of 18 predicted drug targets which did not have homologues in the human host. These candidate targets were inferred to be linked to mitochondrial (e.g., processing proteins or amino acid metabolism (e.g., asparagine t-RNA synthetase. CONCLUSIONS: This study has provided detailed insights into the transcriptome of the adult stage of N. americanus and examines similarities and differences between this species and A. caninum. Future efforts should focus on comparative transcriptomic and

  6. Transcriptome and venom proteome of the box jellyfish Chironex fleckeri

    OpenAIRE

    2015-01-01

    Background The box jellyfish, Chironex fleckeri, is the largest and most dangerous cubozoan jellyfish to humans. It produces potent and rapid-acting venom and its sting causes severe localized and systemic effects that are potentially life-threatening. In this study, a combined transcriptomic and proteomic approach was used to identify C. fleckeri proteins that elicit toxic effects in envenoming. Results More than 40,000,000 Illumina reads were used to de novo assemble ∼ 34,000 contiguous cDN...

  7. Transcriptome profiling of tobacco under water deficit conditions

    Directory of Open Access Journals (Sweden)

    Roel C. Rabara

    2015-09-01

    Full Text Available Drought is one of the limiting environmental factors that affect crop production. Understanding the molecular basis of how plants respond to this water deficit stress is key to developing drought tolerant crops. In this study we generated time course-based transcriptome profiles of tobacco plants under water deficit conditions using microarray technology. In this paper, we describe in detail the experimental procedures and analyses performed in our study. The data set we generated (available in the NCBI/GEO database under GSE67434 has been analysed to identify genes that are involved in the regulation of tobacco's responses to drought.

  8. Single-cell Transcriptome Study as Big Data

    Science.gov (United States)

    Yu, Pingjian; Lin, Wei

    2016-01-01

    The rapid growth of single-cell RNA-seq studies (scRNA-seq) demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing (NGS)-based studies, we propose a workflow that accounts for the unique characteristics of scRNA-seq data and primary objectives of single-cell studies. PMID:26876720

  9. Downstream changes in spring-fed stream invertebrate communities: the effect of increased temperature range?

    Directory of Open Access Journals (Sweden)

    Russell G. DEATH

    2011-09-01

    Full Text Available Reduced thermal amplitude has been highlighted as a limiting factor for aquatic invertebrate diversity in springs. Moving downstream water temperature range increases and invertebrate richness is expected to change accordingly. In the present study temperature patterns were investigated in seven spring-fed streams, between April 2001 and November 2002, and compared to five run-off-fed streams to assess the degree of crenic temperature constancy. Temperature and physico-chemical characteristics of the water, and food resource levels were measured, and the invertebrate fauna collected at 4 distances (0, 100, 500 m and 1 km from seven springs in the North and South Islands of New Zealand. Temperature variability was greater for run-off-fed streams than for springs, and increased in the spring-fed streams with distance from the source. Periphyton and physico-chemical characteristics of the water did not change markedly over the 1 km studied, with the exception of water velocity and organic matter biomass, which increased and decreased, respectively. The rate of increase in temperature amplitude differed greatly for the studied springs, probably being affected by flow, altitude, and the number and type of tributaries (i.e., spring- or run-off-fed joining the spring-fed stream channel. Longitudinal changes in the number and evenness of invertebrate taxa were positively correlated to thermal amplitude (rs = 0.8. Moving downstream, invertebrate communities progressively incorporated taxa with higher mobility and taxa more common in nearby run-off-fed streams. Chironomids and non-insect taxa were denser at the sources. Chironomid larvae also numerically dominated communities 100 and 500 m downstream from the sources, together with Pycnocentria spp. and Zelolessica spp., while taxa such as Hydora sp. and Hydraenidae beetles, the mayflies Deleatidium spp. and Coloburiscus humeralis, and the Trichoptera Pycnocentrodes spp., all had greater abundances 1 km

  10. Explaining Anomalies in Enamine Catalysis: "Downstream Species" as a New Paradigm for Stereocontrol.

    Science.gov (United States)

    Burés, Jordi; Armstrong, Alan; Blackmond, Donna G

    2016-02-16

    Enantioselective organocatalysis by diarylprolinol ethers is remarkably selective and efficient for a wide range of transformations involving a number of different activation modes, including HOMO activation via enamines. A simple steric model based on facial discrimination in the attack of an enamine on an electrophile has been invoked to rationalize high enantioselectivity. In a number of reactions, however, experimental observations have persistently left us with mechanistic puzzles that fail to fit neatly into this simple picture. Further studies involving both kinetic profiling of reaction networks and NMR spectroscopic characterization of the structures of intermediate species helped us to address these puzzles. This work led to the proposal of a new paradigm for stereocontrol in asymmetric aminocatalysis, demonstrating that the ultimate stereochemical outcome may not, in fact, be determined solely in the stereogenic bond-forming step between enamine and electrophile. The identification of stable species occurring downstream from the addition of an electrophile to an enamine, and the discovery of kinetic features that are diagnostic of the presence of such species, allows development of a new mechanistic framework that reveals a hierarchical selection. Both kinetic and thermodynamic processes associated with downstream intermediates can exert an influence on the ultimate enantioselectivity. Interestingly, the role of these species may be either to enhance or to erode selectivity established at the enamine-electrophile step. The reversibility of steps preceding and subsequent to the stereogenic bond-forming step is an important factor, as are reaction parameters that may stabilize or destabilize intermediates, including the nature of the electrophile counterion and the solvent. These concepts hold implications for the future design and optimization of asymmetric catalytic processes, because such design does not necessarily feature the same parameters at the

  11. Effect of Nozzle Material on Downstream Lateral Injection Cold Spray Performance

    Science.gov (United States)

    MacDonald, D.; Leblanc-Robert, S.; Fernández, R.; Farjam, A.; Jodoin, B.

    2016-08-01

    In cold gas dynamic spraying, the gas nature, process stagnation pressure and temperature, and the standoff distance are known to be important parameters that affect the deposition efficiency and coating quality. This investigation attempts to elucidate the effect of nozzle material on coatings produced using a downstream lateral injection cold spray system. Through experimentation, it is shown that the nozzle material has a substantial effect on deposition efficiency and particle velocity. It is proposed that the effects are related to complex interaction between the particles and the internal nozzle walls. The results obtained lead to the conclusion that during the particle/nozzle wall contact, a nozzle with higher thermal diffusivity transfers more heat to the particles. This heat transfer results in lower critical velocities and therefore higher deposition efficiencies, despite a noticeable reduction of particle velocities which is also attributed to particle-nozzle interactions.

  12. Plant GSK3 proteins regulate xylem cell differentiation downstream of TDIF-TDR signalling

    Science.gov (United States)

    Kondo, Yuki; Ito, Tasuku; Nakagami, Hirofumi; Hirakawa, Yuki; Saito, Masato; Tamaki, Takayuki; Shirasu, Ken; Fukuda, Hiroo

    2014-03-01

    During plant radial growth typically seen in trees, procambial and cambial cells act as meristematic cells in the vascular system to self-proliferate and differentiate into xylem cells. These two processes are regulated by a signalling pathway composed of a peptide ligand and its receptor; tracheary element differentiation inhibitory factor (TDIF) and TDIF RECEPTOR (TDR). Here we show that glycogen synthase kinase 3 proteins (GSK3s) are crucial downstream components of the TDIF signalling pathway suppressing xylem differentiation from procambial cells. TDR interacts with GSK3s at the plasma membrane and activates GSK3s in a TDIF-dependent fashion. Consistently, a specific inhibitor of plant GSK3s strongly induces xylem cell differentiation through BRI1-EMS SUPPRESSOR 1 (BES1), a well-known target transcription factor of GSK3s. Our findings provide insight into the regulation of cell fate determination in meristem maintenance.

