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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 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. PMID:27052306

  4. Auxin response under osmotic stress.

    Science.gov (United States)

    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. Up in the air: Untethered Factors of Auxin Response

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    Powers, Samantha K.; Strader, Lucia C.

    2016-01-01

    As a prominent regulator of plant growth and development, the hormone auxin plays an essential role in controlling cell division and expansion. Auxin-responsive gene transcription is mediated through the TRANSPORT INHIBITOR RESPONSE1/AUXIN SIGNALING F-BOX (TIR1/AFB) pathway. Roles for TIR1/AFB pathway components in auxin response are understood best, but additional factors implicated in auxin responses require more study. The function of these factors, including S-Phase Kinase-Associated Protein 2A (SKP2A), SMALL AUXIN UP RNAs (SAURs), INDOLE 3-BUTYRIC ACID RESPONSE5 (IBR5), and AUXIN BINDING PROTEIN1 (ABP1), has remained largely obscure. Recent advances have begun to clarify roles for these factors in auxin response while also raising additional questions to be answered. PMID:26918184

  7. Role of auxin-responsive genes in biotic stress responses

    OpenAIRE

    Ghanashyam, Challa; Jain, Mukesh

    2009-01-01

    Although the phytohormone auxin has been implicated primarily in developmental processes, some recent studies suggest its involvement in stress/defense responses as well. Recently, we identified auxin-responsive genes and reported their comprehensive transcript profiling during various stages of development and abiotic stress responses in crop plant rice. The analysis revealed tissue-specific and overlapping expression profiles of auxin-responsive genes during various stages of reproductive d...

  8. A Review of Auxin Response Factors (ARFs) in Plants

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    Li, Si-Bei; Xie, Zong-Zhou; Hu, Chun-Gen; Zhang, Jin-Zhi

    2016-01-01

    Auxin is a key regulator of virtually every aspect of plant growth and development from embryogenesis to senescence. Previous studies have indicated that auxin regulates these processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs). ARFs are likely components that confer specificity to auxin response through selection of target genes as transcription factors. They bind to auxin response DNA elements (AuxRE) in the promoters of auxin-regulated genes and either activate or repress transcription of these genes depending on a specific domain in the middle of the protein. Genetic studies have implicated various ARFs in distinct developmental processes through loss-of-function mutant analysis. Recent advances have provided information on the regulation of ARF gene expression, the role of ARFs in growth and developmental processes, protein–protein interactions of ARFs and target genes regulated by ARFs in plants. In particular, protein interaction and structural studies of ARF proteins have yielded novel insights into the molecular basis of auxin-regulated transcription. These results provide the foundation for predicting the contributions of ARF genes to the biology of other plants. PMID:26870066

  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

    Science.gov (United States)

    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. Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize

    OpenAIRE

    Xing, Hongyan; Pudake, Ramesh N.; Guo, Ganggang; Xing, Guofang; Hu, Zhaorong; Zhang, Yirong; Sun, Qixin; Ni, Zhongfu

    2011-01-01

    Background Auxin signaling is vital for plant growth and development, and plays important role in apical dominance, tropic response, lateral root formation, vascular differentiation, embryo patterning and shoot elongation. Auxin Response Factors (ARFs) are the transcription factors that regulate the expression of auxin responsive genes. The ARF genes are represented by a large multigene family in plants. The first draft of full maize genome assembly has recently been released, however, to our...

  12. 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.

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

    Institute of Scientific and Technical Information of China (English)

    QI; Mei(齐眉); HUANG; Meijuan(黄美娟); CHEN; Fan(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.

  14. Irrepressible, truncated Auxin Response Factors: Natural roles and applications in dissecting auxin gene regulation pathways

    OpenAIRE

    Ckurshumova, Wenzislava; Krogan, Naden T.; Marcos, Danielle; Caragea, Adriana E.; Berleth, Thomas

    2012-01-01

    The molecularly well-characterized auxin signal transduction pathway involves two evolutionarily conserved families interacting through their C-terminal domains III and IV: the Auxin Response Factors (ARFs) and their repressors the Aux/IAAs, to control auxin-responsive genes, among them genes involved in auxin transport.1,2 We have developed a new genetic tool to study ARF function. Using MONOPTEROS (MP)/ARF5, we have generated a truncated version of MP (MPΔ),3 which has lost the target domai...

  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. Irrepressible, truncated auxin response factors: natural roles and applications in dissecting auxin gene regulation pathways.

    Science.gov (United States)

    Ckurshumova, Wenzislava; Krogan, Naden T; Marcos, Danielle; Caragea, Adriana E; Berleth, Thomas

    2012-08-01

    The molecularly well-characterized auxin signal transduction pathway involves two evolutionarily conserved families interacting through their C-terminal domains III and IV: the Auxin Response Factors (ARFs) and their repressors the Aux/IAAs, to control auxin-responsive genes, among them genes involved in auxin transport. ( 1) (,) ( 2) We have developed a new genetic tool to study ARF function. Using MONOPTEROS (MP)/ARF5, we have generated a truncated version of MP (MPΔ), ( 3) which has lost the target domains for repression by Aux/IAA proteins. Besides exploring genetic interactions between MP and Aux/IAAs, we used this construct to trace MP's role in vascular patterning, a previously characterized auxin dependent process. ( 4) (,) ( 5) Here we summarize examples of naturally occurring truncated ARFs and summarize potential applications of truncated ARFs as analytical tools. PMID:22827953

  18. Auxin-responsive SAUR39 gene modulates auxin level in rice

    OpenAIRE

    Kant, Surya; Rothstein, Steven

    2009-01-01

    The signaling molecule auxin plays a central role in several aspects of plant growth and developmental processes. Underlying optimization of these processes are complex mechanisms orchestrating the expression of genes involved in controlling auxin level, movement and signalling. The small auxin-up RNA (SAUR) family comprises a large set of genes whose expressions are early auxin-responsive. However, the function of these genes is largely unknown. Loss-of-function mutants in a number of Arabid...

  19. 植物生长素响应因子基因的研究进展%Recent advances with auxin response factors (ARFs) : a review

    Institute of Scientific and Technical Information of China (English)

    方佳; 何勇清; 余敏芬; 郑炳松

    2012-01-01

    Auxin response factors (ARFs) are important transcription factors which regulate the expression of auxin response genes in plants and which take on an important role in auxin signal transduction. ARFs can bind specifically to a TGTCTC motif (auxin response element) and mediate auxin responses including activating or inhibiting gene expression. Based on recent advances in the molecular biology of ARFs, structural characteristics as well as biological functions of ARFs and their regulation mechanism are discussed. A typical ARF protein consists of a N-terminal DNA Binding Domain (DBD), a variable middle region that may function as an activation domain (AD) or a repression domain (RD), and one C-terminal Aux/IAA domain (CTD). ARFs promote the transcription of early genes by combining auxin response elements, and they regulate the expression of downstream genes in the process of auxin signal transduction. Different ARFs are expressed in different tissues and organisms. Also, the study of ARF mutants has indicated that different ARFs possess different functions, which are due to differences in temporal and spatial expression and due to affinities with promoters of target genes. Additionally, plant hormones, environmental factors, and non-coding small RNA act as important functions in regulating ARFs. [Ch, 1 fig. 42 ref. ]%生长素响应因子(ARF)是一类调控生长素响应基因表达的转录因子,在生长素的信号传导过程中处于中心位置,它可与生长素响应元件特异结合,促进或抑制基因的表达.介绍了ARF结构特征,生物学功能以及调控机制.植物ARF由3个结构域组成:氨基端的DNA结合结构域(DBD),中间结构域(MR)以及羟基末端的二聚结构域(CTD).中间结构域包括激活结构域(AD)和抑制结构域(RD).在生长素信号转导过程中,ARF主要通过与生长素响应元件结合,促进早期基因转录,从而调节下游基因的表达.不同的ARF在不同的组织和器官中都有特异

  20. 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.

  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. The AUXIN BINDING PROTEIN 1 is required for differential auxin responses mediating root growth.

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    Alexandre Tromas

    Full Text Available BACKGROUND: In plants, the phytohormone auxin is a crucial regulator sustaining growth and development. At the cellular level, auxin is interpreted differentially in a tissue- and dose-dependent manner. Mechanisms of auxin signalling are partially unknown and the contribution of the AUXIN BINDING PROTEIN 1 (ABP1 as an auxin receptor is still a matter of debate. METHODOLOGY/PRINCIPAL FINDINGS: Here we took advantage of the present knowledge of the root biological system to demonstrate that ABP1 is required for auxin response. The use of conditional ABP1 defective plants reveals that the protein is essential for maintenance of the root meristem and acts at least on the D-type CYCLIN/RETINOBLASTOMA pathway to control entry into the cell cycle. ABP1 affects PLETHORA gradients and confers auxin sensitivity to root cells thus defining the competence of the cells to be maintained within the meristem or to elongate. ABP1 is also implicated in the regulation of gene expression in response to auxin. CONCLUSIONS/SIGNIFICANCE: Our data support that ABP1 is a key regulator for root growth and is required for auxin-mediated responses. Differential effects of ABP1 on various auxin responses support a model in which ABP1 is the major regulator for auxin action on the cell cycle and regulates auxin-mediated gene expression and cell elongation in addition to the already well known TIR1-mediated ubiquitination pathway.

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

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    Guo, Hongyan; Zhang, Wei; Tian, Hainan; Zheng, Kaijie; Dai, Xuemei; Liu, Shanda; Hu, Qingnan; Wang, Xianling; Liu, Bao; Wang, Shucai

    2015-01-01

    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. Taken together, our results showed that OsCLE48 is an auxin responsive peptide hormone gene, and it regulates shoot apical

  4. Genome-wide identification and expression profiling of auxin response factor (ARF gene family in maize

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    Zhang Yirong

    2011-04-01

    Full Text Available Abstract Background Auxin signaling is vital for plant growth and development, and plays important role in apical dominance, tropic response, lateral root formation, vascular differentiation, embryo patterning and shoot elongation. Auxin Response Factors (ARFs are the transcription factors that regulate the expression of auxin responsive genes. The ARF genes are represented by a large multigene family in plants. The first draft of full maize genome assembly has recently been released, however, to our knowledge, the ARF gene family from maize (ZmARF genes has not been characterized in detail. Results In this study, 31 maize (Zea mays L. genes that encode ARF proteins were identified in maize genome. It was shown that maize ARF genes fall into related sister pairs and chromosomal mapping revealed that duplication of ZmARFs was associated with the chromosomal block duplications. As expected, duplication of some ZmARFs showed a conserved intron/exon structure, whereas some others were more divergent, suggesting the possibility of functional diversification for these genes. Out of these 31 ZmARF genes, 14 possess auxin-responsive element in their promoter region, among which 7 appear to show small or negligible response to exogenous auxin. The 18 ZmARF genes were predicted to be the potential targets of small RNAs. Transgenic analysis revealed that increased miR167 level could cause degradation of transcripts of six potential targets (ZmARF3, 9, 16, 18, 22 and 30. The expressions of maize ARF genes are responsive to exogenous auxin treatment. Dynamic expression patterns of ZmARF genes were observed in different stages of embryo development. Conclusions Maize ARF gene family is expanded (31 genes as compared to Arabidopsis (23 genes and rice (25 genes. The expression of these genes in maize is regulated by auxin and small RNAs. Dynamic expression patterns of ZmARF genes in embryo at different stages were detected which suggest that maize ARF genes may

  5. 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

  6. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  8. Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes.

    Science.gov (United States)

    Wang, Yijun; Deng, Dexiang; Shi, Yating; Miao, Nan; Bian, Yunlong; Yin, Zhitong

    2012-03-01

    Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3 and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene family.

  9. A tomato phloem-mobile protein regulates the shoot-to-root ratio by mediating the auxin response in distant organs.

    Science.gov (United States)

    Spiegelman, Ziv; Ham, Byung-Kook; Zhang, Zhaoliang; Toal, Ted W; Brady, Siobhan M; Zheng, Yi; Fei, Zhangjun; Lucas, William J; Wolf, Shmuel

    2015-09-01

    The plant vascular system serves as a conduit for delivery of both nutrients and signaling molecules to various distantly located organs. The anucleate sieve tube system of the angiosperm phloem delivers sugars and amino acids to developing organs, and has recently been shown to contain a unique population of RNA and proteins. Grafting studies have established that a number of these macromolecules are capable of moving long distances between tissues, thus providing support for operation of a phloem-mediated inter-organ communication network. Currently, our knowledge of the roles played by such phloem-borne macromolecules is in its infancy. Here, we show that, in tomato, translocation of a phloem-mobile cyclophilin, SlCyp1, from a wild-type scion into a mutant rootstock results in restoration of vascular development and lateral root initiation. This process occurs through reactivation of auxin response pathways and reprogramming of the root transcriptome. Moreover, we show that long-distance trafficking of SlCyp1 is associated with regulation of the shoot-to-root ratio in response to changing light intensities, by modulating root growth. We conclude that long-distance trafficking of SlCyp1 acts as a rheostat to control the shoot-to-root ratio, by mediating root development to integrate photosynthesis and light intensity with requirements for access to water and mineral nutrients. PMID:26173789

  10. Genome-wide small RNA analysis of soybean reveals auxin-responsive microRNAs that are differentially expressed in response to salt stress in root apex

    Directory of Open Access Journals (Sweden)

    Zhengxi eSun

    2016-01-01

    Full Text Available Root growth and the architecture of the root system in Arabidopsis are largely determined by root meristematic activity. Legume roots show strong developmental plasticity in response to both abiotic and biotic stimuli, including symbiotic rhizobia. However, a global analysis of gene regulation in the root meristem of soybean plants is lacking. In this study, we performed a global analysis of the small RNA transcriptome of root tips from soybean seedlings grown under normal and salt stress conditions. In total, 71 miRNA candidates, including known and novel variants of 59 miRNA families, were identified. We found 66 salt-responsive miRNAs in the soybean root meristem; among them, 22 are novel miRNAs. Interestingly, we found auxin-responsive cis-elements in the promoters of many salt-responsive miRNAs, implying that these miRNAs may be regulated by auxin and auxin signaling plays a key role in regulating the plasticity of the miRNAome and root development in soybean. A functional analysis of miR399, a salt-responsive miRNA in the root meristem, indicates the crucial role of this miRNA in modulating soybean root developmental plasticity. Our data provide novel insight into the miRNAome-mediated regulatory mechanism in soybean root growth under salt stress.