  13. The effect of circular bridge piers with different inclination angles toward downstream on scour

    Indian Academy of Sciences (India)

    Mohammad Vaghef; Masoud Ghodsian; Saeid Salimi

    2016-01-01

    A fundamental principle in the safe design of bridge piers is to estimate maximum scour depth. As such, many researchers devoted their efforts to study the phenomenon of scour around bridge piers and to present relationships to estimate maximum scour depth. In the current research, scour around circular bridge piers with two different diameters and different inclination angles toward downstream has been investigated experimentally under clear water and different discharges. The obtained results revealed that increase in the inclination angle leads to a significant decrease in the scour depth, dimensions of sediment ridge and scour hole. Moreover, by comparing the data obtained from vertical bridge pier and well-known relationships, a relationship having the most agreement with the results was selected and modified to estimate equilibrium scour depth around inclined piers.

  14. Arabidopsis MAPKKK18 positively regulates drought stress resistance via downstream MAPKK3.

    Science.gov (United States)

    Li, Yuanyuan; Cai, Huixian; Liu, Pu; Wang, Chunyan; Gao, Huiyang; Wu, Changai; Yan, Kang; Zhang, Shizhong; Huang, Jinguang; Zheng, Chengchao

    2017-03-04

    Mitogen-activated protein kinase (MAPK) cascades are conserved and vital signaling components in the responses to various ambient stresses. Here, we report the identification of MAPKKK18, a drought resistance associated MAPK kinase kinase in Arabidopsis. The mapkkk18 knockout mutants displayed hypersensitivity to drought stress, whereas overaccumulation of MAPKKK18 in transgenic Arabidopsis plants significantly enhanced the resistance to drought. Expression pattern analysis revealed that the inducible expression of MAPKKK18 by osmotic stress was ABA and the canonical ABA signaling pathway dependent. Furthermore, MAPKKK18 mainly exerted its regulatory roles via downstream MAPKK3. These findings uncovered important roles for MAPKKK18 in drought resistance and expanded our understanding of the MAPK pathways in modulating abiotic stress responses.

  15. Targeting Protein Kinase C Downstream of Growth Factor and Adhesion Signalling

    Directory of Open Access Journals (Sweden)

    Catríona M. Dowling

    2015-07-01

    Full Text Available The signaling outputs of Receptor Tyrosine Kinases, G-protein coupled receptors and integrins converge to mediate key cell process such as cell adhesion, cell migration, cell invasion and cell proliferation. Once activated by their ligands, these cell surface proteins recruit and direct a diverse range of proteins to disseminate the appropriate response downstream of the specific environmental cues. One of the key groups of proteins required to regulate these activities is the family of serine/threonine intracellular kinases called Protein Kinase Cs. The activity and subcellular location of PKCs are mediated by a series of tightly regulated events and is dependent on several posttranslational modifications and the availability of second messengers. Protein Kinase Cs exhibit both pro- and anti-tumorigenic effects making them an interesting target for anti-cancer treatment.

  16. Targeting Protein Kinase C Downstream of Growth Factor and Adhesion Signalling

    Energy Technology Data Exchange (ETDEWEB)

    Dowling, Catríona M., E-mail: Catriona.Dowling@ul.ie; Kiely, Patrick A., E-mail: Catriona.Dowling@ul.ie [Department of Life Sciences, Materials and Surface Science Institute and Stokes Institute, University of Limerick, Limerick 78666 (Ireland); Health Research Institute (HRI), University of Limerick, Limerick 78666 (Ireland)

    2015-07-15

    The signaling outputs of Receptor Tyrosine Kinases, G-protein coupled receptors and integrins converge to mediate key cell process such as cell adhesion, cell migration, cell invasion and cell proliferation. Once activated by their ligands, these cell surface proteins recruit and direct a diverse range of proteins to disseminate the appropriate response downstream of the specific environmental cues. One of the key groups of proteins required to regulate these activities is the family of serine/threonine intracellular kinases called Protein Kinase Cs. The activity and subcellular location of PKCs are mediated by a series of tightly regulated events and is dependent on several posttranslational modifications and the availability of second messengers. Protein Kinase Cs exhibit both pro- and anti-tumorigenic effects making them an interesting target for anti-cancer treatment.

  17. Isolation of high-quality RNA from various tissues of Jatropha curcas for downstream applications.

    Science.gov (United States)

    Kumar, G Raja Krishna; Eswaran, Nalini; Johnson, T Sudhakar

    2011-06-01

    A method for isolating transcriptionally active RNA for downstream applications from diverse tissues of Jatropha curcas, a plant rich in latex, lipids, waxes, polysaccharide, polyphenols, and secondary metabolites, is described. The described method uses alkaline borate buffer during tissue homogenization to negate the formation of viscous gel observed in guanidium-salt-containing methods. By this method, quality RNA was extracted from leaf, immature inflorescence, endosperm, and root tissues with yields ranging from 1.80 to 7.80mg/100mg fresh weight (FW). The total RNA obtained was found to be suitable for poly(A)(+)RNA purification, complementary DNA (cDNA) synthesis, cloning of full-length cDNA, and cDNA library construction.

  18. Performance of ESPs operating downstream from spray-drying desulphurisation units

    Energy Technology Data Exchange (ETDEWEB)

    Ollero, P.; Canadas, L.; Salvador, L. [Escuela Superior de Ingenieros Industrials, Sevilla (Spain)] [and others

    1995-06-01

    This paper summarizes data from a Spray Dryer/ESP pilot plant located at the Los Barrios Coal Power Plant (Cadiz, Spain). A series of tests has been conducted to evaluate the performance of an existing ESP operating downstream from a spray dryer in a retrofit application. A factorial design of experiments with two SO{sub 2} levels, two flyash load levels, three Ca/S ratios and three sulfur removal efficiencies, was run during a six-month experimental programme. A global and a field-by-field analysis of the performance of the pilot ESP has shown that the desulphurisation unit enhances ESP efficiency and reduces the emission level. No evidence of electrical dust reentrainment has been found.

  19. Wake Vortices and Tropical Cyclogenesis Downstream of Sumatra over the Indian Ocean

    Science.gov (United States)

    Fine, Caitlin Marie

    A myriad of processes acting singly or in concert may contribute to tropical cyclogenesis, including convectively coupled waves, breakdown of the inter-tropical convergence zone (ITCZ), or upper-level troughs. This thesis investigates the role that topographic effects from the island of Sumatra may play in initiating tropical cyclogenesis (TC genesis) in the eastern Indian Ocean. If easterly flow is split by the mountains of Sumatra, counter-rotating lee vortices may form downstream. Because Sumatra straddles the equator, though the wake vortices rotate in opposite directions, they will both be cyclonic when winds are easterly upon Sumatra, and may intensify further into tropical cyclones. The phenomenon of crossequatorial cyclone pairs, or "twin" tropical cyclones, in the Indian Ocean originating from Sumatra was first noted by Kuettner (1989). TC genesis appears to be particularly favored during the pre-onset phase of the Madden Julian Oscillation (MJO), when easterly flow encroaches upon Sumatra and the resulting cyclonic wake vortices encounter convectively coupled waves and enhanced moisture associated with the MJO in the Indian Ocean. Operational analysis data from the Year of Tropical Convection (YOTC) and Dynamics of the Madden Julian Oscillation (DYNAMO) campaigns were used to evaluate the impacts of Sumatra's topography upon the flow. The YOTC data encompass two years, from May 2008 to April 2010, while the special observing period of DYNAMO was conducted from October to December 2011. This research also presents three case studies of twin tropical cyclones west of Sumatra in the Indian Ocean, which were all determined to originate from Sumatran wake vortices and occurred between October and December of 2008, 2009, and 2011. Multiple cyclonic wake vortices and vorticity streamers were observed downstream of Sumatra during periods of easterly flow, most frequently between October and December. Froude numbers calculated for the region upstream of Sumatra

  20. Estimating the waiting time of multi-priority emergency patients with downstream blocking.

    Science.gov (United States)

    Lin, Di; Patrick, Jonathan; Labeau, Fabrice

    2014-03-01

    To characterize the coupling effect between patient flow to access the emergency department (ED) and that to access the inpatient unit (IU), we develop a model with two connected queues: one upstream queue for the patient flow to access the ED and one downstream queue for the patient flow to access the IU. Building on this patient flow model, we employ queueing theory to estimate the average waiting time across patients. Using priority specific wait time targets, we further estimate the necessary number of ED and IU resources. Finally, we investigate how an alternative way of accessing ED (Fast Track) impacts the average waiting time of patients as well as the necessary number of ED/IU resources. This model as well as the analysis on patient flow can help the designer or manager of a hospital make decisions on the allocation of ED/IU resources in a hospital.

  1. Algorithm of Dynamic Operation Process of Hydraulic Automatically Operated Canals with Constant-Downstream Level Gates

    Institute of Scientific and Technical Information of China (English)

    ZHANG Li-wei; FENG Xiao-bo; WANG Chang-de

    2005-01-01

    On the basis of analysis the governing process of downstream water level gates AVIO and AVIS, a mathematical model for simulation of dynamic operation process of hydraulically automated irrigation canals installed with AVIO and AVIS gates is presented. the main point of this mathematical model is firstly applying a set of unsteady flow equations (St. Venant equations here) and treating the condition of gate movement as its dynamic boundary, and then decoupling this interaction of gate movement with the change of canal flow. In this process, it is necessary to give the gates' open-loop transfer function whose input is water level deviation and output is gate discharge. The result of this simulation for a practical reach has shown it has satisfactory accuracy.

  2. Development of suitable solvent system for downstream processing of biopolymer pullulan using response surface methodology.

    Directory of Open Access Journals (Sweden)

    Anirban Roy Choudhury

    Full Text Available Downstream processing is an important aspect of all biotechnological processes and has significant implications on quality and yield of the final product. Several solvents were examined for their efficacy on pullulan precipitation from fermentation broth. Interactions among four selected solvents and their effect on pullulan yield were studied using response surface methodology. A polynomial model was developed using D-optimal design and three contour plots were generated by performing 20 different experiments and the model was validated by performing optimization experiments. The results indicated that lower concentration of ethanol in combination with the other three solvents has resulted in higher yield of polymer from fermentation broth and the optimized solvent system was able to recover 1.44 times more pullulan as compared to the conventional ethanolic precipitation method. These observations may help in enhancing efficiency of pullulan recovery from fermentation broth and also result in reduced cost of production for the final product.

  3. Trading in the downstream European gas market. A successive oligopoly approach

    Energy Technology Data Exchange (ETDEWEB)

    Boots, M.G. [ECN Policy Studies, Petten (Netherlands); Rijkers, F.A.M. [Office of Energy Regulation DTe, Den Haag (Netherlands); Hobbs, B.F. [Whiting School of Engineering, Johns Hopkins University, Baltimore, MD (United States)

    2005-01-01

    A model of successive oligopoly is applied to the European natural gas market. The model has a two-level structure, in which Cournot producers are also Stackelberg leaders with respect to traders, who may be Cournot oligopolists or price takers. Several conclusions emerge. First, successive oligopoly (''double marginalization'') yields higher prices and lower consumer welfare than if oligopoly exists only on one level. Second, due to the high concentration of traders, prices are distorted more by market power in trading than in production. Third, trader profits depend on whether producers can price discriminate among consuming sectors; if so, producers collect a greater share of the profits. Finally, when traders increase in number, prices approach competitive levels. Thus, it is important to prevent concentration in the downstream gas market. If oligopolistic trading cannot be prevented, vertical integration should not be discouraged, especially if it would increase the number of traders.

  4. Ovary transcriptome profiling via artificial intelligence reveals a transcriptomic fingerprint predicting egg quality in striped bass, Morone saxatilis.

    Science.gov (United States)

    Chapman, Robert W; Reading, Benjamin J; Sullivan, Craig V

    2014-01-01

    Inherited gene transcripts deposited in oocytes direct early embryonic development in all vertebrates, but transcript profiles indicative of embryo developmental competence have not previously been identified. We employed artificial intelligence to model profiles of maternal ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in the striped bass (Morone saxatilis), a farmed species with serious egg quality problems. In models developed using artificial neural networks (ANNs) and supervised machine learning, collective changes in the expression of a limited suite of genes (233) representing 90% of the eventual variance in embryo survival. Egg quality related to minor changes in gene expression (<0.2-fold), with most individual transcripts making a small contribution (<1%) to the overall prediction of egg quality. These findings indicate that the predictive power of the transcriptome as regards egg quality resides not in levels of individual genes, but rather in the collective, coordinated expression of a suite of transcripts constituting a transcriptomic "fingerprint". Correlation analyses of the corresponding candidate genes indicated that dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence. The affected gene networks are centrally involved in regulation of early development in all vertebrates, including humans. By assessing collective levels of the relevant ovarian transcripts via ANNs we were able, for the first time in any vertebrate, to accurately predict the subsequent embryo developmental potential of eggs from individual females. Our results show that the transcriptomic fingerprint evidencing developmental dysfunction is highly predictive of, and therefore likely to regulate, egg quality, a biologically complex trait crucial to reproductive fitness.

  5. Ovary transcriptome profiling via artificial intelligence reveals a transcriptomic fingerprint predicting egg quality in striped bass, Morone saxatilis.

    Directory of Open Access Journals (Sweden)

    Robert W Chapman

    Full Text Available Inherited gene transcripts deposited in oocytes direct early embryonic development in all vertebrates, but transcript profiles indicative of embryo developmental competence have not previously been identified. We employed artificial intelligence to model profiles of maternal ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in the striped bass (Morone saxatilis, a farmed species with serious egg quality problems. In models developed using artificial neural networks (ANNs and supervised machine learning, collective changes in the expression of a limited suite of genes (233 representing 90% of the eventual variance in embryo survival. Egg quality related to minor changes in gene expression (<0.2-fold, with most individual transcripts making a small contribution (<1% to the overall prediction of egg quality. These findings indicate that the predictive power of the transcriptome as regards egg quality resides not in levels of individual genes, but rather in the collective, coordinated expression of a suite of transcripts constituting a transcriptomic "fingerprint". Correlation analyses of the corresponding candidate genes indicated that dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence. The affected gene networks are centrally involved in regulation of early development in all vertebrates, including humans. By assessing collective levels of the relevant ovarian transcripts via ANNs we were able, for the first time in any vertebrate, to accurately predict the subsequent embryo developmental potential of eggs from individual females. Our results show that the transcriptomic fingerprint evidencing developmental dysfunction is highly predictive of, and therefore likely to regulate, egg quality, a biologically complex trait crucial to reproductive fitness.