  11. Genome-Wide Small RNA Analysis of Soybean Reveals Auxin-Responsive microRNAs that are Differentially Expressed in Response to Salt Stress in Root Apex

    Science.gov (United States)

    Sun, Zhengxi; Wang, Youning; Mou, Fupeng; Tian, Yinping; Chen, Liang; Zhang, Senlei; Jiang, Qiong; Li, Xia

    2016-01-01

    Root growth and the architecture of the root system in Arabidopsis are largely determined by root meristematic activity. Legume roots show strong developmental plasticity in response to both abiotic and biotic stimuli, including symbiotic rhizobia. However, a global analysis of gene regulation in the root meristem of soybean plants is lacking. In this study, we performed a global analysis of the small RNA transcriptome of root tips from soybean seedlings grown under normal and salt stress conditions. In total, 71 miRNA candidates, including known and novel variants of 59 miRNA families, were identified. We found 66 salt-responsive miRNAs in the soybean root meristem; among them, 22 are novel miRNAs. Interestingly, we found auxin-responsive cis-elements in the promoters of many salt-responsive miRNAs, implying that these miRNAs may be regulated by auxin and auxin signaling plays a key role in regulating the plasticity of the miRNAome and root development in soybean. A functional analysis of miR399, a salt-responsive miRNA in the root meristem, indicates the crucial role of this miRNA in modulating soybean root developmental plasticity. Our data provide novel insight into the miRNAome-mediated regulatory mechanism in soybean root growth under salt stress. PMID:26834773

  12. The auxin response factor transcription factor family in soybean: genome-wide identification and expression analyses during development and water stress.

    Science.gov (United States)

    Ha, Chien Van; Le, Dung Tien; Nishiyama, Rie; Watanabe, Yasuko; Sulieman, Saad; Tran, Uyen Thi; Mochida, Keiichi; Dong, Nguyen Van; Yamaguchi-Shinozaki, Kazuko; Shinozaki, Kazuo; Tran, Lam-Son Phan

    2013-10-01

    In plants, the auxin response factor (ARF) transcription factors play important roles in regulating diverse biological processes, including development, growth, cell division and responses to environmental stimuli. An exhaustive search of soybean genome revealed 51 GmARFs, many of which were formed by genome duplications. The typical GmARFs (43 members) contain a DNA-binding domain, an ARF domain and an auxin/indole acetic acid (AUX/IAA) dimerization domain, whereas the remaining eight members lack the dimerization domain. Phylogenetic analysis of the ARFs from soybean and Arabidopsis revealed both similarity and divergence between the two ARF families, as well as enabled us to predict the functions of the GmARFs. Using quantitative real-time polymerase chain reaction (qRT-PCR) and available soybean Affymetrix array and Illumina transcriptome sequence data, a comprehensive expression atlas of GmARF genes was obtained in various organs and tissues, providing useful information about their involvement in defining the precise nature of individual tissues. Furthermore, expression profiling using qRT-PCR and microarray data revealed many water stress-responsive GmARFs in soybean, albeit with different patterns depending on types of tissues and/or developmental stages. Our systematic analysis has identified excellent tissue-specific and/or stress-responsive candidate GmARF genes for in-depth in planta functional analyses, which would lead to potential applications in the development of genetically modified soybean cultivars with enhanced drought tolerance. PMID:23810914

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

    Science.gov (United States)

    Meir, Sagit; Panizel, Irina; Puig, Clara Pons; Hao, Yanwei; Yifhar, Tamar; Yasuor, Hagai; Zouine, Mohamed; Bouzayen, Mondher; Granell Richart, Antonio; Rogachev, Ilana; Aharoni, Asaph

    2016-01-01

    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. PMID:26959229

  14. 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.

  15. AUXIN RESPONSE FACTOR8 is a negative regulator of fruit initiation in Arabidopsis.

    Science.gov (United States)

    Goetz, Marc; Vivian-Smith, Adam; Johnson, Susan D; Koltunow, Anna M

    2006-08-01

    Fruit and seed formation in plants is normally initiated after pollination and fertilization, and, in the absence of fertilization, flowers senesce. In the Arabidopsis thaliana mutant fruit without fertilization, a mutation in AUXIN RESPONSE FACTOR8 (ARF8) results in the uncoupling of fruit development from pollination and fertilization and gives rise to seedless (parthenocarpic) fruit. Parthenocarpy was confirmed in two additional recessive alleles and was caused by mutations within the coding region of ARF8. Genetic experiments indicate that ARF8 acts as an inhibitor to stop further carpel development in the absence of fertilization and the generation of signals required to initiate fruit and seed development. Expression of ARF8 was found to be regulated at multiple levels, and transcriptional autoregulation of ARF8 was observed. Analysis of plants transformed with a transcriptional P(ARF8):beta-glucuronidase (GUS) construct or a translational ARF8:GUS fusion construct displayed distinct developmental regulation of the reporter in floral tissues involved in pollination and fertilization and in the carpel wall. After fertilization, the level of GUS activity declined in the developing seed, while in unfertilized ovules that are destined to senesce, ARF8:GUS expression spread throughout the ovule. This is consistent with a proposed role for ARF8 in restricting signal transduction processes in ovules and growth in pistils until the fruit initiation cue. PMID:16829592

  16. 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. PMID:26959229

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

    Science.gov (United States)

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

    2016-06-01

    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 replum of the developing fruit. It was proposed that IND specifies the separation layer by inducing a local auxin minimum at late stages of fruit development. Here we show that morphological differences between the ind mutant and wild-type fruit already arise at early stages of fruit development, coinciding with strong IND expression in the valve margin. We show that IND-reduced PIN-FORMED3 (PIN3) auxin efflux carrier abundance leads to an increased auxin response in the valve margin during early fruit development, and that the concomitant cell divisions that form the dehiscence zone are lacking in ind mutant fruit. Moreover, IND promoter-driven ectopic expression of the AGC kinases PINOID (PID) and WAG2 induced indehiscence by expelling auxin from the valve margin at stages 14-16 of fruit development through increased PIN3 abundance. Our results show that IND, besides its role at late stages of Arabidopsis fruit development, functions at early stages to facilitate the auxin-triggered cell divisions that form the dehiscence zone. PMID:26995296

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

    Science.gov (United States)

    Xu, Zhichao; Ji, Aijia; Chen, Shilin

    2016-01-01

    ABSTRACT 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. PMID:27230647

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

    Science.gov (United States)

    Xu, Zhichao; Ji, Aijia; Song, Jingyuan; Chen, Shilin

    2016-01-01

    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. PMID:27230647

  20. 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.

  1. Genome-wide identification and expression profiling of auxin response factor (ARF) gene family in maize

    OpenAIRE

    Zhang Yirong; Hu Zhaorong; Xing Guofang; Guo Ganggang; Pudake Ramesh N; Xing Hongyan; Sun Qixin; Ni Zhongfu

    2011-01-01

    Abstract Background Auxin signaling is vital for plant growth and development, and plays important role in apical dominance, tropic response, lateral root formation, vascular differentiation, embryo patterning and shoot elongation. Auxin Response Factors (ARFs) are the transcription factors that regulate the expression of auxin responsive genes. The ARF genes are represented by a large multigene family in plants. The first draft of full maize genome assembly has recently been released, howeve...

  2. 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.

  3. 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.

  4. 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.

  5. 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.

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

    OpenAIRE

    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 Ci...

  7. Expression of aberrant forms of AUXIN RESPONSE FACTOR8 stimulates parthenocarpy in Arabidopsis and tomato.

    Science.gov (United States)

    Goetz, Marc; Hooper, Lauren C; Johnson, Susan D; Rodrigues, Julio Carlyle Macedo; Vivian-Smith, Adam; Koltunow, Anna M

    2007-10-01

    Fruit initiation in Arabidopsis (Arabidopsis thaliana) is generally repressed until fertilization occurs. However, mutations in AUXIN RESPONSE FACTOR8 (ARF8) uncouple fruit initiation from fertilization, resulting in the formation of seedless, parthenocarpic fruit. Here we induced parthenocarpy in wild-type Arabidopsis by introducing either the mutant genomic (g) Atarf8-4 sequence or gAtARF8:beta-glucuronidase translational fusion constructs by plant transformation. Silencing of endogenous AtARF8 transcription was not observed, indicating that the introduced, aberrant ARF8 transcripts were compromising the function of endogenous ARF8 and/or associated factors involved in suppressing fruit initiation. To analyze the role of ARF8 in tomato (Solanum lycopersicum) we initially emasculated 23 tomato cultivars to test for background parthenocarpy. Surprisingly, all had a predisposition to initiate fertilization-independent fruit growth. Expression of gAtarf8-4 in transgenic tomato ('Monalbo') resulted in a significant increase in the number and size of parthenocarpic fruit. Isolation of tomato ARF8 cDNA indicated significant sequence conservation with AtARF8. SlARF8 may therefore control tomato fruit initiation in a similar manner as AtARF8 does in Arabidopsis. Two SlARF8 cDNAs differing in size by 5 bp were found, both arising from the same gene. The smaller cDNA is a splice variant and is also present in Arabidopsis. We propose that low endogenous levels of the splice variant products might interfere with efficient formation/function of a complex repressing fruit initiation, thereby providing an explanation for the observed ovary expansion in tomato and also Arabidopsis after emasculation. Increasing the levels of aberrant Atarf8-4 transcripts may further destabilize formation/function of the complex in a dosage-dependent manner enhancing tomato parthenocarpic fruit initiation frequency and size and mimicking the parthenocarpic dehiscent silique phenotype found in

  8. Genome-wide characterization and expression profiling of the AUXIN RESPONSE FACTOR (ARF gene family in Eucalyptus grandis.

    Directory of Open Access Journals (Sweden)

    Hong Yu

    Full Text Available Auxin is a central hormone involved in a wide range of developmental processes including the specification of vascular stem cells. Auxin Response Factors (ARF are important actors of the auxin signalling pathway, regulating the transcription of auxin-responsive genes through direct binding to their promoters. The recent availability of the Eucalyptus grandis genome sequence allowed us to examine the characteristics and evolutionary history of this gene family in a woody plant of high economic importance. With 17 members, the E. grandis ARF gene family is slightly contracted, as compared to those of most angiosperms studied hitherto, lacking traces of duplication events. In silico analysis of alternative transcripts and gene truncation suggested that these two mechanisms were preeminent in shaping the functional diversity of the ARF family in Eucalyptus. Comparative phylogenetic analyses with genomes of other taxonomic lineages revealed the presence of a new ARF clade found preferentially in woody and/or perennial plants. High-throughput expression profiling among different organs and tissues and in response to environmental cues highlighted genes expressed in vascular cambium and/or developing xylem, responding dynamically to various environmental stimuli. Finally, this study allowed identification of three ARF candidates potentially involved in the auxin-regulated transcriptional program underlying wood formation.

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

    OpenAIRE

    si-bei eli; wei-zhi eouyang; xiao-jin ehou; liang-liang eXie; chun-gen ehu; Jin-Zhi eZhang

    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 homologues of auxin response genes. A total of 19 non-redundant ARF genes (CiARF) were identified and validated from the sweet orange genome. A c...

  10. Solution structure of the PsIAA4 oligomerization domain reveals interaction modes for transcription factors in early auxin response.

    Science.gov (United States)

    Dinesh, Dhurvas Chandrasekaran; Kovermann, Michael; Gopalswamy, Mohanraj; Hellmuth, Antje; Calderón Villalobos, Luz Irina A; Lilie, Hauke; Balbach, Jochen; Abel, Steffen

    2015-05-12

    The plant hormone auxin activates primary response genes by facilitating proteolytic removal of auxin/indole-3-acetic acid (AUX/IAA)-inducible repressors, which directly bind to transcriptional auxin response factors (ARF). Most AUX/IAA and ARF proteins share highly conserved C-termini mediating homotypic and heterotypic interactions within and between both protein families. The high-resolution NMR structure of C-terminal domains III and IV of the AUX/IAA protein PsIAA4 from pea (Pisum sativum) revealed a globular ubiquitin-like β-grasp fold with homologies to the Phox and Bem1p (PB1) domain. The PB1 domain of wild-type PsIAA4 features two distinct surface patches of oppositely charged amino acid residues, mediating front-to-back multimerization via electrostatic interactions. Mutations of conserved basic or acidic residues on either face suppressed PsIAA4 PB1 homo-oligomerization in vitro and confirmed directional interaction of full-length PsIAA4 in vivo (yeast two-hybrid system). Mixing of oppositely mutated PsIAA4 PB1 monomers enabled NMR mapping of the negatively charged interface of the reconstituted PsIAA4 PB1 homodimer variant, whose stoichiometry (1:1) and equilibrium binding constant (KD ∼ 6.4 μM) were determined by isothermal titration calorimetry. In silico protein-protein docking studies based on NMR and yeast interaction data derived a model of the PsIAA4 PB1 homodimer, which is comparable with other PB1 domain dimers, but indicated considerable differences between the homodimeric interfaces of AUX/IAA and ARF PB1 domains. Our study provides an impetus for elucidating the molecular determinants that confer specificity to complex protein-protein interaction circuits between members of the two central families of transcription factors important to the regulation of auxin-responsive gene expression. PMID:25918389

  11. 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.

  12. 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.

  13. The eta7/csn3-3 auxin response mutant of Arabidopsis defines a novel function for the CSN3 subunit of the COP9 signalosome.

    Directory of Open Access Journals (Sweden)

    He Huang

    Full Text Available The COP9 signalosome (CSN is an eight subunit protein complex conserved in all higher eukaryotes. In Arabidopsis thaliana, the CSN regulates auxin response by removing the ubiquitin-like protein NEDD8/RUB1 from the CUL1 subunit of the SCF(TIR1/AFB ubiquitin-ligase (deneddylation. Previously described null mutations in any CSN subunit result in the pleiotropic cop/det/fus phenotype and cause seedling lethality, hampering the study of CSN functions in plant development. In a genetic screen to identify enhancers of the auxin response defects conferred by the tir1-1 mutation, we identified a viable csn mutant of subunit 3 (CSN3, designated eta7/csn3-3. In addition to enhancing tir1-1 mutant phenotypes, the csn3-3 mutation alone confers several phenotypes indicative of impaired auxin signaling including auxin resistant root growth and diminished auxin responsive gene expression. Unexpectedly however, csn3-3 plants are not defective in either the CSN-mediated deneddylation of CUL1 or in SCF(TIR1-mediated degradation of Aux/IAA proteins. These findings suggest that csn3-3 is an atypical csn mutant that defines a novel CSN or CSN3-specific function. Consistent with this possibility, we observe dramatic differences in double mutant interactions between csn3-3 and other auxin signaling mutants compared to another weak csn mutant, csn1-10. Lastly, unlike other csn mutants, assembly of the CSN holocomplex is unaffected in csn3-3 plants. However, we detected a small CSN3-containing protein complex that is altered in csn3-3 plants. We hypothesize that in addition to its role in the CSN as a cullin deneddylase, CSN3 functions in a distinct protein complex that is required for proper auxin signaling.

  14. 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.

  15. Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.

    Science.gov (United States)

    Pashkovskiy, Pavel P; Kartashov, Alexander V; Zlobin, Ilya E; Pogosyan, Sergei I; Kuznetsov, Vladimir V

    2016-07-01

    The effect of blue LED (450 nm) on the photomorphogenesis of Arabidopsis thaliana Col-0 plants and the transcript levels of several genes, including miRNAs, photoreceptors and auxin response factors (ARF) was investigated. It was observed that blue light accelerated the generative development, reduced the rosette leaf number, significantly reduced the leaf area, dry biomass and led to the disruption of conductive tissue formation. The blue LED differentially influenced the transcript levels of several phytochromes (PHY a, b, c, d, and e), cryptochromes (CRY 1 and 2) and phototropins (PHOT 1 and 2). At the same time, the blue LED significantly increased miR167 expression compared to a fluorescent lamp or white LEDs. This increase likely resulted in the enhanced transcription of the auxin response factor genes ARF4 and ARF8, which are regulated by this miRNA. These findings support the hypothesis that the effects of blue light on A. thaliana are mediated by auxin signalling pathway involving miRNA-dependent regulation of ARF gene expression. PMID:27031426

  16. 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.

  17. SlTPR1, a tomato tetratricopeptide repeat protein, interacts with the ethylene receptors NR and LeETR1, modulating ethylene and auxin responses and development.

    Science.gov (United States)

    Lin, Zhefeng; Arciga-Reyes, Luis; Zhong, Silin; Alexander, Lucy; Hackett, Rachel; Wilson, Ian; Grierson, Don

    2008-01-01

    The gaseous hormone ethylene is perceived by a family of ethylene receptors which interact with the Raf-like kinase CTR1. SlTPR1 encodes a novel TPR (tetratricopeptide repeat) protein from tomato that interacts with the ethylene receptors NR and LeETR1 in yeast two-hybrid and in vitro protein interaction assays. SlTPR1 protein with a GFP fluorescent tag was localized in the plasmalemma and nuclear membrane in Arabidopsis, and SlTPR1-CFP and NR-YFP fusion proteins were co-localized in the plasmalemma and nuclear membrane following co-bombardment of onion cells. Overexpression of SlTPR1 in tomato resulted in ethylene-related pleiotropic effects including reduced stature, delayed and reduced production of inflorescences, abnormal and infertile flowers with degenerate styles and pollen, epinasty, reduced apical dominance, inhibition of abscission, altered leaf morphology, and parthenocarpic fruit. Similar phenotypes were seen in Arabidopsis overexpressing SlTPR1. SlTPR1 overexpression did not increase ethylene production but caused enhanced accumulation of mRNA from the ethylene responsive gene ChitB and the auxin-responsive gene SlSAUR1-like, and reduced expression of the auxin early responsive gene LeIAA9, which is known to be inhibited by ethylene and to be associated with parthenocarpy. Cuttings from the SlTPR1-overexpressors produced fewer adventitious roots and were less responsive to indole butyric acid. It is suggested that SlTPR1 overexpression enhances a subset of ethylene and auxin responses by interacting with specific ethylene receptors. SlTPR1 shares features with human TTC1, which interacts with heterotrimeric G-proteins and Ras, and competes with Raf-1 for Ras binding. Models for SlTPR1 action are proposed involving modulation of ethylene signalling or receptor levels. PMID:19036844

  18. The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress.

    Science.gov (United States)

    Hu, Wei; Zuo, Jiao; Hou, Xiaowan; Yan, Yan; Wei, Yunxie; Liu, Juhua; Li, Meiying; Xu, Biyu; Jin, Zhiqiang

    2015-01-01

    Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF) and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47 ARF genes were identified in banana based on its genome sequence. Phylogenetic analysis of the ARFs from banana, rice, and Arabidopsis suggested that the ARFs could be divided into four subgroups, among which most ARFs from the banana showed a closer relationship with those from rice than those from Arabidopsis. Conserved motif analysis showed that all identified MaARFs had typical DNA-binding and ARF domains, but 12 members lacked the dimerization domain. Gene structure analysis showed that the number of exons in MaARF genes ranged from 5 to 21, suggesting large variation amongst banana ARF genes. The comprehensive expression profiles of MaARF genes yielded useful information about their involvement in diverse tissues, different stages of fruit development and ripening, and responses to abiotic stresses in different varieties. Interaction networks and co-expression assays indicated the strong transcriptional response of banana ARFs and ARF-mediated networks in early fruit development for different varieties. Our systematic analysis of MaARFs revealed robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MaARF genes for further functional assays in planta. These findings could lead to potential applications in the genetic improvement of banana cultivars, and yield new insights into the complexity of the control of MaARF gene expression at the transcriptional level. Finally, they support the hypothesis that ARFs are a crucial component of the auxin signaling pathway, which regulates a wide range of physiological processes. PMID:26442055

  19. The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress

    Directory of Open Access Journals (Sweden)

    Wei eHu

    2015-09-01

    Full Text Available Auxin signaling regulates various auxin-responsive genes via two types of transcriptional regulators, Auxin Response Factors (ARF and Aux/IAA. ARF transcription factors act as critical components of auxin signaling that play important roles in modulating various biological processes. However, limited information about this gene family in fruit crops is currently available. Herein, 47 ARF genes were identified in banana based on its genome sequence. Phylogenetic analysis of the ARFs from banana, rice, and Arabidopsis suggested that the ARFs could be divided into four subgroups, among which most ARFs from the banana showed a closer relationship with those from rice than those from Arabidopsis. Conserved motif analysis showed that all identified MaARFs had typical DNA-binding and ARF domains, but 12 members lacked the dimerization domain. Gene structure analysis showed that the number of exons in MaARF genes ranged from 5 to 21, suggesting large variation amongst banana ARF genes. The comprehensive expression profiles of MaARF genes yielded useful information about their involvement in diverse tissues, different stages of fruit development and ripening, and responses to abiotic stresses in different varieties. Interaction networks and co-expression assays indicated the strong transcriptional response of banana ARFs and ARF-mediated networks in early fruit development for different varieties. Our systematic analysis of MaARFs revealed robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MaARF genes for further functional assays in planta. These findings could lead to potential applications in the genetic improvement of banana cultivars, and yield new insights into the complexity of the control of MaARF gene expression at the transcriptional level. Finally, they support the hypothesis that ARFs are a crucial component of the auxin signaling pathway, which regulates a wide range of physiological processes.

  20. 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.

  1. The auxin response factor MONOPTEROS controls meristem function and organogenesis in both the shoot and root through the direct regulation of PIN genes.

    Science.gov (United States)

    Krogan, Naden T; Marcos, Danielle; Weiner, Aaron I; Berleth, Thomas

    2016-10-01

    The regulatory effect auxin has on its own transport is critical in numerous self-organizing plant patterning processes. However, our understanding of the molecular mechanisms linking auxin signal transduction and auxin transport is still fragmentary, and important regulatory genes remain to be identified. To track a key link between auxin signaling and auxin transport in development, we established an Arabidopsis thaliana genetic background in which fundamental patterning processes in both shoot and root were essentially abolished and the expression of PIN FORMED (PIN) auxin efflux facilitators was dramatically reduced. In this background, we demonstrate that activating a steroid-inducible variant of the auxin response factor (ARF) MONOPTEROS (MP) is sufficient to restore patterning and PIN gene expression. Further, we show that MP binds to distinct promoter elements of multiple genetically defined PIN genes. Our work identifies a direct regulatory link between central, well-characterized genes involved in auxin signal transduction and auxin transport. The steroid-inducible MP system directly demonstrates the importance of this molecular link in multiple patterning events in embryos, shoots and roots, and provides novel options for interrogating the properties of self-regulated auxin-based patterning in planta. PMID:27441727

  2. Hydrolases of the ILR1-like family of Arabidopsis thaliana modulate auxin response by regulating auxin homeostasis in the endoplasmic reticulum.

    Science.gov (United States)

    Sanchez Carranza, Ana Paula; Singh, Aparajita; Steinberger, Karoline; Panigrahi, Kishore; Palme, Klaus; Dovzhenko, Alexander; Dal Bosco, Cristina

    2016-01-01

    Amide-linked conjugates of indole-3-acetic acid (IAA) have been identified in most plant species. They function in storage, inactivation or inhibition of the growth regulator auxin. We investigated how the major known endogenous amide-linked IAA conjugates with auxin-like activity act in auxin signaling and what role ILR1-like proteins play in this process in Arabidopsis. We used a genetically encoded auxin sensor to show that IAA-Leu, IAA-Ala and IAA-Phe act through the TIR1-dependent signaling pathway. Furthermore, by using the sensor as a free IAA reporter, we followed conjugate hydrolysis mediated by ILR1, ILL2 and IAR3 in plant cells and correlated the activity of the hydrolases with a modulation of auxin response. The conjugate preferences that we observed are in agreement with available in vitro data for ILR1. Moreover, we identified IAA-Leu as an additional substrate for IAR3 and showed that ILL2 has a more moderate kinetic performance than observed in vitro. Finally, we proved that IAR3, ILL2 and ILR1 reside in the endoplasmic reticulum, indicating that in this compartment the hydrolases regulate the rates of amido-IAA hydrolysis which results in activation of auxin signaling. PMID:27063913

  3. 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

    [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 seedlings and plants of the transgenic Line 3 and Line 5 as well as wild type (WT) were cultured to determine the growth features and to assay the fresh and dry weights of roots and aboveground tissues under the conditions of Pi sufficiency and Pi deficiency. [Results] 1) TaARF6 encodes a transcription factor categoried into auxin response factor family and shares the conserved domains of ARF proteins in plants, such as the DNA binding domain and the auxin response domain. It shares a high identity to BdARF6 and OsARF6, two ARF family members in B. distachyon and

  4. Downstream in Mawrth Valles

    Science.gov (United States)

    2005-01-01

    [figure removed for brevity, see original site] The THEMIS VIS camera is capable of capturing color images of the Martian surface using five different color filters. In this mode of operation, the spatial resolution and coverage of the image must be reduced to accommodate the additional data volume produced from using multiple filters. To make a color image, three of the five filter images (each in grayscale) are selected. Each is contrast enhanced and then converted to a red, green, or blue intensity image. These three images are then combined to produce a full color, single image. Because the THEMIS color filters don't span the full range of colors seen by the human eye, a color THEMIS image does not represent true color. Also, because each single-filter image is contrast enhanced before inclusion in the three-color image, the apparent color variation of the scene is exaggerated. Nevertheless, the color variation that does appear is representative of some change in color, however subtle, in the actual scene. Note that the long edges of THEMIS color images typically contain color artifacts that do not represent surface variation. This false color image is from further downstream in Mawrth Valles than yesterday's image. The channel here is at the end of the vallis. This image was collected during the Northern Spring season. Image information: VIS instrument. Latitude 26.7, Longitude 340.2 East (19.8 West). 37 meter/pixel resolution. Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time. NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey

  5. Arabic downstream crushes competition; Arabische downstream verpletterd concurrentie

    Energy Technology Data Exchange (ETDEWEB)

    Widdershoven, C. [Capgemini International, Utrecht (Netherlands)

    2007-07-01

    Oil producers in the Middle East have enormous advantages while the costs for resources are very low. The petrochemical industry in this region shows a considerable growth. The question, however, is whether this situation will continue for a long time. [Dutch] Veel downstream-bedrijven in het Westen hebben hun activiteiten afgebouwd wegens zeer lage of negatieve winstmarges. Op hetzelfde moment is er een exponentiele groei van de downstream-sector te zien in het Midden-Oosten, West-Afrika en Azie. De komende jaren wordt er wereldwijdvoor meer dan zeshonderd miljard dollar aan nieuwe downstream-projecten op poten gezet. Een substantieel deel van deze projecten is in het Midden-Oosten gepland, waarbij Saudi-Arabie, Qatar, Verenigde Arabische Emiraten, Iran en Egypte het voortouw nemen. De Arabische nationale olie- en gasmaatschappijen - Saudi Aramco, Qatargas, NIOC and EGPC - onderkennen dat het strategisch en financieel interessant is om deze sector in handen te krijgen.

  6. 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.)

  7. Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants.

    Science.gov (United States)

    Huang, Zhinan; Duan, Weike; Song, Xiaoming; Tang, Jun; Wu, Peng; Zhang, Bei; Hou, Xilin

    2016-02-01

    Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion, and expression patterns of Aux/IAAs and ARFs in Brassica rapa and their evolution in eight other plant species, including algae, bryophytes, lycophytes, and angiosperms. All 33 of the ARFs, including 1 ARF-like (AL) (a type of ARF-like protein) and 53 Aux/IAAs, were identified in the B. rapa genome. The genes mainly diverged approximately 13 Ma. After the split, no Aux/IAA was completely lost, and they were more preferentially retained than ARFs. In land plants, compared with ARFs, which increased in stability, Aux/IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants adapt to complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of Aux/IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both Aux/IAAs and ARFs. PMID:26721260

  8. Retention, Molecular Evolution, and Expression Divergence of the Auxin/Indole Acetic Acid and Auxin Response Factor Gene Families in Brassica Rapa Shed Light on Their Evolution Patterns in Plants

    Science.gov (United States)

    Huang, Zhinan; Duan, Weike; Song, Xiaoming; Tang, Jun; Wu, Peng; Zhang, Bei; Hou, Xilin

    2016-01-01

    Auxin/indole acetic acids (Aux/IAAs) and auxin response factors (ARFs), major components of the Aux signaling network, are involved in many developmental processes in plants. Investigating their evolution will provide new sight on the relationship between the molecular evolution of these genes and the increasing morphotypes of plants. We constructed comparative analyses of the retention, structure, expansion, and expression patterns of Aux/IAAs and ARFs in Brassica rapa and their evolution in eight other plant species, including algae, bryophytes, lycophytes, and angiosperms. All 33 of the ARFs, including 1 ARF-like (AL) (a type of ARF-like protein) and 53 Aux/IAAs, were identified in the B. rapa genome. The genes mainly diverged approximately 13 Ma. After the split, no Aux/IAA was completely lost, and they were more preferentially retained than ARFs. In land plants, compared with ARFs, which increased in stability, Aux/IAAs expanded more rapidly and were under more relaxed selective pressure. Moreover, BraIAAs were expressed in a more tissue-specific fashion than BraARFs and demonstrated functional diversification during gene duplication under different treatments, which enhanced the cooperative interaction of homologs to help plants adapt to complex environments. In addition, ALs existed widely and had a closer relationship with ARFs, suggesting that ALs might be the initial structure of ARFs. Our results suggest that the rapid expansion and preferential retention of Aux/IAAs are likely paralleled by the increasingly complex morphotypes in Brassicas and even in land plants. Meanwhile, the data support the hypothesis that the PB1 domain plays a key role in the origin of both Aux/IAAs and ARFs. PMID:26721260

  9. ASYMMETRIC-LEAVES2 and an ortholog of eukaryotic NudC domain proteins repress expression of AUXIN-RESPONSE-FACTOR and class 1 KNOX homeobox genes for development of flat symmetric leaves in Arabidopsis

    Directory of Open Access Journals (Sweden)

    Nanako Ishibashi

    2012-01-01

    Leaf primordia form around the shoot apical meristem, which consists of indeterminate stem cells. Upon initiation of leaf development, adaxial-abaxial patterning is crucial for appropriate lateral expansion, via cellular proliferation, and the formation of flat symmetric leaves. Many genes that specify such patterning have been identified, but regulation by upstream factors of the expression of relevant effector genes remains poorly understood. In Arabidopsis thaliana, ASYMMETRIC LEAVES2 (AS2 and AS1 play important roles in repressing transcription of class 1 KNOTTED1-like homeobox (KNOX genes and leaf abaxial-determinant effector genes. We report here a mutation, designated enhancer of asymmetric leaves2 and asymmetric leaves1 (eal, that is associated with efficient generation of abaxialized filamentous leaves on the as2 or as1 background. Levels of transcripts of many abaxial-determinant genes, including ETTIN (ETT/AUXIN RESPONSE FACTOR3 (ARF3, and all four class 1 KNOX genes were markedly elevated in as2 eal shoot apices. Rudimentary patterning in as2 eal leaves was suppressed by the ett mutation. EAL encodes BOBBER1 (BOB1, an Arabidopsis ortholog of eukaryotic NudC domain proteins. BOB1 was expressed in plant tissues with division potential and bob1 mutations resulted in lowered levels of transcripts of some cell-cycle genes and decreased rates of cell division in shoot and root apices. Coordinated cellular proliferation, supported by BOB1, and repression of all class 1 KNOX genes, ETT/ARF3 by AS2 (AS1 and BOB1 might be critical for repression of the indeterminate state and of aberrant abaxialization in the presumptive adaxial domain of leaf primordia, which might ensure the formation of flat symmetric leaves.