  6. Ovary Transcriptome Profiling via Artificial Intelligence Reveals a Transcriptomic Fingerprint Predicting Egg Quality in Striped Bass, Morone saxatilis

    Science.gov (United States)

    2014-01-01

    Inherited gene transcripts deposited in oocytes direct early embryonic development in all vertebrates, but transcript profiles indicative of embryo developmental competence have not previously been identified. We employed artificial intelligence to model profiles of maternal ovary gene expression and their relationship to egg quality, evaluated as production of viable mid-blastula stage embryos, in the striped bass (Morone saxatilis), a farmed species with serious egg quality problems. In models developed using artificial neural networks (ANNs) and supervised machine learning, collective changes in the expression of a limited suite of genes (233) representing 90% of the eventual variance in embryo survival. Egg quality related to minor changes in gene expression (<0.2-fold), with most individual transcripts making a small contribution (<1%) to the overall prediction of egg quality. These findings indicate that the predictive power of the transcriptome as regards egg quality resides not in levels of individual genes, but rather in the collective, coordinated expression of a suite of transcripts constituting a transcriptomic “fingerprint”. Correlation analyses of the corresponding candidate genes indicated that dysfunction of the ubiquitin-26S proteasome, COP9 signalosome, and subsequent control of the cell cycle engenders embryonic developmental incompetence. The affected gene networks are centrally involved in regulation of early development in all vertebrates, including humans. By assessing collective levels of the relevant ovarian transcripts via ANNs we were able, for the first time in any vertebrate, to accurately predict the subsequent embryo developmental potential of eggs from individual females. Our results show that the transcriptomic fingerprint evidencing developmental dysfunction is highly predictive of, and therefore likely to regulate, egg quality, a biologically complex trait crucial to reproductive fitness. PMID:24820964

  7. A computational fluid dynamics modeling study of guide walls for downstream fish passage

    Science.gov (United States)

    Mulligan, Kevin; Towler, Brett; Haro, Alexander J.; Ahlfeld, David P.

    2017-01-01

    A partial-depth, impermeable guidance structure (or guide wall) for downstream fish passage is typically constructed as a series of panels attached to a floating boom and anchored across a water body (e.g. river channel, reservoir, or power canal). The downstream terminus of the wall is generally located nearby to a fish bypass structure. If guidance is successful, the fish will avoid entrainment in a dangerous intake structure (i.e. turbine intakes) while passing from the headpond to the tailwater of a hydroelectric facility through a safer passage route (i.e. the bypass). The goal of this study is to determine the combination of guide wall design parameters that will most likely increase the chance of surface-oriented fish being successfully guided to the bypass. To evaluate the flow field immediately upstream of a guide wall, a parameterized computational fluid dynamics model of an idealized power canal was constructed in © ANSYS Fluent v 14.5 (ANSYS Inc., 2012). The design parameters investigated were the angle and depth of the guide wall and the average approach velocity in the power canal. Results call attention to the importance of the downward to sweeping flow ratio and demonstrate how a change in guide wall depth and angle can affect this important hydraulic cue to out-migrating fish. The key findings indicate that a guide wall set at a small angle (15° is the minimum in this study) and deep enough such that sweeping flow dominant conditions prevail within the expected vertical distribution of fish approaching the structure will produce hydraulic conditions that are more likely to result in effective passage.

  8. Mammalian TBX1 preferentially binds and regulates downstream targets via a tandem T-site repeat.

    Science.gov (United States)

    Castellanos, Raquel; Xie, Qing; Zheng, Deyou; Cvekl, Ales; Morrow, Bernice E

    2014-01-01

    Haploinsufficiency or mutation of TBX1 is largely responsible for the etiology of physical malformations in individuals with velo-cardio-facial/DiGeorge syndrome (VCFS/DGS/22q11.2 deletion syndrome). TBX1 encodes a transcription factor protein that contains an evolutionarily conserved DNA binding domain termed the T-box that is shared with other family members. All T-box proteins, examined so far, bind to similar but not identical consensus DNA sequences, indicating that they have specific binding preferences. To identify the TBX1 specific consensus sequence, Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was performed. In contrast to other TBX family members recognizing palindrome sequences, we found that TBX1 preferentially binds to a tandem repeat of 5'-AGGTGTGAAGGTGTGA-3'. We also identified a second consensus sequence comprised of a tandem repeat with a degenerated downstream site. We show that three known human disease-causing TBX1 missense mutations (F148Y, H194Q and G310S) do not alter nuclear localization, or disrupt binding to the tandem repeat consensus sequences, but they reduce transcriptional activity in cell culture reporter assays. To identify Tbx1-downstream genes, we performed an in silico genome wide analysis of potential cis-acting elements in DNA and found strong enrichment of genes required for developmental processes and transcriptional regulation. We found that TBX1 binds to 19 different loci in vitro, which may correspond to putative cis-acting binding sites. In situ hybridization coupled with luciferase gene reporter assays on three gene loci, Fgf8, Bmper, Otog-MyoD, show that these motifs are directly regulated by TBX1 in vitro. Collectively, the present studies establish new insights into molecular aspects of TBX1 binding to DNA. This work lays the groundwork for future in vivo studies, including chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) to further elucidate the molecular

  9. Evaluation of the In-vessel Downstream Effects for the APR1400 Design and License

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Jeong-kwan; Kim, Jae-won; Kwon, Sun-guk; Lee, Jae-yong [KHNP Central Research Institute, Daejeon (Korea, Republic of)

    2015-10-15

    These reports include the licensing issues as follows; the effect of a flow channel gap change, the effect of debris settling, the accuracy of the GF630 flow meter, the effect of bubbles impinging on the bottom nozzle, and the bypass fiber amount. In this paper, the valuation results of the in-vessel downstream effects for the APR1400 were described. In addition, the effect of a flow channel gap change and the bypass fiber amount were evaluated. In-vessel downstream effect tests with a mock-up PLUS7 fuel assembly were performed to confirm that the head losses caused by debris meet the available driving head following a LOCA. All the test results showed lower pressure drops than the available head limits. Therefore, a sufficient driving force is available to maintain an adequate flow rate, and the LTCC capability is adequately maintained in the APR1400. A sensitivity test was conducted to assess the effect of a change in the gap size between the mock-up fuel assembly and the test column. The maximum pressure drop recorded for the test was 19.73 kPa under the re-manufactured condition. This value is larger by 1.6% than the previous test result (19.4 kPa) under the same conditions. As such, changing the gap of the flow path between the mock-up fuel assembly and the test column from the previous manufactured conditions to the re-manufactured conditions is expected to result in a slight increase in the differential pressure. However, this is a negligible amount compared to the test uncertainty value of 25%.

  10. Use of Bone Scan During Initial Prostate Cancer Workup, Downstream Procedures, and Associated Medicare Costs

    Energy Technology Data Exchange (ETDEWEB)

    Falchook, Aaron D. [Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Salloum, Ramzi G. [Department of Health Services Policy and Management, University of South Carolina, Columbia, South Carolina (United States); Hendrix, Laura H. [Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Chen, Ronald C., E-mail: ronald_chen@med.unc.edu [Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Cecil G. Sheps Center for Health Services Research, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States); Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (United States)

    2014-06-01

    Purpose: For patients with a high likelihood of having metastatic disease (high-risk prostate cancer), bone scan is the standard, guideline-recommended test to look for bony metastasis. We quantified the use of bone scans and downstream procedures, along with associated costs, in patients with high-risk prostate cancer, and their use in low- and intermediate-risk patients for whom these tests are not recommended. Methods and Materials: Patients in the Surveillance, Epidemiology, and End Results (SEER)-Medicare database diagnosed with prostate cancer from 2004 to 2007 were included. Prostate specific antigen (PSA), Gleason score, and clinical T stage were used to define D'Amico risk categories. We report use of bone scans from the date of diagnosis to the earlier of treatment or 6 months. In patients who underwent bone scans, we report use of bone-specific x-ray, computed tomography (CT), and magnetic resonance imaging (MRI) scans, and bone biopsy within 3 months after bone scan. Costs were estimated using 2012 Medicare reimbursement rates. Results: In all, 31% and 48% of patients with apparent low- and intermediate-risk prostate cancer underwent a bone scan; of these patients, 21% underwent subsequent x-rays, 7% CT, and 3% MRI scans. Bone biopsies were uncommon. Overall, <1% of low- and intermediate-risk patients were found to have metastatic disease. The annual estimated Medicare cost for bone scans and downstream procedures was $11,300,000 for low- and intermediate-risk patients. For patients with apparent high-risk disease, only 62% received a bone scan, of whom 14% were found to have metastasis. Conclusions: There is overuse of bone scans in patients with low- and intermediate-risk prostate cancers, which is unlikely to yield clinically actionable information and results in a potential Medicare waste. However, there is underuse of bone scans in high-risk patients for whom metastasis is likely.