  10. Downstream fining - a literature review -

    NARCIS (Netherlands)

    Frings, R.M.

    2004-01-01

    In this report a detailed overview is given of the present knowledge about downstream fining. The influence of abrasion (chapter 2), selective transport (chapter 3), sediment addition, extraction and redistribution (chapter 4) is described and discussed. Then some attention is attained to a very str

  11. 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.

  12. 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.

  13. 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....

  14. 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

  15. 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)

  16. Transcriptome sequencing of Zhikong scallop (Chlamys farreri and comparative transcriptomic analysis with Yesso scallop (Patinopecten yessoensis.

    Directory of Open Access Journals (Sweden)

    Shan Wang

    Full Text Available BACKGROUND: Bivalves play an important role in the ecosystems they inhabit and represent an important food source all over the world. So far limited genetic research has focused on this group of animals largely due to the lack of sufficient genetic or genomic resources. Here, we performed de novo transcriptome sequencing to produce the most comprehensive expressed sequence tag resource for Zhikong scallop (Chlamys farreri, and conducted the first transcriptome comparison for scallops. RESULTS: In a single 454 sequencing run, 1,033,636 reads were produced and then assembled into 26,165 contigs. These contigs were then clustered into 24,437 isotigs and further grouped into 20,056 isogroups. About 47% of the isogroups showed significant matches to known proteins based on sequence similarity. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified through Gene ontology (GO and KEGG pathway analyses. Transcriptome comparison with Yesso scallop (Patinopecten yessoensis revealed similar patterns of GO representation. Moreover, 38 putative fast-evolving genes were identified through analyzing the orthologous gene pairs between the two scallop species. More than 46,000 single nucleotide polymorphisms (SNPs and 350 simple sequence repeats (SSRs were also detected. CONCLUSION: Our study provides the most comprehensive transcriptomic resource currently available for C. farreri. Based on this resource, we performed the first large-scale transcriptome comparison between the two scallop species, C. farreri and P. yessoensis, and identified a number of putative fast-evolving genes, which may play an important role in scallop speciation and/or local adaptation. A large set of single nucleotide polymorphisms and simple sequence repeats were identified, which are ready for downstream marker development. This transcriptomic resource should lay an important foundation for future genetic or genomic studies on C. farreri.

  17. 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

  18. A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs

    Directory of Open Access Journals (Sweden)

    Mingming Liu

    2014-01-01

    Full Text Available With the rapid development of high throughput sequencing technologies, new transcriptomes can be sequenced for little cost with high coverage. Sequence assembly approaches have been modified to meet the requirements for de novo transcriptomes, which have complications not found in traditional genome assemblies such as variation in coverage for each candidate mRNA and alternative splicing. As a consequence, de novo assembly strategies tend to generate a large number of redundant contigs due to sequence variations, which adversely affects downstream analysis and experiments. In this work we proposed TransPS, a transcriptome post-scaffolding method, to generate high quality, nonredundant de novo transcriptomes. TransPS shows promising results on the test transcriptome datasets, where redundancy is greatly reduced by more than 50% and, at the same time, coverage is improved considerably. The web server and source code are available.

  19. Transcriptome 2002 Conference

    Energy Technology Data Exchange (ETDEWEB)

    Quackenbush, John

    2002-01-01

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

  20. 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.

  1. 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.

  2. 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).

  3. Regulatory network of inflammation downstream of proteinase-activated receptors

    Directory of Open Access Journals (Sweden)

    Hurst Robert E

    2007-03-01

    Full Text Available Abstract Background Protease-activated receptors (PAR are present in the urinary bladder, and their expression is altered in response to inflammation. PARs are a unique class of G protein-coupled that carry their own ligands, which remain cryptic until unmasked by proteolytic cleavage. Although the canonical signal transduction pathway downstream of PAR activation and coupling with various G proteins is known and leads to the rapid transcription of genes involved in inflammation, the effect of PAR activation on the downstream transcriptome is unknown. We have shown that intravesical administration of PAR-activating peptides leads to an inflammatory reaction characterized by edema and granulocyte infiltration. Moreover, the inflammatory response to intravesical instillation of known pro-inflammatory stimuli such as E. coli lipopolysaccharide (LPS, substance P (SP, and antigen was strongly attenuated by PAR1- and to a lesser extent by PAR2-deficiency. Results Here, cDNA array experiments determined inflammatory genes whose expression is dependent on PAR1 activation. For this purpose, we compared the alteration in gene expression in wild type and PAR1-/- mice induced by classical pro-inflammatory stimuli (LPS, SP, and antigen. 75 transcripts were considered to be dependent on PAR-1 activation and further annotated in silico by Ingenuity Pathways Analysis (IPA and gene ontology (GO. Selected transcripts were target validated by quantitative PCR (Q-PCR. Among PAR1-dependent transcripts, the following have been implicated in the inflammatory process: b2m, ccl7, cd200, cd63, cdbpd, cfl1, dusp1, fkbp1a, fth1, hspb1, marcksl1, mmp2, myo5a, nfkbia, pax1, plaur, ppia, ptpn1, ptprcap, s100a10, sim2, and tnfaip2. However, a balanced response to signals of injury requires a transient cellular activation of a panel of genes together with inhibitory systems that temper the overwhelming inflammation. In this context, the activation of genes such as dusp1 and

  4. 黄瓜生长素反应因子(ARF)家族鉴定及表达特异性分析%Genome-wide Identification and Expression Analysis of Auxin Response Factor (ARF) Family in Cucumber

    Institute of Scientific and Technical Information of China (English)

    盛慧; 秦智伟; 李文滨; 周秀艳; 武涛; 辛明

    2014-01-01

    [Objective]The objective of this study is to identify the cucumber auxin response factor (ARF), forecast the small RNAs and verify the relationship between ARF with small RNAs and auxin. The expression pattern of ARF during seed germination was analyzed and the effect of ARF on the process of parthenocarpy and seed germination was deduced.[Method]The Arabidopsis and rice ARF proteins were used to search the cucumber genome database. Then, the retrieved cucumber ARF family structure was analyzed and the small RNAs were predicted. The predicted gma-MIR160o precursur was built into the pCAMBIA2301. By Agrobacterium-mediated method, it was imported into parthenocarpy cucumber varieties. Transgenic plants were validated by RT-PCR. Using real-time RT-PCR method, the expression patterns of ARF were analyzed in auxin treatment, flowing and seed germination. [Result] By comparison with the Arabidopsis and rice ARF protein sequences, there are 18 cucumber ARF protein sequences. ARF proteins were divided into four classes. The number of exons varied from 2 to 18, and the structure was similar among the same class. Phylogenetic tree showed that the similarity of 18 genes was not high. Small RNAs corresponds to ARF genes in cucumber were found. Csa010564, Csa011935, Csa015176, Csa020560 and Csa022361 were miR160 targets. Transgenic test further exhibited mRNA abundance of Csa010564, Csa011935 and Csa015176 decreased, while Csa020560 and Csa022361 rose slightly, indicating that Csa010564, Csa011935 and Csa015176 were miR160 targets. The results of real-time RT-PCR exhibited that mRNA abundance of Csa007296, Csa011935 and Csa015176 in roots, stems and leaves were higher than wild type, indicating the expressions of these genes were positively regulated by auxin. Meanwhile, the expressions in leaves and female flowers were decreased on the second flowering day, while the expression of the ovary was the opposite, especially Csa011935 and Csa015176, indicating that ARF genes play a

  5. 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

  6. Genome wide transcriptome analysis reveals ABA mediated response in Arabidopsis during gold (AuCl(-) 4) treatment.

    Science.gov (United States)

    Shukla, Devesh; Krishnamurthy, Sneha; Sahi, Shivendra V

    2014-01-01

    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 AuCl(-) 4 In this study, we carried out global transcriptome analysis in root tissue of Arabidopsis grown for 12- h 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 AuCl(-) 4 exposure. Overall, this study presents a useful picture of plant-gold interaction with an identification of candidate genes

  7. 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.

  8. 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.

  9. Transcriptomics using axolotls.

    Science.gov (United States)

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

    2015-01-01

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

  10. The downstream industry compared to market

    International Nuclear Information System (INIS)

    J.L. Schilansky introduces here the difficult question of the downstream industry compared to market in recalling the recent structural changes (behaviour of customers, behaviour of the USA- and China-governments), the increase of the European and French regulations, the climatic change and the conjectural impact of the crisis on the refining industry. (O.M.)

  11. 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

  12. 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

  13. Upstream versus Downstream Implementation of Climate Policy

    OpenAIRE

    Erin T. Mansur

    2010-01-01

    This chapter examines the tradeoffs of regulating upstream (e.g., coal, natural gas, and refined petroleum product producers) versus regulating downstream (e.g., direct sources of greenhouse gases (GHG)). In general, regulating at the source provides polluters with incentives to choose among more opportunities to abate pollution. This chapter develops a simple theoretical model that shows why this added flexibility achieves the lowest overall costs. I broaden the theory to incorporate several...

  14. Mechanical downstream processing of Single Cell Oils

    OpenAIRE

    De Coninck, Maarten; Van Hecke, Renaat; Deprez, Koen; De Baerdemaeker, Josse

    2011-01-01

    During the last years, the third generation of bio fuels has been arousing more and more interest. Under certain conditions some micro organisms: yeasts, algae, fungi and bacteria, can accumulate up to 50% oil (based on dry weight). These so-called ‘Single cell oils’ (SCO) are well known in this context. Nowadays, harvesting and recovery of interesting products from microalgae is one of the most problematic areas of algal biofuel production technology. The traditional downstream process,...

  15. 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.

  16. Downstream mode of competition with upstream market power

    OpenAIRE

    Manasakis, Constantine; Vlassis, Minas

    2013-01-01

    In a two-tier oligopoly, where the downstream firms are locked in pair-wise exclusive relationships with their upstream input suppliers, the equilibrium mode of competition in the downstream market is endogenously determined as a renegotiation-proof contract signed between each downstream firm and its exclusive upstream input supplier. We find that the upstream-downstream exclusive relationships credibly sustain the Cournot (Bertrand) mode of competition in the downstream market, when the goo...

  17. Vertical Integration and Market Foreclosure with Convex Downstream Costs

    OpenAIRE

    Baake, Pio; Kamecke, Ulrich; Normann, Hans-Theo

    2001-01-01

    In a framework with an upstream monopoly and a downstream duopoly, we analyze the impact of convex costs on the downstream level. In contrast to the case of constant marginal costs, vertical integration does not imply complete market foreclosure. While the non-integrated downstream firm receives a strictly positive amount of the intermediate good, the downstream allocation is inefficient. However, a parametrized example indicates that competition at the downstream level may increase aggregate...

  18. Integration of small RNAs, degradome and transcriptome sequencing in hyperaccumulator Sedum alfredii uncovers a complex regulatory network and provides insights into cadmium phytoremediation.

    Science.gov (United States)

    Han, Xiaojiao; Yin, Hengfu; Song, Xixi; Zhang, Yunxing; Liu, Mingying; Sang, Jiang; Jiang, Jing; Li, Jihong; Zhuo, Renying

    2016-06-01

    The hyperaccumulating ecotype of Sedum alfredii Hance is a cadmium (Cd)/zinc/lead co-hyperaccumulating species of Crassulaceae. It is a promising phytoremediation candidate accumulating substantial heavy metal ions without obvious signs of poisoning. However, few studies have focused on the regulatory roles of miRNAs and their targets in the hyperaccumulating ecotype of S. alfredii. Here, we combined analyses of the transcriptomics, sRNAs and the degradome to generate a comprehensive resource focused on identifying key regulatory miRNA-target circuits under Cd stress. A total of 87 721 unigenes and 356 miRNAs were identified by deep sequencing, and 79 miRNAs were differentially expressed under Cd stress. Furthermore, 754 target genes of 194 miRNAs were validated by degradome sequencing. A gene ontology (GO) enrichment analysis of differential miRNA targets revealed that auxin, redox-related secondary metabolism and metal transport pathways responded to Cd stress. An integrated analysis uncovered 39 pairs of miRNA targets that displayed negatively correlated expression profiles. Ten miRNA-target pairs also exhibited negative correlations according to a real-time quantitative PCR analysis. Moreover, a coexpression regulatory network was constructed based on profiles of differentially expressed genes. Two hub genes, ARF4 (auxin response factor 4) and AAP3 (amino acid permease 3), which might play central roles in the regulation of Cd-responsive genes, were uncovered. These results suggest that comprehensive analyses of the transcriptomics, sRNAs and the degradome provided a useful platform for investigating Cd hyperaccumulation in S. alfredii, and may provide new insights into the genetic engineering of phytoremediation. PMID:26801211

  19. OCT4 and downstream factors are expressed in human somatic urogenital epithelia and in culture of epididymal spheres

    DEFF Research Database (Denmark)

    Audouze, Karine Marie Laure; Brunak, Søren; Kristensen, DM;

    2010-01-01

    microdissected tissues, in situ hybridisation, immunohistochemistry, and Western blotting to show that OCT4 and SOX2 together with downstream targets, UTF1 and REX1, are expressed in the human male urogenital tract. We further supported these results by analysis of DNA methylation of a region in the OCT4...... promoter. In culture, human primary epididymis cells formed spheres that continued to express the investigated genes for at least 20 days. Transcriptomic analysis of cultured cells showed up-regulation of CD29, CD44, and CD133 that are normally associated with sphere-forming cancer stem cells. Furthermore...

  20. Oomycete transcriptomics database: A resource for oomycete transcriptomes

    Directory of Open Access Journals (Sweden)

    Tripathy Sucheta

    2012-07-01

    Full Text Available Abstract Background Oomycete pathogens have attracted significant attention in recent years due to their economic impact. With improving sequencing technologies, large amounts of oomycete transcriptomics data are now available which have great biological utility. A known bottleneck with next generation sequencing data however lies with their analysis, interpretation, organization, storage and visualization. A number of efforts have been made in this respect resulting in development of a myriad of resources. Most of the existing NGS browsers work as standalone applications that need processed data to be uploaded to the browser locally for visualization. At the same time, several oomycete EST databases such as PFGD, ESTAP and SPC, are not available anymore, so there is an immediate need for a database resource that can store and disseminate this legacy information in addition to NGS data. Description Oomycetes Transcriptomics Database is an integrated transcriptome and EST data resource for oomycete pathogens. The database currently stores processed ABI SOLiD transcript sequences from Phytophthora sojae and its host soybean (P. sojae mycelia, healthy soybean and P. sojae-infected soybean as well as Illumina transcript sequences from five Hyaloperonospora arabidopsidis libraries. In addition to those resources, it has also a complete set of Sanger EST sequences from P. sojae, P. infestans and H. arabidopsidis grown under various conditions. A web-based transcriptome browser was created for visualization of assembled transcripts, their mapping to the reference genome, expression profiling and depth of read coverage for particular locations on the genome. The transcriptome browser merges EST-derived contigs with NGS-derived assembled transcripts on the fly and displays the consensus. OTD possesses strong query features and the database interacts with the VBI Microbial Database as well as the Phytophthora Transcriptomics Database. Conclusion Oomycete

  1. Plasma waves downstream of weak collisionless shocks

    Science.gov (United States)

    Coroniti, F. V.; Greenstadt, E. W.; Moses, S. L.; Smith, E. J.; Tsurutani, B. T.

    1993-01-01

    In September 1983 the International Sun Earth Explorer 3 (ISEE 3) International Cometary Explorer (ICE) spacecraft made a long traversal of the distant dawnside flank region of the Earth's magnetosphere and had many encounters with the low Mach number bow shock. These weak shocks excite plasma wave electric field turbulence with amplitudes comparable to those detected in the much stronger bow shock near the nose region. Downstream of quasi-perpendicular (quasi-parallel) shocks, the E field spectra exhibit a strong peak (plateau) at midfrequencies (1 - 3 kHz); the plateau shape is produced by a low-frequency (100 - 300 Hz) emission which is more intense behind downstream of two quasi-perpendicular shocks show that the low frequency signals are polarized parallel to the magnetic field, whereas the midfrequency emissions are unpolarized or only weakly polarized. A new high frequency (10 - 30 kHz) emission which is above the maximum Doppler shift exhibit a distinct peak at high frequencies; this peak is often blurred by the large amplitude fluctuations of the midfrequency waves. The high-frequency component is strongly polarized along the magnetic field and varies independently of the lower-frequency waves.

  2. 40 CFR 80.69 - Requirements for downstream oxygenate blending.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Requirements for downstream oxygenate... downstream oxygenate blending. The requirements of this section apply to all reformulated gasoline blendstock... annual compliance period; (D) A process for notifying oxygenate blenders and other downstream parties...

  3. 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.

  4. Experimental Study on Scours Downstream of Floodgates

    Institute of Scientific and Technical Information of China (English)

    张玮; 陈锡林; 徐金环; 李国臣; 王志谦

    2000-01-01

    The river reach downstream of a floodgate at the estuary of the Xinyihe River is about 1.3km long, and the riverbed is composed of clotty clay. In the experiment, soil samples are taken from the construction site, and the incipient velocity is determined in a laboratory flume, and it is used to design the scour model and to select model sand material. The experimental results show that scours below the floodgate is unavoidable due to large discharge and low tidal level. Scours is caused by two factors: the rapid flow passing though the floodgate and the water drop near the river mouth during low tide, and the scour below the floodgate is more critical to the structural design. It is suggested that anti-scour walls should be used instead of riprap. The ideas and methods adopted in the experiment can be used as reference in the study on river scour under similar conditions.

  5. Downstream process options for the ABE fermentation.

    Science.gov (United States)

    Friedl, Anton

    2016-05-01

    Butanol is a very interesting substance both for the chemical industry and as a biofuel. The classical distillation process for the removal of butanol is far too energy demanding, at a factor of 220% of the energy content of butanol. Alternative separation processes studied are hybrid processes of gas-stripping, liquid-liquid extraction and pervaporation with distillation and a novel adsorption/drying/desorption hybrid process. Compared with the energy content of butanol, the resulting energy demand for butanol separation and concentration of optimized hybrid processes is 11%-22% for pervaporation/distillation and 11%-17% for liquid-liquid extraction/distillation. For a novel adsorption/drying/desorption process, the energy demand is 9.4%. But all downstream process options need further proof of industrial applicability. PMID:27020411

  6. Modeling of channel erosion downstream spillway dams

    Directory of Open Access Journals (Sweden)

    M.A. Mikhalev

    2013-03-01

    Full Text Available The channel erosion downstream spillway dams in non-cohesive materials has been analyzed from the viewpoint of methods of similarity and dimension theory. The obtained criterion equation connects the maximum depth of the local erosion with its determining parameters: length of concrete lining of bed in the down water of the spillway dam; Froude number at the contracted cross section; Archimedes and Reynolds criterions; submergence factor of hydraulic jump. The problem may be formulated as follows: the geometric size of the structure, kinematics and dynamics of the flows in the model are similar to that in the prototype. Conditions under which the characteristic depth of the local erosion in the model would be recomputed into the prototype, like any geometric size, are being discussed.

  7. The jet membrane-experiment: downstream sampling

    International Nuclear Information System (INIS)

    The invasion separation effect of the free jet structure was found in 1966 at Saclay. In the Downstream Sampling Configuration patended by Campargue (1967), the light fraction is withdrawn from the supersonic central core, by skimming the separating free jet. From experimental and theoretical results obtained for gas and isotopic mixtures, the following points linked to operation and equipment costs, are considered: system description; influence of mass ratio, expansion ratio, nature of separating gas, ratio of upflow to separating jet flow, rarefaction. Fron an uninteresting aspect of Jet Membrane (elimination of background penetration), a new principle has been discovered to produce nozzle beams which may be of great interest for other separation processes involving free jets and/or molecular beams

  8. 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.

  9. Transcriptomic Analysis of Grapevine (cv. Summer Black Leaf, Using the Illumina Platform.

    Directory of Open Access Journals (Sweden)

    Tariq Pervaiz

    Full Text Available Proceeding to illumina sequencing, determining RNA integrity numbers for poly RNA were separated from each of the four developmental stages of cv. Summer Black leaves by using Illumina HiSeq™ 2000. The sums of 272,941,656 reads were generated from vitis vinifera leaf at four different developmental stages, with more than 27 billion nucleotides of the sequence data. At each growth stage, RNA samples were indexed through unique nucleic acid identifiers and sequenced. KEGG annotation results depicted that the highest number of transcripts in 2,963 (2Avs4A followed by 1Avs4A (2,920, and 3Avs4A (2,294 out of 15,614 (71% transcripts were recorded. In comparison, a total of 1,532 transcripts were annotated in GOs, including Cellular component, with the highest number in "Cell part" 251 out of 353 transcripts (71.1%, followed by intracellular organelle 163 out of 353 transcripts (46.2%, while in molecular function and metabolic process 375 out of 525 (71.4% transcripts, multicellular organism process 40 out of 525 (7.6% transcripts in biological process were most common in 1Avs2A. While in case of 1Avs3A, cell part 476 out of 662 transcripts (71.9%, and membrane-bounded organelle 263 out of 662 transcripts (39.7% were recorded in Cellular component. In the grapevine transcriptome, during the initial stages of leaf development 1Avs2A showed single transcript was down-regulated and none of them were up-regulated. While in comparison of 1A to 3A showed one up-regulated (photosystem II reaction center protein C and one down regulated (conserved gene of unknown function transcripts, during the hormone regulating pathway namely SAUR-like auxin-responsive protein family having 2 up-regulated and 7 down-regulated transcripts, phytochrome-associated protein showed 1 up-regulated and 9 down-regulated transcripts, whereas genes associated with the Leucine-rich repeat protein kinase family protein showed 7 up-regulated and 1 down-regulated transcript, meanwhile

  10. Transcriptomic Analysis of Grapevine (cv. Summer Black) Leaf, Using the Illumina Platform.

    Science.gov (United States)

    Pervaiz, Tariq; Haifeng, Jia; Salman Haider, Muhammad; Cheng, Zhang; Cui, Mengjie; Wang, Mengqi; Cui, Liwen; Wang, Xicheng; Fang, Jinggui

    2016-01-01

    Proceeding to illumina sequencing, determining RNA integrity numbers for poly RNA were separated from each of the four developmental stages of cv. Summer Black leaves by using Illumina HiSeq™ 2000. The sums of 272,941,656 reads were generated from vitis vinifera leaf at four different developmental stages, with more than 27 billion nucleotides of the sequence data. At each growth stage, RNA samples were indexed through unique nucleic acid identifiers and sequenced. KEGG annotation results depicted that the highest number of transcripts in 2,963 (2Avs4A) followed by 1Avs4A (2,920), and 3Avs4A (2,294) out of 15,614 (71%) transcripts were recorded. In comparison, a total of 1,532 transcripts were annotated in GOs, including Cellular component, with the highest number in "Cell part" 251 out of 353 transcripts (71.1%), followed by intracellular organelle 163 out of 353 transcripts (46.2%), while in molecular function and metabolic process 375 out of 525 (71.4%) transcripts, multicellular organism process 40 out of 525 (7.6%) transcripts in biological process were most common in 1Avs2A. While in case of 1Avs3A, cell part 476 out of 662 transcripts (71.9%), and membrane-bounded organelle 263 out of 662 transcripts (39.7%) were recorded in Cellular component. In the grapevine transcriptome, during the initial stages of leaf development 1Avs2A showed single transcript was down-regulated and none of them were up-regulated. While in comparison of 1A to 3A showed one up-regulated (photosystem II reaction center protein C) and one down regulated (conserved gene of unknown function) transcripts, during the hormone regulating pathway namely SAUR-like auxin-responsive protein family having 2 up-regulated and 7 down-regulated transcripts, phytochrome-associated protein showed 1 up-regulated and 9 down-regulated transcripts, whereas genes associated with the Leucine-rich repeat protein kinase family protein showed 7 up-regulated and 1 down-regulated transcript, meanwhile Auxin

  11. 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.

  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. New challenges in downstream retail markets

    International Nuclear Information System (INIS)

    The role and purposes of deregulation in the natural gas industry and the way in which downstream markets operate today were reviewed. The question of what form deregulation will take in the future, and how it will affect market participants was also addressed. Load imbalance has been identified as the most significant system inefficiency. It was argued that as long as LCDs hold control over the imbalances, end-users will be in a position where they will have no control over a variable which can significantly affect their cost. It is this lack of control that can be viewed as a system inefficiency. It was suggested that in the future deregulation will focus on load balancing, and will support the continued development of a retail market for products and services which exist independently of the wholesale market. Security of supply and control of the transportation and storage assets were identified as the principal issues associated with end-user customers gaining more control over their gas accounts

  14. Identification of novel auxin responses during Arabidopsis embryogenesis

    NARCIS (Netherlands)

    Rademacher, E.H.

    2009-01-01

    Plants normally form one embryo per seed. Under special circumstances, such as death of the embryo, a second embryo can develop from a supportive structure called the suspensor. These suspensor cells therefore provide a reservoir of stem cells for the generation of secondary embryos. At the start of

  15. Context, Specificity, and Self-Organization in Auxin Response

    OpenAIRE

    Del Bianco, Marta; Kepinski, Stefan

    2011-01-01

    Auxin is a simple molecule with a remarkable ability to control plant growth, differentiation, and morphogenesis. The mechanistic basis for this versatility appears to stem from the highly complex nature of the networks regulating auxin metabolism, transport and response. These heavily feedback-regulated and inter-dependent mechanisms are complicated in structure and complex in operation giving rise to a system with self-organizing properties capable of generating highly context-specific resp...

  16. Reporters for sensitive and quantitative measurement of auxin response

    NARCIS (Netherlands)

    Liao, C.Y.; Smet, W.M.S.; Brunoud, G.; Yoshida, S.; Vernoux, T.; Weijers, D.

    2015-01-01

    The visualization of hormonal signaling input and output is key to understanding how multicellular development is regulated. The plant signaling molecule auxin triggers many growth and developmental responses, but current tools lack the sensitivity or precision to visualize these. We developed a set

  17. Dependence of mountain moisture retention on downstream saturation

    CERN Document Server

    November, L J

    2007-01-01

    We derive 1D steady equilibria for partially saturated downslope flow as a solution to the reposed vadose-zone problem. The equilibria are determined by two free parameters: a mean flow and a downstream saturation. Where there is no downstream saturation, a uniform outflow of constant saturation is obtained, but if an isolated zone of excess downstream saturation exists, the upstream flow speed is reduced and saturation increased. The saturated zone produces a capillary head jump that blocks the downward percolation. With a fully saturated downstream zone in medium clay mixtures, flow backs up more than 20 km projected vertically, but with 90% downstream saturation, the back up is reduced to less than a km. The drying of downstream saturated zones with the increased rate of mountain moisture outflow gives a viable quantitative explanation for the mysterious 56% unaccounted drop seen in the output of the southern NM La Luz / Fresnal Watershed at Alamogordo's upstream spring-box diversions.

  18. Pyrvinium attenuates Hedgehog signaling downstream of smoothened.

    Science.gov (United States)

    Li, Bin; Fei, Dennis Liang; Flaveny, Colin A; Dahmane, Nadia; Baubet, Valérie; Wang, Zhiqiang; Bai, Feng; Pei, Xin-Hai; Rodriguez-Blanco, Jezabel; Hang, Brian; Orton, Darren; Han, Lu; Wang, Baolin; Capobianco, Anthony J; Lee, Ethan; Robbins, David J

    2014-09-01

    The Hedgehog (HH) signaling pathway represents an important class of emerging developmental signaling pathways that play critical roles in the genesis of a large number of human cancers. The pharmaceutical industry is currently focused on developing small molecules targeting Smoothened (Smo), a key signaling effector of the HH pathway that regulates the levels and activity of the Gli family of transcription factors. Although one of these compounds, vismodegib, is now FDA-approved for patients with advanced basal cell carcinoma, acquired mutations in Smo can result in rapid relapse. Furthermore, many cancers also exhibit a Smo-independent activation of Gli proteins, an observation that may underlie the limited efficacy of Smo inhibitors in clinical trials against other types of cancer. Thus, there remains a critical need for HH inhibitors with different mechanisms of action, particularly those that act downstream of Smo. Recently, we identified the FDA-approved anti-pinworm compound pyrvinium as a novel, potent (IC50, 10 nmol/L) casein kinase-1α (CK1α) agonist. We show here that pyrvinium is a potent inhibitor of HH signaling, which acts by reducing the stability of the Gli family of transcription factors. Consistent with CK1α agonists acting on these most distal components of the HH signaling pathway, pyrvinium is able to inhibit the activity of a clinically relevant, vismodegib -resistant Smo mutant, as well as the Gli activity resulting from loss of the negative regulator suppressor of fused. We go on to demonstrate the utility of this small molecule in vivo, against the HH-dependent cancer medulloblastoma, attenuating its growth and reducing the expression of HH biomarkers. PMID:24994715

  19. Auxin responsive factor基因转化烟草的初探%Transformation of auxin responsive factor to tobacco

    Institute of Scientific and Technical Information of China (English)

    陆艳; 徐刚标; 陈建华

    2006-01-01

    如何改进烟叶的品质、提高烟叶的产量、特别是提高烟株对病虫害的抗性,是烟草研究专家的重要课题.由于烟草较易进行组织培养和基因转化,因而成为植物基因工程中的模式植物之一,是植物界的"果蝇",许多非烟草研究专家也在用它进行转基因的研究,这就使得烟草的转基因研究特别丰富,研究成果很多,这是烟草得天独厚之处.但研究的成果真正转化到生产上的数量却相当少,这正是烟草研究者们要努力解决的问题.