  11. Swim performance and energy homeostasis in spottail shiner (Notropis hudsonius) collected downstream of a uranium mill.

    Science.gov (United States)

    Goertzen, Meghan M; Hauck, Dominic W; Phibbs, James; Weber, Lynn P; Janz, David M

    2012-01-01

    The Key Lake uranium milling operation (Saskatchewan, Canada) releases complex effluent into the local watershed. The objective of the current study was to investigate whether fish from an effluent-receiving waterbody exhibited differences in swimming performance and energy homeostasis compared to fish from a local reference site. Juvenile spottail shiner (Notropis hudsonius) were collected from a lake downstream of the uranium mill, and compared to fish collected from a nearby reference lake. Critical swimming speed (U(crit); fatigue velocity), tail beat frequency, and tail amplitude did not differ significantly when comparing fish collected from the exposure lake and reference lake. Captured shiner used in swim tests were considered fatigued, and metabolic endpoints were compared between this group and non-fatigued fish, which were treated similarly but not subjected to swim tests. In both non-fatigued and fatigued shiner, liver glycogen was significantly greater in fish collected from the exposure lake compared to the reference lake. However, it is unclear if this effect, and others related to condition, were the result of contaminant exposure or other environmental factors. While there were no differences in plasma lactate, hematocrit or liver triglycerides in non-fatigued fish between sites, only fatigued reference fish had increased lactate and hematocrit and decreased triglycerides. In non-fatigued fish, plasma glucose did not significantly differ between sites, but significantly decreased after swimming only in fish from the exposure lake. In summary, shiner from the exposure site demonstrated similar swim endurance and possessed greater energy stores despite metabolic alterations compared to shiner from the reference site. Therefore, because fish collected downstream of the uranium mill operation had similar swimming ability as fish from the reference lake, U(crit) test results presented here may not reflect or be indicative of metabolic effects of complex

  12. Phosphorus release potential and pollution characteristics of sediment in downstream Nansi Lake, China

    Institute of Scientific and Technical Information of China (English)

    Zhijian LI; Qinyan YUE; Baoyu GAO; Yanwen WANG; Qing LIU

    2012-01-01

    The research aimed to evaluate present and potential phosphorous pollution due to high sedimentary phosphorus load and release from sediment, when external phosphorus was reduced in downstream Nansi Lake. Pollution load of the sediment and overlying water was investigated. Kinetics and isotherms of adsorption/release of sedimentary phosphorus were studied to determine equilibrium phosphate concentration (EPCo) and release potential. Kinetics of phosphorus adsorption on sediment and release from sediment were well described by both the pseudo-first-order rate equation and the pseudo-second- order rate equation, but more appropriate to the pseudo- second-order rate equation with the adsorption/release capacity more close to the measured values, suggesting that the processes were chemically rate controlled and dependent on adsorption capacity. Soluble reactive phosphorus (SRP) sorption isotherms on sediment were best fitted by the modified Langmuir model indicating a monolayer adsorption. By comparing EPC0 and SRP of water, the status (adsorption, releasing or in equilibrium) of sediment phosphorus could be determined. The sediments at site S l, S3, S4, S5, and S7 where the EPC0s were greater than the SRPs, had a potential to release phosphorus into the water column. However, those sediments at S9, S10, and S 12, where the EPC0s were approximately equal to the SRPs, were in impermanent equilibrium with overlying water in status of phosphorus, the sediments can be likely to release phosphorus to the water column once the equilibrium was broken. Therefore, sedimentary phos- phorus can be a secondary pollution source in downstream Nansi Lake.

  13. Mammalian TBX1 preferentially binds and regulates downstream targets via a tandem T-site repeat.

    Directory of Open Access Journals (Sweden)

    Raquel Castellanos

    Full Text Available Haploinsufficiency or mutation of TBX1 is largely responsible for the etiology of physical malformations in individuals with velo-cardio-facial/DiGeorge syndrome (VCFS/DGS/22q11.2 deletion syndrome. TBX1 encodes a transcription factor protein that contains an evolutionarily conserved DNA binding domain termed the T-box that is shared with other family members. All T-box proteins, examined so far, bind to similar but not identical consensus DNA sequences, indicating that they have specific binding preferences. To identify the TBX1 specific consensus sequence, Systematic Evolution of Ligands by Exponential Enrichment (SELEX was performed. In contrast to other TBX family members recognizing palindrome sequences, we found that TBX1 preferentially binds to a tandem repeat of 5'-AGGTGTGAAGGTGTGA-3'. We also identified a second consensus sequence comprised of a tandem repeat with a degenerated downstream site. We show that three known human disease-causing TBX1 missense mutations (F148Y, H194Q and G310S do not alter nuclear localization, or disrupt binding to the tandem repeat consensus sequences, but they reduce transcriptional activity in cell culture reporter assays. To identify Tbx1-downstream genes, we performed an in silico genome wide analysis of potential cis-acting elements in DNA and found strong enrichment of genes required for developmental processes and transcriptional regulation. We found that TBX1 binds to 19 different loci in vitro, which may correspond to putative cis-acting binding sites. In situ hybridization coupled with luciferase gene reporter assays on three gene loci, Fgf8, Bmper, Otog-MyoD, show that these motifs are directly regulated by TBX1 in vitro. Collectively, the present studies establish new insights into molecular aspects of TBX1 binding to DNA. This work lays the groundwork for future in vivo studies, including chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq to further elucidate the

  14. Assessing the Downstream Impact of the Integrated Use of Socioeconomic and Remote Sensing Data

    Science.gov (United States)

    Chen, R. S.; Downs, R. R.; Schumacher, J.

    2014-12-01

    The interdisciplinary use of data from multiple disciplines to address both research and applied problems has received increasing attention in the sciences, but understanding remains limited on the specific modalities of data use and their impact not only in enabling new research insights but also in facilitating the application of research to societal problems. In our previous work, we used citation analysis to investigate the use of data from the NASA Socioeconomic Data and Applications Center (SEDAC) and identify the extent of interdisciplinary use, based on the subject classifications of citing journals. We also proposed and tested a taxonomy of data integration and use on a selection of peer-reviewed scientific articles that cited both remote sensing data and socioeconomic data from SEDAC. We extend both of these analyses here. We analyze the interdisciplinary use of SEDAC data over a seven-year period including the types and topical areas of application observed. We also explore the degree to which different types of data integration and use are leading to further "downstream" research and applications, and if objective measures can be developed using bibliometric methods to quantify downstream use and impact in meaningful ways. These methods include both traditional citation analysis and searches of the informal literature and online resources. Better understanding of how disparate data and information has been utilized to address new interdisciplinary problems will help the data user and provider communities improve the effectiveness and efficiency of their efforts. It should also provide justification for further investments in linking different data resources and networks across scientific fields, in methods of interdisciplinary data integration, and in application of integrated data to societal problems.

  15. Environmental radiological studies downstream from Rancho Seco Nuclear Power Generating Station

    Energy Technology Data Exchange (ETDEWEB)

    Noshkin, V.E.; Wong, K.M.; Eagle, R.J.; Dawson, J.W.; Brunk, J.L.; Jokela, T.A.