  20. 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

  1. Integration of transcriptomics and metabonomics

    DEFF Research Database (Denmark)

    Bjerrum, Jacob Tveiten; Rantalainen, Mattias; Wang, Yulan;

    2014-01-01

    A systems biology approach to multi-faceted diseases has provided an opportunity to establish a holistic understanding of the processes at play. Thus, the current study merges transcriptomics and metabonomics data in order to improve diagnostics, biomarker identification and to explore the possib......A systems biology approach to multi-faceted diseases has provided an opportunity to establish a holistic understanding of the processes at play. Thus, the current study merges transcriptomics and metabonomics data in order to improve diagnostics, biomarker identification and to explore...... profiles were generated using (1)H Nuclear magnetic resonance spectroscopy (Bruker 600 MHz, Bruker BioSpin, Rheinstetten, Germany). Data were analyzed with the use of orthogonal-projection to latent structure-discriminant analysis and a multivariate logistic regression model fitted by lasso. Prediction....... These combined panels improve diagnostics and more importantly also the molecular phenotyping in UC and provide insight into the pathophysiological processes at play, making optimized and personalized medication a possibility....

  2. Tricks to translating TB transcriptomics.

    Science.gov (United States)

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

    2015-05-01

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

  3. 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...

  4. Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse.

    Directory of Open Access Journals (Sweden)

    Maria Augusta Crivelente Horta

    Full Text Available Profiling the transcriptome that underlies biomass degradation by the fungus Trichoderma harzianum allows the identification of gene sequences with potential application in enzymatic hydrolysis processing. In the present study, the transcriptome of T. harzianum IOC-3844 was analyzed using RNA-seq technology. The sequencing generated 14.7 Gbp for downstream analyses. De novo assembly resulted in 32,396 contigs, which were submitted for identification and classified according to their identities. This analysis allowed us to define a principal set of T. harzianum genes that are involved in the degradation of cellulose and hemicellulose and the accessory genes that are involved in the depolymerization of biomass. An additional analysis of expression levels identified a set of carbohydrate-active enzymes that are upregulated under different conditions. The present study provides valuable information for future studies on biomass degradation and contributes to a better understanding of the role of the genes that are involved in this process.

  5. 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

  6. 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

  7. Using Transcriptomics to Understand the Wheat Genome

    Science.gov (United States)

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

  8. Transcriptome sequencing goals, assembly, and assessment.

    Science.gov (United States)

    Wheat, Christopher W; Vogel, Heiko

    2011-01-01

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

  9. 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.

  10. Corrosion rate and downstream effect in liquid metal systems

    International Nuclear Information System (INIS)

    Results of experiments performed, especially of runs 1.10 and 1.12 have been evaluated with respect to the downstream effect in isothermal test sections in sodium at 1000 K. It is evident that there is not dependence of the selective Ni loss on position. This loss will be reduced considerably with high Ni concentration in sodium. The downstream function is influenced by different causes for short and extended exposure periods. Up to 400h Cr, together with impurities in sodium dominates the downstream effect. After longer exposure periods the steel surface will become equilibrated with respect to sodium conditions and the downstream effect will be dominated by elemental dissolution, essentially of Fe and saturation of dissolved elements in sodium. (author)

  11. Downstream influence scaling of turbulent flow past expansion corners

    Science.gov (United States)

    Lu, Frank K.; Chung, Kung-Ming

    1992-01-01

    Previous studies of the high-speed viscous inviscid interaction between a turbulent boundary layer and an expansion at a convex corner have noted that surface pressure decreases toward the downstream inviscid value yielded by a Prandtl-Meyer expansion. A downstream influence on the corner is presently identified which is based on the mean surface pressure distribution; a scaling law is proposed for this distance.

  12. Modelling Downstream Effects in the Presence of Technological Change

    OpenAIRE

    Duncan Mortimer

    2008-01-01

    Downstream effects are typically evaluated given current technology and current practice patterns rather than for technology and practice patterns that will be available at the time when downstream effects accrue. Where a relatively short time horizon can be expected to capture all relevant costs and effects, the current approach is unlikely to introduce substantial error into estimates of the costs and benefits attributed to an intervention; the estimates will remain valid so long as the con...

  13. 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.

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

    OpenAIRE

    Gilbert-López, Bienvenida; Mendiola, José A.; Fontecha, Javier; SIJTSMA Lolke; Cifuentes, Alejandro; Herrero, Miguel; Ibáñez, Elena; van den Broek, Lambertus A. M.

    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 chemistry, it will end-up with sustainable processes. In the present study, a downstream processing platform has been developed to extract bioactive compounds from the microalga Isochrysis galbana using v...

  15. Modeling Neutral Densities Downstream of a Gridded Ion Thruster

    Science.gov (United States)

    Soulas, George C.

    2010-01-01

    The details of a model for determining the neutral density downstream of a gridded ion thruster are presented. An investigation of the possible sources of neutrals emanating from and surrounding a NEXT ion thruster determined that the most significant contributors to the downstream neutral density include discharge chamber neutrals escaping through the perforated grids, neutrals escaping from the neutralizer, and vacuum facility background neutrals. For the neutral flux through the grids, near- and far-field equations are presented for rigorously determining the neutral density downstream of a cylindrical aperture. These equations are integrated into a spherically-domed convex grid geometry with a hexagonal array of apertures for determining neutral densities downstream of the ion thruster grids. The neutrals escaping from an off-center neutralizer are also modeled assuming diffuse neutral emission from the neutralizer keeper orifice. Finally, the effect of the surrounding vacuum facility neutrals is included and assumed to be constant. The model is used to predict the neutral density downstream of a NEXT ion thruster with and without neutralizer flow and a vacuum facility background pressure. The impacts of past simplifying assumptions for predicting downstream neutral densities are also examined for a NEXT ion thruster.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. The olfactory transcriptomes of mice.

    Science.gov (United States)

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

    2014-09-01

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

  1. The olfactory transcriptomes of mice.

    Directory of Open Access Journals (Sweden)

    Ximena Ibarra-Soria

    2014-09-01

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

  2. Characterization of the Asian Citrus Psyllid Transcriptome.

    Science.gov (United States)

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

    2014-01-01

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

  3. Characterization of the Asian Citrus Psyllid Transcriptome.

    Science.gov (United States)

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

    2014-01-01

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

  4. Comparative transcriptomics in the Triticeae

    Directory of Open Access Journals (Sweden)

    Waugh Robbie

    2009-06-01

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

  5. Modeling downstream fining in sand-bed rivers. I: Formulation

    Science.gov (United States)

    Wright, S.; Parker, G.

    2005-01-01

    In this paper a numerical modeling formulation is presented for simulation of the development of the longitudinal profile and bed sediment distribution in sand-bed rivers. The objective of the model application, which is presented in the companion paper (Wright and Parker, 2005), is to study the development of two characteristics of large, low-slope, sand-bed rivers: (1) a downstream decrease in bed slope (i.e. concave upward longitudinal profile) and (2) a downstream decrease in characteristic bed sediment diameter (e.g. the median bed surface size D50). Three mechanisms that lead to an upward concave profile and downstream fining are included in the modeling formulation: (1) a delta prograding into standing water at the downstream boundary, (2) sea-level rise, and (3) tectonic subsidence. In the companion paper (Wright and Parker, 2005) the model is applied to simulate the development of the longitudinal profile and downstream fining in sand-bed rivers flowing into the ocean during the past 5000 years of relatively slow sea-level rise. ?? 2005 International Association of Hydraulic Engineering and Research.

  6. Mortality of zebra mussel, Dreissena polymorpha, veligers during downstream transport

    Science.gov (United States)

    Horvath, T.G.; Lamberti, G.A.

    1999-01-01

    1. Streams flowing from lakes which contain zebra mussels, Dreissena polymorpha, provide apparently suitable habitats for mussel colonization and downstream range expansion, yet most such streams contain few adult mussels. We postulated that mussel veligers experience high mortality during dispersal via downstream transport. They tested this hypothesis in Christiana Creek, a lake-outlet stream in south-western Michigan, U.S.A., in which adult mussel density declined exponentially with distance downstream. 2. A staining technique using neutral red was developed and tested to distinguish quickly live and dead veligers. Live and dead veligers were distinguishable after an exposure of fresh samples to 13.3 mg L-1 of neutral red for 3 h. 3. Neutral red was used to determine the proportion of live veligers in samples taken longitudinally along Christiana Creek. The proportion of live veligers (mean ?? SE) declined from 90 ?? 3% at the lake outlet to 40 ?? 8% 18 km downstream. 4. Veligers appear to be highly susceptible to damage by physical forces (e.g. shear), and therefore, mortality in turbulent streams could be an important mechanism limiting zebra mussel dispersal to downstream reaches. Predictions of zebra mussel spread and population growth should consider lake-stream linkages and high mortality in running waters.

  7. Downstream Yangtze River levels impacted by Three Gorges Dam

    Science.gov (United States)

    Wang, Jida; Sheng, Yongwei; Gleason, Colin J.; Wada, Yoshihide

    2013-12-01

    Changes in the Yangtze River level induced by large-scale human water regulation have profound implications on the inundation dynamics of surrounding lakes/wetlands and the integrity of related ecosystems. Using in situ measurements and hydrological simulation, this study reveals an altered Yangtze level regime downstream from the Three Gorges Dam (TGD) to the Yangtze estuary in the East China Sea as a combined result of (i) TGD’s flow regulation and (ii) Yangtze channel erosion due to reduced sediment load. During the average annual cycle of TGD’s regular flow control in 2009-2012, downstream Yangtze level variations were estimated to have been reduced by 3.9-13.5% at 15 studied gauging stations, manifested as evident level decrease in fall and increase in winter and spring. The impacts on Yangtze levels generally diminished in a longitudinal direction from the TGD to the estuary, with a total time lag of ˜9-12 days. Chronic Yangtze channel erosion since the TGD closure has lowered water levels in relation to flows at most downstream stations, which in turn counteracts the anticipated level increase by nearly or over 50% in winter and spring while reinforcing the anticipated level decrease by over 20% in fall. Continuous downstream channel erosion in the near future may further counteract the benefit of increased Yangtze levels during TGD’s water supplement in winter and accelerate the receding of inundation areas/levels of downstream lakes in fall.

  8. Critical effects of downstream boundary conditions on vortex breakdown

    Science.gov (United States)

    Kandil, Osama; Kandil, Hamdy A.; Liu, C. H.

    1992-01-01

    The unsteady, compressible, full Navier-Stokes (NS) equations are used to study the critical effects of the downstream boundary conditions on the supersonic vortex breakdown. The present study is applied to two supersonic vortex breakdown cases. In the first case, quasi-axisymmetric supersonic swirling flow is considered in a configured circular duct, and in the second case, quasi-axisymmetric supersonic swirling jet, that is issued from a nozzle into a supersonic jet of lower Mach number, is considered. For the configured duct flow, four different types of downstream boundary conditions are used, and for the swirling jet flow from the nozzle, two types of downstream boundary conditions are used. The solutions are time accurate which are obtained using an implicit, upwind, flux-difference splitting, finite-volume scheme.

  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. 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.

  11. Characterization of the Asian Citrus Psyllid Transcriptome

    OpenAIRE

    Reese, Justin; Christenson, Matthew K.; Leng, Nan; Saha, Surya; Cantarel, Brandi; Lindeberg, Magdalen; Tamborindeguy, Cecilia; MacCarthy, Justin; Weaver, Daniel; Trease, Andrew J.; Ready, Steven V.; Davis, Vincent M.; McCormick, Courtney; Haudenschild, Christian; Han, Shunsheng

    2014-01-01

    The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insectici...

  12. Transition duct with divided upstream and downstream portions

    Science.gov (United States)

    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.

  13. Interaction of fan rotor flow with downstream struts

    Science.gov (United States)

    Obrien, W. F., Jr.; Reimers, S. L.; Richardson, S. W.

    1983-01-01

    The detailed unsteady pressure field produced on the rotor blades of an axial-flow fan by interaction with downstream struts was investigated. The experimental arrangement was similar to that found in the fan casings of turbofan aircraft engines. Acoustically significant pressure fluctuations were measured on both thy suction and pressure sides of the rotor blades for several positions of the downstream struts. The level of the observed interaction decreased with increased spacing of the struts behind the rotor. An inviscid flow analysis for the disturbance level is compared with trends of the measured results.

  14. 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.

  15. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Tsai, I-Lin [Department of Pharmacy, National Taiwan University, No. 1, Jen-Ai Road, Section 1 Taipei 10051, Taiwan (China); The Metabolomics Group, National Taiwan University, Taipei 106, Taiwan (China); Center for Genomic Medicine, National Taiwan University, Taipei 10051, Taiwan (China); Kuo, Tien-Chueh [The Metabolomics Group, National Taiwan University, Taipei 106, Taiwan (China); Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Room 410 BL Building, No. 1, Roosevelt Road, Sec. 4, Taipei 106, Taiwan (China); Ho, Tsung-Jung [The Metabolomics Group, National Taiwan University, Taipei 106, Taiwan (China); Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan (China); Harn, Yeu-Chern [The Metabolomics Group, National Taiwan University, Taipei 106, Taiwan (China); Graduate Institute of Networking and Multimedia, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan (China); Wang, San-Yuan [The Metabolomics Group, National Taiwan University, Taipei 106, Taiwan (China); Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan (China); Fu, Wen-Mei [Department of Pharmacology, National Taiwan University, 11 F No. 1 Sec. 1, Ren-ai Rd., Taipei 10051, Taiwan (China); Kuo, Ching-Hua, E-mail: kuoch@ntu.edu.tw [Department of Pharmacy, National Taiwan University, No. 1, Jen-Ai Road, Section 1 Taipei 10051, Taiwan (China); The Metabolomics Group, National Taiwan University, Taipei 106, Taiwan (China); Center for Genomic Medicine, National Taiwan University, Taipei 10051, Taiwan (China); Tseng, Yufeng Jane, E-mail: kuoch@ntu.edu.tw [Department of Pharmacy, National Taiwan University, No. 1, Jen-Ai Road, Section 1 Taipei 10051, Taiwan (China); The Metabolomics Group, National Taiwan University, Taipei 106, Taiwan (China); Center for Genomic Medicine, National Taiwan University, Taipei 10051, Taiwan (China); Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Room 410 BL Building, No. 1, Roosevelt Road, Sec. 4, Taipei 106, Taiwan (China); Department of Computer Science and Information Engineering, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan (China)

    2013-05-03

    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.

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

    International Nuclear Information System (INIS)

    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

  18. 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.

  19. 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

  20. 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.

  1. 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...

  2. Peru's Downstream Natural Gas Sector : A Preliminary Assessment

    OpenAIRE

    Reinstein, David; Benítez, Daniel A. Benítez; Todd M. Johnson

    2011-01-01

    This study assesses the natural gas market in Peru. In the process of evaluating the downstream market, the study identifies opportunities for meeting the Government s aspirational goals with respect to energy and natural gas development, including the efficient use of natural gas in the power and other sectors, strengthening and coordinating national energy planning for the gas sector, in...

  3. Methylation of Hg downstream from the Bonanza Hg mine, Oregon

    Science.gov (United States)

    Gray, John E.; Hines, Mark E.; Krabbenhoft, David P.; Thoms, Bryn

    2012-01-01

    Speciation of Hg and conversion to methyl-Hg were evaluated in stream sediment, stream water, and aquatic snails collected downstream from the Bonanza Hg mine, Oregon. Total production from the Bonanza mine was >1360t of Hg, during mining from the late 1800s to 1960, ranking it as an intermediate sized Hg mine on an international scale. The primary objective of this study was to evaluate the distribution, transport, and methylation of Hg downstream from a Hg mine in a coastal temperate climatic zone. Data shown here for methyl-Hg, a neurotoxin hazardous to humans, are the first reported for sediment and water from this area. Stream sediment collected from Foster Creek flowing downstream from the Bonanza mine contained elevated Hg concentrations that ranged from 590 to 71,000ng/g, all of which (except the most distal sample) exceeded the probable effect concentration (PEC) of 1060ng/g, the Hg concentration above which harmful effects are likely to be observed in sediment-dwelling organisms. Concentrations of methyl-Hg in stream sediment collected from Foster Creek varied from 11 to 62ng/g and were highly elevated compared to regional baseline concentrations (0.11-0.82ng/g) established in this study. Methyl-Hg concentrations in stream sediment collected in this study showed a significant correlation with total organic C (TOC, R2=0.62), generally indicating increased methyl-Hg formation with increasing TOC in sediment. Isotopic-tracer methods indicated that several samples of Foster Creek sediment exhibited high rates of Hg-methylation. Concentrations of Hg in water collected downstream from the mine varied from 17 to 270ng/L and were also elevated compared to baselines, but all were below the 770ng/L Hg standard recommended by the USEPA to protect against chronic effects to aquatic wildlife. Concentrations of methyl-Hg in the water collected from Foster Creek ranged from 0.17 to 1.8ng/L, which were elevated compared to regional baseline sites upstream and downstream

  4. 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

  5. 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.

  6. Genome-wide transcriptome directed pathway analysis of maternal pre-eclampsia susceptibility genes.

    Directory of Open Access Journals (Sweden)

    Hannah E J Yong

    Full Text Available Preeclampsia (PE is a serious hypertensive pregnancy disorder with a significant genetic component. Numerous genetic studies, including our own, have yielded many susceptibility genes from distinct functional groups. Additionally, transcriptome profiling of tissues at the maternal-fetal interface has likewise yielded many differentially expressed genes. Often there is little overlap between these two approaches, although genes identified in both approaches are significantly associated with PE. We have thus taken a novel integrative bioinformatics approach of analysing pathways common to the susceptibility genes and the PE transcriptome.Using Illumina Human Ht12v4 and Wg6v3 BeadChips, transcriptome profiling was conducted on n = 65 normotensive and n = 60 PE decidua basalis tissues collected at delivery. The R software package libraries lumi and limma were used to preprocess transcript data for pathway analysis. Pathways were analysed and constructed using Pathway Studio. We examined ten candidate genes, which are from these functional groups: activin/inhibin signalling-ACVR1, ACVR1C, ACVR2A, INHA, INHBB; structural components-COL4A1, COL4A2 and M1 family aminopeptidases-ERAP1, ERAP2 and LNPEP.Major common regulators/targets of these susceptibility genes identified were AGT, IFNG, IL6, INHBA, SERPINE1, TGFB1 and VEGFA. The top two categories of pathways associated with the susceptibility genes, which were significantly altered in the PE decidual transcriptome, were apoptosis and cell signaling (p < 0.001. Thus, susceptibility genes from distinct functional groups share similar downstream pathways through common regulators/targets, some of which are altered in PE. This study contributes to a better understanding of how susceptibility genes may interact in the development of PE. With this knowledge, more targeted functional analyses of PE susceptibility genes in these key pathways can be performed to examine their contributions to the pathogenesis

  7. [Transcriptome analysis of Dunaliella viridis].

    Science.gov (United States)

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

    2015-08-01

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

  8. 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.

  9. Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis

    OpenAIRE

    Li, Wenli; Turner, Amy; Aggarwal, Praful; Matter, Andrea; Storvick, Erin; Donna K Arnett; Broeckel, Ulrich

    2015-01-01

    Background Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitati...

  10. 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.

  11. Collusion and downstream entry in a vertically integrated industry

    OpenAIRE

    Éric Avenel; Stéphane Caprice

    2012-01-01

    We analyse the impact of an entry threat at the downstream level on the ability of a pair of vertically integrated incumbents to collude. We present an original model of horizontal product differentiation on the final market and characterize the structures of this market for which an entry threat facilitates collusion between incumbents. While the entry threat leaves collusion and deviation profits unchanged, it lowers profits in punishment periods. Consequently, an entry threat discourages d...

  12. Corner waves downstream from a partially submerged vertical plate

    OpenAIRE

    Martínez-Legazpi Aguiló, Pablo

    2011-01-01

    In this dissertation, the high-Reynolds-number flow near the corner of a vertical at plate partially submerged across an uniform stream has been studied using a combination of experimental, numerical and analytical tools. In this configuration, a three dimensional wave forms at the corner of the plate which evolves downstream in a similar way as a time-evolving two dimensional plunging or spilling breaker, depending the occurrence of one or the other type of breaker on the flow conditions. Ex...

  13. Microalgae downstream processing and economical approaches of biodiesel producton processes

    OpenAIRE

    Ríos, Sergio Daniel

    2013-01-01

    Microalgae oil has been identified as a reliable resource for biodiesel production due to its high lipid productivity and potential cultivation in non-fertile locations. However, high scale production of microalgae based biodiesel depends on the optimization of the entire process to be economically feasible. The present work combine the optimization of microalgae downstream processes with computational tools for the modeling of different scenarios of the harvesting, oil extraction and transes...

  14. 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.

  15. 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 (pcomplex 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 number of downstream proteins. Indeed, we verify that this property is independent of the hubness in

  16. Strigolactone acts downstream of auxin to regulate bud outgrowth in pea and Arabidopsis.

    Science.gov (United States)

    Brewer, Philip B; Dun, Elizabeth A; Ferguson, Brett J; Rameau, Catherine; Beveridge, Christine A

    2009-05-01

    During the last century, two key hypotheses have been proposed to explain apical dominance in plants: auxin promotes the production of a second messenger that moves up into buds to repress their outgrowth, and auxin saturation in the stem inhibits auxin transport from buds, thereby inhibiting bud outgrowth. The recent discovery of strigolactone as the novel shoot-branching inhibitor allowed us to test its mode of action in relation to these hypotheses. We found that exogenously applied strigolactone inhibited bud outgrowth in pea (Pisum sativum) even when auxin was depleted after decapitation. We also found that strigolactone application reduced branching in Arabidopsis (Arabidopsis thaliana) auxin response mutants, suggesting that auxin may act through strigolactones to facilitate apical dominance. Moreover, strigolactone application to tiny buds of mutant or decapitated pea plants rapidly stopped outgrowth, in contrast to applying N-1-naphthylphthalamic acid (NPA), an auxin transport inhibitor, which significantly slowed growth only after several days. Whereas strigolactone or NPA applied to growing buds reduced bud length, only NPA blocked auxin transport in the bud. Wild-type and strigolactone biosynthesis mutant pea and Arabidopsis shoots were capable of instantly transporting additional amounts of auxin in excess of endogenous levels, contrary to predictions of auxin transport models. These data suggest that strigolactone does not act primarily by affecting auxin transport from buds. Rather, the primary repressor of bud outgrowth appears to be the auxin-dependent production of strigolactones. PMID:19321710

  17. Meta-analysis of transcriptome data identified TGTCNN motif variants associated with the response to plant hormone auxin in Arabidopsis thaliana L.

    Science.gov (United States)

    Zemlyanskaya, Elena V; Wiebe, Daniil S; Omelyanchuk, Nadezhda A; Levitsky, Victor G; Mironova, Victoria V

    2016-04-01

    Auxin is the major regulator of plant growth and development. It regulates gene expression via a family of transcription factors (ARFs) that bind to auxin responsive elements (AuxREs) in the gene promoters. The canonical AuxREs found in regulatory regions of many auxin responsive genes contain the TGTCTC core motif, whereas ARF binding site is a degenerate TGTCNN with TGTCGG strongly preferred. Thereby two questions arise: which TGTCNN variants are functional AuxRE cores and whether different TGTCNN variants have distinct functional roles? In this study, we performed meta-analysis of microarray data to reveal TGTCNN variants essential for auxin response and to characterize their functional features. Our results indicate that four TGTCNN motifs (TGTCTC, TGTCCC, TGTCGG, and TGTCTG) are associated with auxin up-regulation and two (TGTCGG, TGTCAT) with auxin down-regulation, but to a lesser extent. The genes having some of these motifs in their regulatory regions showed time-specific auxin response. Functional annotation of auxin up- and down-regulated genes also revealed GO terms specific for the auxin-regulated genes with certain TGTCNN variants in their promoters. Our results provide an idea that various TGTCNN motifs may play distinct roles in the auxin regulation of gene expression. PMID:27122321

  18. 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

  19. 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.

  20. The transcriptome landscape of early maize meiosis

    Science.gov (United States)

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

  1. Mastitis associated transcriptomic disruptions in cattle

    Science.gov (United States)

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

  2. Climate change issue table : petroleum downstream sector industry foundation paper

    International Nuclear Information System (INIS)

    An analysis of the impact of the Kyoto Protocol on the Canadian downstream petroleum industry is presented. The downstream sector includes petroleum refining, plus all activities regarding distribution, marketing and retailing of petroleum products. In 1990, the carbon dioxide (CO2) emissions resulting from the production and consumption of petroleum products were about 207 megatons which is about 45 per cent of total Canadian CO2 emissions. This report includes the analysis of the Base Case and the Kyoto Case. The Base Case is premised on the implementation of fuel sulphur reductions to meet cleaner fuels requirements and an enhanced program of refinery efficiency initiatives. Under the Base Case assumptions the CO2 emissions from refinery operations in 2010 would be about 3.4 below 1990 levels. The Kyoto Case was developed on the basis of reductions in Canadian petroleum product demand that would be sufficient to achieve a 6 per cent reduction in GHG emissions from the production and consumption of petroleum products relative to 1990 levels. The model demonstrates the dramatic economic impact of the Kyoto Case reductions on the Canadian downstream petroleum sector. Investment requirements for capital improvements to further distillate production and to further desulphurization are estimated at $ 1.5 billion between 2005 and 2015. The reduced volume of gasoline sales would be expected to result in rationalization of retail outlets, resulting in the closure of some 2,000 retail outlets with a combined loss of about 12,000 jobs. It is suggested that similar impact in other countries that are signatory to the Kyoto Protocol could result in the shift of refining, refining industry jobs and related economic benefits to countries which are not participants in the Kyoto Protocol. 14 tabs., 6 figs., 5 appendices

  3. Growth Characteristics Downstream of a Shallow Bump: Computation and Experiment

    Science.gov (United States)

    Joslin, Ronald D.; Grosch, Chester E.

    1996-01-01

    Measurements of the velocity field created by a shallow bump on a wall revealed that an energy peak in the spanwise spectrum associated with the driver decays and an initially small-amplitude secondary mode rapidly grows with distance downstream of the bump. Linear theories could not provide an explanation for this growing mode. The present Navier-Stokes simulation replicates and confirms the experimental results. Insight into the structure of the flow was obtained from a study of the results of the calculations and is presented.

  4. 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.

  5. The flow field downstream of a hydraulic jump

    OpenAIRE

    Hornung, Hans G.; Willert, Christian; Turner, Stewart

    1995-01-01

    A control-volume analysis of a hydraulic jump is used to obtain the mean vorticity downstream of the jump as a function of the Froude number. To do this it is necessary to include the conservation of angular momentum. The mean vorticity increases from zero as the cube of Froude number minus one, and, in dimensionless form, approaches a constant at large Froude number. Digital particle imaging velocimetry was applied to travelling hydraulic jumps giving centre-plane velocity field images at a ...

  6. Experiments in a combined up stream downstream slug flow

    Directory of Open Access Journals (Sweden)

    Toledo-Velázquez M.

    2013-04-01

    Full Text Available Slug flow induced by the combination of a downstream and an upstream two phase flow is very common in the oil industry, mainly when the pipelines are installed on hilly terrains. This phenomenon can be dangerous for the equipment operation because it induces vibrations due to the slugs intermittent movement into the separators. A loop, where it is possible to change the flow conditions and the loop geometrical parameters as the length and inclination angle of the pipe sections was built. Instruments for slug detection and for measuring their characteristic parameters as hold up, frequency, length, and velocity were installed. Three conductive probes were used for the hold-up measurement in different points; all of them were designed, constructed, tested andcalibrated. Experimental runs for a set of four alternated sections upstream downstream W shaped pipe have been undertaken. The gas and liquid flow rates were selected in order to obtain stratified flow at the inlet, which is the condition to induce the severe slugging. The main conclusions of the experimental results analysis are presented in this paper. The Barnea's criterion has been compared against our experimental results, three slugging regions have been found.

  7. Initial PVO Evidence of Electron Depletion Signatures Downstream of Venus

    Science.gov (United States)

    Intriligator, D. S.; Hartle, R. E.; Perez-de-Tejada, H.; Siscoe, G. L.

    1993-01-01

    This first analysis of Pioneer Venus Orbiter (PVO) plasma analyzer electron measurements obtained in early 1992 during the PVO entry phase of the mission indicates the presence downstream from the terminator of a depletion or "bite out" of energetic ionosheath electrons similar to that observed on Mariner 10. There is more than one possible explanation for this energetic electron depletion. If it is due to atmospheric scattering, the electrons traveling along draped magnetic flux tubes that thread through the Venus neutral atmosphere would lose energy from impact ionization with oxygen. The cross-section for such electron impact ionization of oxygen has a peak near 100 eV, and it remains high above this energy, so atmospheric loss could provide a natural process for electrons at these energies to be selectively removed. In this case, our results are consistent with the Kar et al. (1994) study of PVO atmospheric entry ion mass spectrometer data which indicates that electron impact plays a significant role in maintaining the nightside ionosphere. Although it is appealing to interpret the energetic electron depletion in terms of direct atmospheric scattering, alternatively it could result from strong draping which connects the depletion region magnetically to the weak downstream bow shock and thereby reduces the electron source strength.

  8. Flow downstream of the heliospheric terminal shock. I - Irrotational flow

    Science.gov (United States)

    Suess, Steven T.; Nerney, Steven

    1990-01-01

    Recent reports of remote detection of the heliospheric terminal shock place it near 50 AU. These conflict with standard models which, when combined with current data on the local interstellar medium, place the shock beyod 100 AU. Resolution of this discrepancy has led to hypotheses that invoke cosmic ray pressure, momentum exchange with interstellar neutrals, and magnetic field effects between the shock and the contact discontinuity dividing the solar wind from interstellar plasma. These hypotheses depend not only on properties of the interstellar medium, but also on the downstream three-dimensional flow between the shock and the contact discontinuity, in the region called the 'heliosheath'. The downstream flow field in the absence of magnetic fields is examined here under the assumptions that the flow everywhere outside the shock can be approximated as irrotational and incompressible. It is found, in particular, that the distance between the terminal shock and the contact discontinuity is less than the heliocentric distance to the terminal shock, effectively eliminating magnetic field effects in the heliosheath as being dynamically important.