    1985-03-22

    This report summarizes the information compiled in 1984 while assessing the environmental impact of radionuclides in aquatic releases from the Rancho Seco Nuclear Power Generating Station. Gamma-emitting radionuclides discharged since 1981 are found in many of the dietary components derived from the creeks receiving the effluent wastewater. Some soils and crops are found to contain radionuclides that originate from the contaminated water that was transferred to land during the irrigation season. /sup 134/Cs and /sup 137/Cs are the primary gamma-emitting radionuclides detected in the edible flesh of fish from the creeks. Concentrations in the flesh of fish decreased exponentially with distance from the plant. No significant differences in the /sup 137/Cs activity were found between male and female fish of equal size, but concentrations may vary in fish of different size, with the season and diet. 21% of the total /sup 137/Cs and /sup 134/Cs discharged between 1981 and 1984 is associated with the creek sediments to a distance of 27 km from the plant. Fractions of the missing inventory have been transferred to land during the irrigation season or to downstream regions more distant than 27 km from the plant. The radiocesium content of the sediments in 1984 decreased significantly in a downstream direction, much in the same manner as concentrations decreased in fish. Radioactivity originating from the plant was not above detection limits in any terrestrial food item sampled beyond 6.5 km from the plant. Based on the usage factors provided by individuals interviewed in a 1984 survey, the fish and aquatic-organism ingestion pathway contributed the largest radiological dose to humans utilizing products contaminated with the radionuclides in the liquid wastes discharged from the Rancho Seco Nuclear Power Generating Station in 1984.

  16. Downstream changes of water quality in a lowland river due to groundwater inflows.

    Science.gov (United States)

    Zieba, Damian; Bar-Michalczyk, Dominika; Kania, Jarosław; Malina, Grzegorz; Michalczyk, Tomasz; Rozanski, Kazimierz; Witczak, Stanislaw; Wachniew, Przemyslaw; Zurek, Anna J.

    2016-04-01

    The Kocinka catchment (ca. 250 km2) in southern Poland receives substantial inflows of groundwater from a major fissured-carbonate aquifer polluted with nitrates originating from agriculture and domestic sewage. The 40 km long Kocinka river reveals large spatial variations in physical and chemical water properties with large downstream changes of nitrate concentrations. Detailed longitudinal surveys of such water characteristics as nitrate concentration, water temperature, pH, electric conductivity, stable isotopic composition, tritium concentration were performed in order to identify and quantify groundwater inflows. The river gains groundwater down to the 25 km from the source and a looses water further downstream. The subsequent increase and decrease of nitrate concentration in the upper and middle reaches of the river are caused by inflows of the, respectively, polluted and non-polluted groundwaters. The range of such changes can be even five-fold while the drop of nitrate concentration along the semi natural, 18 km long, lower reach where the river is well connected to its riparian and hyporheic zones nitrate loss is of the order of 10%. More significant nitrate losses were observed in the dammed reaches and in a small reservoir in the upper part of the river. Results of the study have implications for identification of measures that can be undertaken to reduce nitrate export from the catchment. Because of the role of groundwater in river runoff reduction of nitrate loads to the aquifer should be primary objective. Acknowledgements. The work was carried out as part of the BONUS Soils2Sea project on groundwater system (http:/www.soils2sea.eu) financed by the European Commission 7 FP contract 226536 and the statutory funds of the AGH University of Science and Technology (project No.11.11.140.026 and 11.11.220.01).

  17. PIV measurements of the flow field just downstream of an oscillating collapsible tube.

    Science.gov (United States)

    Bertram, C D; Truong, N K; Hall, S D

    2008-12-01

    We probed the time-varying flow field immediately downstream of a flexible tube conveying an aqueous flow, during flow-induced oscillation of small amplitude, at time-averaged Reynolds numbers (Re) in the range 300-550. Velocity vector components in the plane of a laser sheet were measured by high-speed ("time-resolved") particle image velocimetry. The sheet was aligned alternately with both the major axis and the minor axis of the collapsing tube by rotating the pressure chamber in which the tube was mounted. The Womersley number of the oscillations was approximately 10. In the major-axis plane the flow fields were characterized by two jets that varied in lateral spacing. The rapid deceleration of flow at maximal collapse caused the jets momentarily to merge about one diameter into the downstream pipe, and strengthened and enlarged the existing retrograde flow lateral to each jet. Collapse also spread the jets maximally, allowing retrograde flow between them during the ascent from its minimum of the pressure at the end of the flexible tube. The minor-axis flow fields showed that the between-jet retrograde flow at this time extended all the way across the pipe. Whereas the retrograde flow lateral to the jets terminated within three diameters of the tube end at Re=335 at all times, it extended beyond three diameters at Re=525 for some 25% of the cycle including the time of maximal flow deceleration. Off-axis sheet positioning revealed the lateral jets to be crescent shaped. When the pressure outside the tube was increased, flattening the tube more, the jets retained a more consistent lateral position. These results illuminate the flows created by collapsible-tube oscillation in a laminar regime accessible to numerical modeling.

  18. Screening level dose assessment of aquatic biota downstream of the Marcoule nuclear complex in southern France.

    Science.gov (United States)

    St-Pierre, S; Chambers, D B; Lowe, L M; Bontoux, J G

    1999-09-01

    Aquatic biota in the Rhone River downstream of the Marcoule nuclear complex in France are exposed to natural sources of radiation and to radioactivity released from the Marcoule complex. A simple conservative screening level model was used to estimate the range of concentrations in aquatic media (water, sediments, and aquatic organisms) of both artificial and natural radionuclides and the consequent absorbed (whole body) dose rates for aquatic organisms. Five categories of aquatic organisms were studied, namely, submerged aquatic plants (phanerogam), non-bottom-feeding fish, bottom-feeding fish, mollusca, and fish-eating birds. The analysis was based on the radionuclide concentrations reported in four consecutive annual radioecological monitoring reports published by French agencies with nuclear regulatory responsibilities. The results of this assessment were used to determine, qualitatively, the magnitude of any potential health impacts on each of the five categories of aquatic organisms studied. The range of dose rate estimates ranged over three orders of magnitude, with maximum dose rates estimated to be in the order of 1 to 10 microGy h(-1). These maximum dose rates are a factor 40 or more below the international guideline intended to ensure the protection of aquatic populations (about 400 microGy h(-1)), and a factor ten or more below the level which may trigger the need for a more detailed evaluation of potential ecological consequences to the exposed populations (about 100 microGy h(-1)). As a result, chronic levels of radioactivity, artificial and natural, measured in aquatic media downstream of Marcoule are unlikely to result in adverse health impacts on the categories and species of aquatic organisms studied. Thus, based on the screening level analysis discussed in this paper, a more detailed evaluation of the dose rates does not appear to be warranted.

  19. A Hydraulic Nexus between Geographically Isolated Wetlands and Downstream Water Bodies

    Science.gov (United States)

    Mclaughlin, D. L.; Kaplan, D. A.; Cohen, M. J.

    2014-12-01

    Geographic isolation does not imply hydrological isolation; indeed, local groundwater exchange between geographically isolated wetlands (GIWs) and surrounding uplands may yield important controls on regional hydrology. Differences in specific yield (Sy) between aquifers and inundated GIWs drive differences in water level responses to atmospheric fluxes, leading to frequent reversals in hydraulic gradients that cause GIWs to act as both groundwater sinks and sources. When distributed across the landscape, these reversals in local groundwater fluxes are predicted to collectively buffer the surficial aquifer and its regulation of baseflow delivery, a process we refer to as landscape hydrologic capacitance. To test this hypothesis, we integrated models of daily soil moisture, upland water table, and wetland stage dynamics to simulate hydrology of a low-relief landscape with GIWs. Simulations explored the influences of cumulative wetland area, individual wetland size, climate, and soil texture on water table and baseflow variation. Increasing cumulative wetland area and decreasing individual wetland size reduced water table variation and the frequency of extremely shallow and deep water tables. This buffering effect extended to baseflow deliveries, decreasing the standard deviation of daily baseflow by as much as 50%. For the same total wetland area, landscapes with fewer (i.e., larger) wetlands exhibited markedly lower hydrologic capacitance than those with more (i.e., smaller) wetlands, highlighting the important role of small GIWs in regulating regional hydrology. Recent U.S. Supreme Court rulings have limited federal protections for GIWs except where a "significant nexus" to a navigable water body is demonstrated. Our results suggest that GIWs regulate downstream baseflow, even where water in GIWs may never physically reach downstream systems, providing a significant "hydraulic" nexus to distant water bodies.

  20. Human Cytomegalovirus Immediate-Early 1 Protein Rewires Upstream STAT3 to Downstream STAT1 Signaling Switching an IL6-Type to an IFNγ-Like Response.

    Directory of Open Access Journals (Sweden)

    Thomas Harwardt

    2016-07-01

    Full Text Available The human cytomegalovirus (hCMV major immediate-early 1 protein (IE1 is best known for activating transcription to facilitate viral replication. Here we present transcriptome data indicating that IE1 is as significant a repressor as it is an activator of host gene expression. Human cells induced to express IE1 exhibit global repression of IL6- and oncostatin M-responsive STAT3 target genes. This repression is followed by STAT1 phosphorylation and activation of STAT1 target genes normally induced by IFNγ. The observed repression and subsequent activation are both mediated through the same region (amino acids 410 to 445 in the C-terminal domain of IE1, and this region serves as a binding site for STAT3. Depletion of STAT3 phenocopies the STAT1-dependent IFNγ-like response to IE1. In contrast, depletion of the IL6 receptor (IL6ST or the STAT kinase JAK1 prevents this response. Accordingly, treatment with IL6 leads to prolonged STAT1 instead of STAT3 activation in wild-type IE1 expressing cells, but not in cells expressing a mutant protein (IE1dl410-420 deficient for STAT3 binding. A very similar STAT1-directed response to IL6 is also present in cells infected with a wild-type or revertant hCMV, but not an IE1dl410-420 mutant virus, and this response results in restricted viral replication. We conclude that IE1 is sufficient and necessary to rewire upstream IL6-type to downstream IFNγ-like signaling, two pathways linked to opposing actions, resulting in repressed STAT3- and activated STAT1-responsive genes. These findings relate transcriptional repressor and activator functions of IE1 and suggest unexpected outcomes relevant to viral pathogenesis in response to cytokines or growth factors that signal through the IL6ST-JAK1-STAT3 axis in hCMV-infected cells. Our results also reveal that IE1, a protein considered to be a key activator of the hCMV productive cycle, has an unanticipated role in tempering viral replication.

  1. Targeting downstream transcription factors and epigenetic modifications following Toll-like receptor 7/8 ligation to forestall tissue injury in anti-Ro60 associated heart block.

    Science.gov (United States)

    Clancy, Robert M; Markham, Androo J; Reed, Joanne H; Blumenberg, Miroslav; Halushka, Marc K; Buyon, Jill P

    2016-02-01

    Based on the consistent demonstration of fibrosis of the atrioventricular node surrounded by macrophages and multinucleated giant cells in anti-Ro antibody exposed fetuses dying with heart block, this study focuses on macrophage signaling stimulated by ssRNA associated with the Ro60 protein and the impact of antagonizing innate cell drivers such as TLR7/8. Transcriptome and epigenetic modifications which affect transcription factors, NF-κB and STAT1, were selected to evaluate the phenotype of macrophages in which TLR7/8 was ligated following treatment with either anti-Ro60/Ro60/hY3 RNA immune complexes or transfection with hY3. Based on microarray, TNF and IL6 were among the most highly upregulated genes in both stimulated conditions, each of which was significantly inhibited by preincubation with hydroxychloroquine (HCQ). In contrast, following stimulation of macrophages with either TNF-α or IFN-α, which do not signal through TLR, the resultant gene expression was refractory to HCQ. Ligation of TLR7/8 resulted in increased histone methylation as measured by increased H3K4me2, a requirement for binding of NF-κB at certain promoters, specifically the kB1 region in the TNF promoter (ChIP-qPCR), which was significantly decreased by HCQ. In summary, these results support that the HCQ-sensitive phenotype of hY3 stimulated macrophages reflects the bifurcation of TLR downstream signals involving NF-κB and STAT 1 pathways and for the former dimethylation of H3K4. Accordingly, HCQ may act more as a preventive measure in downregulating the initial production of IFN-α or TNF-α and not affect the resultant autocoid stimulation reflected in TNF-α and IFN-α responsive genes. The beneficial scope of antimalarials in the prevention of organ damage, inclusive of heart block in an anti-Ro offspring or more broadly SLE, may include in part, a mechanism targeting TLR-dependent epigenetic modification.

  2. Identification and expression analysis of primary auxin-responsive Aux/IAA gene family in cucumber (Cucumis sativus)

    Indian Academy of Sciences (India)

    Defang Gan; Dan Zhuang; Fei Ding; Zhenzhou Yu; Yang Zhao

    2013-12-01

    Aux/IAA is an important gene family involved in many aspects of growth and development. Aux/IAA proteins are short-lived nuclear proteins that are induced primarily by various phytohormones. In this study, 29 Aux/IAA family genes (CsIAA01–CsIAA29) were identified and characterized in cucumber, including gene structures, phylogenetic relationships, conserved protein motifs and chromosomal locations. These genes show distinct organizational patterns of their putative motifs. The distributions of the genes vary: except for five CsIAA genes in cucumber that were not located, seven CsIAA genes were found on scaffold, while the other 17 CsIAA genes were distributed on seven other chromosomes. Based on a phylogenetic analysis of the Aux/IAA protein sequences from cucumber, Arabidopsis and other plants, the Aux/IAA genes in cucumber were categorized into seven subfamilies. To investigate whether the expression of CsIAA genes is associated with auxin induction, their transcript levels were monitored in seedlings treated with IAA (indole-3-acetic acid), and their expression patterns were analysed by semiquantitative reverse transcription-polymerase chain reaction (RT-PCR). The results showed that 11/29 CsIAA genes were expressed in leaves whether treated with IAA or not and the time course of processing and compared with the control, five CsIAA genes showed low expression only after 60 min treatment with IAA, while 11 genes showed no expression. These results provide useful information for further functional analysis of Aux/IAA gene family in cucumber.

  3. Under-expression of the Auxin Response Factor Sl-ARF4 improves postharvest behavior of tomato fruits.

    Science.gov (United States)

    Sagar, Maha; Chervin, Christian; Roustant, Jean-Paul; Bouzayen, Mondher; Zouine, Mohamed

    2013-10-01

    Auxin is one of the most prominent phytohormones regulating many aspects of fleshy fruit development including fruit set, fruit size through the control of cell division and cell expansion, and fruit ripening. To shed light on the role of auxin fruit ripening, we have previously shown that Sl-ARF4 is a major player in mediating the auxin control of sugar metabolism in tomato fruit (cv MicroTom). Further extending this study, we show here that down-regulation of Sl-ARF4 in tomato alters some ripening-related fruit quality traits including enhanced fruit density at mature stage, increased firmness, prolonged shelf-life and reduced water (weight) loss at red ripe stage. These findings suggest that Sl-ARF4 plays a role in determining fruit cell wall architecture and thus providing a potential genetic marker for improving post-harvest handling and shelf life of tomato fruits.

  4. Transcriptome profiling of Cucumis melo fruit development and ripening.

    Science.gov (United States)

    Zhang, Hong; Wang, Huaisong; Yi, Hongping; Zhai, Wenqiang; Wang, Guangzhi; Fu, Qiushi

    2016-01-01

    Hami melon (Cucumis melo) is the most important melon crop grown in the north-western provinces of China. In order to elucidate the genetic and molecular basis of developmental changes related to size, flesh, sugar and sour content, we performed a transcriptome profiling of its fruit development. Over 155 000 000 clean reads were mapped to MELONOMICS genome, yielding a total of 23 299 expressed genes. Of these, 554 genes were specifically expressed in flowers, and 3260 genes in fruit flesh tissues. The 7892 differentially expressed genes (DEGs) were related to fruit development and mediated diverse metabolic processes and pathways; 83 DEGs and 13 DEGs were possibly associated with sucrose and citric acid accumulation, respectively. The quantitative real-time PCR results showed that six out of eight selected candidate genes displayed expression trends similar to our DEGs. This study profiled the gene expression related to different growing stages of flower and fruit at the whole transcriptome level to provide an insight into the regulatory mechanism underlying Hami melon fruit development.

  5. Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree.

    Science.gov (United States)

    Kuravadi, Nagesh A; Yenagi, Vijay; Rangiah, Kannan; Mahesh, H B; Rajamani, Anantharamanan; Shirke, Meghana D; Russiachand, Heikham; Loganathan, Ramya Malarini; Shankara Lingu, Chandana; Siddappa, Shilpa; Ramamurthy, Aishwarya; Sathyanarayana, B N; Gowda, Malali

    2015-01-01

    Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC-600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways.

  6. High-throughput sequencing of black pepper root transcriptome

    Directory of Open Access Journals (Sweden)

    Gordo Sheila MC

    2012-09-01

    Full Text Available Abstract Background Black pepper (Piper nigrum L. is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host’s root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant’s root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.

  7. Genome scale transcriptomics of baculovirus-insect interactions.

    Science.gov (United States)

    Nguyen, Quan; Nielsen, Lars K; Reid, Steven

    2013-11-12

    Baculovirus-insect cell technologies are applied in the production of complex proteins, veterinary and human vaccines, gene delivery vectors' and biopesticides. Better understanding of how baculoviruses and insect cells interact would facilitate baculovirus-based production. While complete genomic sequences are available for over 58 baculovirus species, little insect genomic information is known. The release of the Bombyx mori and Plutella xylostella genomes, the accumulation of EST sequences for several Lepidopteran species, and especially the availability of two genome-scale analysis tools, namely oligonucleotide microarrays and next generation sequencing (NGS), have facilitated expression studies to generate a rich picture of insect gene responses to baculovirus infections. This review presents current knowledge on the interaction dynamics of the baculovirus-insect system' which is relatively well studied in relation to nucleocapsid transportation, apoptosis, and heat shock responses, but is still poorly understood regarding responses involved in pro-survival pathways, DNA damage pathways, protein degradation, translation, signaling pathways, RNAi pathways, and importantly metabolic pathways for energy, nucleotide and amino acid production. We discuss how the two genome-scale transcriptomic tools can be applied for studying such pathways and suggest that proteomics and metabolomics can produce complementary findings to transcriptomic studies.

  8. Bamboo Flowering from the Perspective of Comparative Genomics and Transcriptomics.

    Science.gov (United States)

    Biswas, Prasun; Chakraborty, Sukanya; Dutta, Smritikana; Pal, Amita; Das, Malay

    2016-01-01

    Bamboos are an important member of the subfamily Bambusoideae, family Poaceae. The plant group exhibits wide variation with respect to the timing (1-120 years) and nature (sporadic vs. gregarious) of flowering among species. Usually flowering in woody bamboos is synchronous across culms growing over a large area, known as gregarious flowering. In many monocarpic bamboos this is followed by mass death and seed setting. While in sporadic flowering an isolated wild clump may flower, set little or no seed and remain alive. Such wide variation in flowering time and extent means that the plant group serves as repositories for genes and expression patterns that are unique to bamboo. Due to the dearth of available genomic and transcriptomic resources, limited studies have been undertaken to identify the potential molecular players in bamboo flowering. The public release of the first bamboo genome sequence Phyllostachys heterocycla, availability of related genomes Brachypodium distachyon and Oryza sativa provide us the opportunity to study this long-standing biological problem in a comparative and functional genomics framework. We identified bamboo genes homologous to those of Oryza and Brachypodium that are involved in established pathways such as vernalization, photoperiod, autonomous, and hormonal regulation of flowering. Additionally, we investigated triggers like stress (drought), physiological maturity and micro RNAs that may play crucial roles in flowering. We also analyzed available transcriptome datasets of different bamboo species to identify genes and their involvement in bamboo flowering. Finally, we summarize potential research hurdles that need to be addressed in future research.

  9. Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

    Directory of Open Access Journals (Sweden)

    Nagesh A. Kuravadi

    2015-08-01

    Full Text Available Neem (Azadirachta indica A. Juss is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC. Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways.

  10. An RNA-Seq-based reference transcriptome for Citrus.

    Science.gov (United States)

    Terol, Javier; Tadeo, Francisco; Ventimilla, Daniel; Talon, Manuel

    2016-03-01

    Previous RNA-Seq studies in citrus have been focused on physiological processes relevant to fruit quality and productivity of the major species, especially sweet orange. Less attention has been paid to vegetative or reproductive tissues, while most Citrus species have never been analysed. In this work, we characterized the transcriptome of vegetative and reproductive tissues from 12 Citrus species from all main phylogenetic groups. Our aims were to acquire a complete view of the citrus transcriptome landscape, to improve previous functional annotations and to obtain genetic markers associated with genes of agronomic interest. 28 samples were used for RNA-Seq analysis, obtained from 12 Citrus species: C. medica, C. aurantifolia, C. limon, C. bergamia, C. clementina, C. deliciosa, C. reshni, C. maxima, C. paradisi, C. aurantium, C. sinensis and Poncirus trifoliata. Four different organs were analysed: root, phloem, leaf and flower. A total of 3421 million Illumina reads were produced and mapped against the reference C. clementina genome sequence. Transcript discovery pipeline revealed 3326 new genes, the number of genes with alternative splicing was increased to 19,739, and a total of 73,797 transcripts were identified. Differential expression studies between the four tissues showed that gene expression is overall related to the physiological function of the specific organs above any other variable. Variants discovery analysis revealed the presence of indels and SNPs in genes associated with fruit quality and productivity. Pivotal pathways in citrus such as those of flavonoids, flavonols, ethylene and auxin were also analysed in detail.

  11. The capsicum transcriptome DB: a "hot" tool for genomic research.

    Science.gov (United States)

    Góngora-Castillo, Elsa; Fajardo-Jaime, Rubén; Fernández-Cortes, Araceli; Jofre-Garfias, Alba E; Lozoya-Gloria, Edmundo; Martínez, Octavio; Ochoa-Alejo, Neftalí; Rivera-Bustamante, Rafael

    2012-01-01

    Chili pepper (Capsicum annuum) is an economically important crop with no available public genome sequence. We describe a genomic resource to facilitate Capsicum annuum research. A collection of Expressed Sequence Tags (ESTs) derived from five C. annuum organs (root, stem, leaf, flower and fruit) were sequenced using the Sanger method and multiple leaf transcriptomes were deeply sampled using with GS-pyrosequencing. A hybrid assembly of 1,324,516 raw reads yielded 32,314 high quality contigs as validated by coverage and identity analysis with existing pepper sequences. Overall, 75.5% of the contigs had significant sequence similarity to entries in nucleic acid and protein databases; 23% of the sequences have no