  9. 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.

  10. Evaluation of Intracellular Signaling Downstream Chimeric Antigen Receptors.

    Directory of Open Access Journals (Sweden)

    Hannah Karlsson

    Full Text Available CD19-targeting CAR T cells have shown potency in clinical trials targeting B cell leukemia. Although mainly second generation (2G CARs carrying CD28 or 4-1BB have been investigated in patients, preclinical studies suggest that third generation (3G CARs with both CD28 and 4-1BB have enhanced capacity. However, little is known about the intracellular signaling pathways downstream of CARs. In the present work, we have analyzed the signaling capacity post antigen stimulation in both 2G and 3G CARs. 3G CAR T cells expanded better than 2G CAR T cells upon repeated stimulation with IL-2 and autologous B cells. An antigen-driven accumulation of CAR+ cells was evident post antigen stimulation. The cytotoxicity of both 2G and 3G CAR T cells was maintained by repeated stimulation. The phosphorylation status of intracellular signaling proteins post antigen stimulation showed that 3G CAR T cells had a higher activation status than 2G. Several proteins involved in signaling downstream the TCR were activated, as were proteins involved in the cell cycle, cell adhesion and exocytosis. In conclusion, 3G CAR T cells had a higher degree of intracellular signaling activity than 2G CARs which may explain the increased proliferative capacity seen in 3G CAR T cells. The study also indicates that there may be other signaling pathways to consider when designing or evaluating new generations of CARs.

  11. Transcriptome and metabolome analysis of plant sulphate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulphur, nitrogen and phosphorus nutritional responses in Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Monika eBielecka

    2015-01-01

    Full Text Available Sulphur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulphur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulphate starvation have been studied in the past, knowledge of the regulation of sulphur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs using ‘omics technologies. For this purpose a short term sulphate-starvation / re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulphate starvation. Categorization by response behaviors under sulphate-starvation / re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

  12. 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

  13. 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.

  14. 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.

  15. From gravel to sand. Downstream fining of bed sediments in the lower river Rhine

    NARCIS (Netherlands)

    Frings, R.M.

    2007-01-01

    A common characteristic of many rivers is the tendency for bed sediments to become finer in downstream direction. This phenomenon, which is generally known as downstream fining, has a strong effect on the morphologic and hydrodynamic behaviour of a river. The fundamental causes of downstream finin

  16. 19 CFR 351.223 - Procedures for initiation of downstream product monitoring.

    Science.gov (United States)

    2010-04-01

    ... 19 Customs Duties 3 2010-04-01 2010-04-01 false Procedures for initiation of downstream product... initiation of downstream product monitoring. (a) Introduction. Section 780 of the Act establishes a mechanism for monitoring imports of “downstream products.” In general, section 780 is aimed at situations...

  17. 40 CFR 80.210 - What sulfur standards apply to gasoline downstream from refineries and importers?

    Science.gov (United States)

    2010-07-01

    ... gasoline downstream from refineries and importers? 80.210 Section 80.210 Protection of Environment... Gasoline Sulfur Gasoline Sulfur Standards § 80.210 What sulfur standards apply to gasoline downstream from... downstream from refineries and import facilities, including gasoline at facilities of distributors,...

  18. Flow downstream of the heliospheric terminal shock - Magnetic field kinematics

    Science.gov (United States)

    Nerney, S.; Suess, S. T.; Schmahl, E. J.

    1991-01-01

    A kinematic model of the interplanetary magnetic field in the heliosheath beyond the solar wind terminal shock is presented in order to evaluate the possible importance of MHD effects in that region of space. The need for this evaluation arises because the interplanetary magnetic field is compressed across the terminal shock and further amplified by the decreasing flow speed beyond the shock. Streamlines which approach the stagnation point before turning in the downstream direction lead to the strongest effects due to the extreme slowing of the solar wind and consequent compression of the embedded magnetic field. The magnetic volume force therefore cannot be neglected on streamlines that approach the heliopause in the upstream direction, where the volume containing them is a large fraction of the overall of the heliosheath in the upstream direction. The increase in the magnetic pressure may act to bring the upstream terminal shock significantly closer to the sun, potentially reconciling a conflict between models and observations.

  19. Downstream properties of magnetic flux transfer events. [in magnetosphere

    Science.gov (United States)

    Sibeck, D. G.; Siscoe, G. L.

    1984-01-01

    Attention is given to the downstream evolution of the field line tubes known as 'flux transfer events' (FTEs), whose magnetic field and plasma properties are distinct from those of the nearby unmerged magnetosheath and magnetosphere field lines. After the FTE has moved 200 earth radii down the tail, its drained portion reaches 25 earth radii radially outward from the tail boundary. It is suggested that most multiple crossings of the tail boundary observed by spacecraft are encounters with tailward-moving FTEs, thereby explaining both the behavior of boundary normals during multiple crossings and how the sign of the IMF causes the observed dawn-dusk asymmetries in the thickness of the magnetotail boundary layer.

  20. 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.

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

    DEFF Research Database (Denmark)

    Howells, John

    Merges and Nelson have provided an empirically grounded argument that firms use pioneer patents of 'broad' scope to block downstream technological development (Merges and Nelson 1990). If this is a regular occurrence then, as they claim, they have faulted Kitch's 'prospect theory' of patents (Kitch...... 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...... in development in these same technologies. The paper finds that, first, the award of 'broad' scope is only implicated in one of the examples presented, second, that strict development block (understood as a retardation of development rate below some demonstrable and potentially higher rate) is not illustrated...

  2. Downstream and upstream extension of the House of Quality

    DEFF Research Database (Denmark)

    Holmen, Elsebeth; Kristensen, Preben Sander

    Executive summary 1. During 1993-94 the authors followed a product development process in a Danish butter cookie company. The process was structured according to the Quality Function Deployment technique House of Quality. Originally, the intention was to study the prototyping process that we...... for product development, we suggest ad incompatibility matrix to the traditional House of Quality. 3. Upstream, most product characteristics were deployed to internal company functions. In addition, some characteristics were deployed to potential suppliers. In this way the departments and firms that seemed...... a discussion in a diabetics end-user focus group. During a series of meetings, the production manager and the sales manager transformed attributes int characteristics and constructed Houses of Quality for a sugar-free cookie. 2. Downstream on its way to the end-user, the product passes through a chain of users...

  3. 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)

  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. 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

  6. Downstream cumulative effects of land use on freshwater communities

    Science.gov (United States)

    Kuglerová, L.; Kielstra, B. W.; Moore, D.; Richardson, J. S.

    2015-12-01

    Many streams and rivers are subject to disturbance from intense land use such as urbanization and agriculture, and this is especially obvious for small headwaters. Streams are spatially organized into networks where headwaters represent the tributaries and provide water, nutrients, and organic material to the main stems. Therefore perturbations within the headwaters might be cumulatively carried on downstream. Although we know that the disturbance of headwaters in urban and agricultural landscapes poses threats to downstream river reaches, the magnitude and severity of these changes for ecological communities is less known. We studied stream networks along a gradient of disturbance connected to land use intensity, from urbanized watersheds to watersheds placed in agricultural settings in the Greater Toronto Area. Further, we compared the patterns and processes found in the modified watershed to a control watershed, situated in a forested, less impacted landscape. Preliminary results suggest that hydrological modifications (flash floods), habitat loss (drainage and sewer systems), and water quality issues of small streams in urbanized and agricultural watersheds represent major disturbances and threats for aquatic and riparian biota on local as well as larger spatial scales. For example, communities of riparian plants are dominated by species typical of the land use on adjacent uplands as well as the dominant land use on the upstream contributing area, instead of riparian obligates commonly found in forested watersheds. Further, riparian communities in disturbed environments are dominated by invasive species. The changes in riparian communities are vital for various functions of riparian vegetation. Bank erosion control is suppressed, leading to severe channel transformations and sediment loadings in urbanized watersheds. Food sources for instream biota and thermal regimes are also changed, which further triggers alterations of in-stream biological communities

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

    Science.gov (United States)

    Yang, In Seok; Kim, Sangwoo

    2015-12-01

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

  8. Novel Approaches for Fungal Transcriptomics from Host Samples

    OpenAIRE

    Amorim-Vaz, Sara; Sanglard, Dominique

    2016-01-01

    Candida albicans adaptation to the host requires a profound reprogramming of the fungal transcriptome as compared to in vitro laboratory conditions. A detailed knowledge of the C. albicans transcriptome during the infection process is necessary in order to understand which of the fungal genes are important for host adaptation. Such genes could be thought of as potential targets for antifungal therapy. The acquisition of the C. albicans transcriptome is, however, technically challenging due to...

  9. Applications of new sequencing technologies for transcriptome analysis.

    Science.gov (United States)

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

    2009-01-01

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

  10. 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.

  11. 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.

  12. 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.

  13. Transcriptomic changes of Legionella pneumophila in water

    OpenAIRE

    Li, Laam; Mendis, Nilmini; Trigui, Hana; Faucher, Sébastien P.

    2015-01-01

    Background Legionella pneumophila (Lp) is a water-borne opportunistic pathogen. In water, Lp can survive for an extended period of time until it encounters a permissive host. Therefore, identifying genes that are required for survival in water may help develop strategies to prevent Legionella outbreaks. Results We compared the global transcriptomic response of Lp grown in a rich medium to that of Lp exposed to an artificial freshwater medium (Fraquil) for 2, 6 and 24 hours. We uncovered succe...

  14. Transcriptome Analysis of Sarracenia, an Insectivorous Plant

    OpenAIRE

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

    2011-01-01

    Sarracenia species (pitcher plants) are carnivorous plants which obtain a portion of their nutrients from insects captured in the pitchers. To investigate these plants, we sequenced the transcriptome of two species, Sarracenia psittacina and Sarracenia purpurea, using Roche 454 pyrosequencing technology. We obtained 46 275 and 36 681 contigs by de novo assembly methods for S. psittacina and S. purpurea, respectively, and further identified 16 163 orthologous contigs between them. Estimation o...

  15. 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.

  16. 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

  17. 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

  18. Electron acceleration at nearly perpendicular collisionless shocks. 3: Downstream distributions

    Science.gov (United States)

    Krauss-Varban, D.

    1994-01-01

    Spacecraft observations at the Earth's bow shock and at interplanetary shocks have established that the largest fluxes of accelerated suprathermal electrons occur in so-called shock spike events immediately downstream of the shock ramp. Previous theoretical efforts have mainly focused on explaining upstream energetic electron beams. Here we investigate the general motion and acceleration of energetic electrons in a curved, nearly perpendicular shock by numerically integrating the orbits of solar wind halo electrons in shock fields generated by a hybrid simulation (core electron fluid and kinetic ions). Close to the angle Theta(sub Bn) = 90 degs between the upstream magnetic field and shock normal, the calculations result in a (perpendicular) temperature increase proportional to the magnetic field ratio and give the highest phase space densities in the overshoot. For a steep distribution, the temperature change can correspond to an enhancement of the distribution by several orders of magnitude. These results are in agreement with predictions from adiabatic mapping. With smaller angles Theta(sub Bn), the overshoot and downstream densities fall off quickly, because the adiabatic energy gain is less and fewer electrons transmit. The shock curvature also leads to an accumulation of electrons close to 90 degs. Without pitch angle scattering, energization is only significant within a few (approximately 5 to 10 degs) degrees of the point of tangency. However, shock spike events appear to be observed more easily and farther away from 90 degs. Given that over a region of several degrees around 90 degs the theory gives enhancements of up to approximately 4 orders of magnitude, such electrons could in principle account for the typically observed enhancements of 1 to 2 orders of magnitude, if they were distributed over Theta(sub Bn). To test the idea that scattering could efficiently redistribute the energetic electrons, we have conducted test particle simulations in which

  19. 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

  20. Simulation of hanging dams downstream of Ossauskoski power plant

    Energy Technology Data Exchange (ETDEWEB)

    Aaltonen, J.; Huokuna, M. [Finnish Environment Inst., Helsinki (Finland); Severinkangas, K.; Talvensaari, M. [Kemijoki Oy, Rovaniemi (Finland)

    2008-07-01

    Sixteen power plants have been constructed along Finland's Kemijoki River for hydroelectric power production. The Ossauskoski facility has recently undergone major renovations and upgrade, making it the sixth largest hydroelectric power plant in Finland, with a new capacity of 124 MW and an annual energy output of 501 GWh. The increase in power output and discharge may cause changes in ice conditions downstream of the power plant. The section of the river is already subjected to frazil ice problems and hanging dam formation. Discharges and adverse effects of frazil ice phenomena are likely to increase due to climate change, resulting in harm for hydropower production and the environment, particularly in flow regulated rivers where winter discharges are higher than natural discharges. As such, a study was launched to investigate a dredge plan suggested by by the electric utility Kemijoki Oy. The project involved mapping the river bed topography to identify the location and extent of hanging dams. A sounding device and ground penetrating radar was used to find the thaw regions in the ice cover. The JJT numerical river ice model was effectively used to study the effect of hanging dams on water levels. However, the ice bridging phenomena was not modelled in a reliable way by the JJT model and will be modelled in the future using the CRISSP2D numerical model. 5 refs., 11 figs.

  1. Expression pattern of GASA, downstream genes of DELLA, in Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    ZHANG ShengChun; WANG XiaoJing

    2008-01-01

    Separation and functional research of related components involved in gibberellins (GAs) signaling are important to clarify the mechanism of GA functioning. Research on the downstream components of DELLA, the key factor of the GA signaling pathway, is limited at present. GASA (GA-Stimulated in Arabidopsis) family contains 15 genes usually regulated by GA in Arabidopsis thaliana. All GASA proteins have a cleavable signal peptide in N terminus and a conserved GASA domain including 12 cysteines in C terminus. RT-PCR analysis revealed that the expression of GASA4 and GASA6 were down-regulated, but GASA1 and GASA9were up-regulated in the DELLA mutants, gai-t6 and rga-24, as well as the double mutant, consisting with the results that GASA4 and GASA6 were induced, but GASA1 and GASA9 were inhibited by exogenous GA3. In addition, the expression patterns of other GASA genes were regulated by GA and ABA, separately or cooperatively. Most of GASA genes were expressed in roots, stems, leaves, flowers and developing siliques. GUS gene driven by the promoters of GASA6, GASA7, GASAS, GASA9, GASA10, GASA11 and GASA12were used as reporters and it was found that all GASA genes expressed in the growing and differentiating organs and abscission zones,suggesting the role of these genes in cell growth and differentiation. This study provided an important basis for functional study of the GASA gene family in the GA and ABA signaling pathway.

  2. 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.

  3. 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.

  4. Non-Uniform Sediment Transport Downstream from Reservoir

    Institute of Scientific and Technical Information of China (English)

    LI Yitian; CHEN Fei

    2008-01-01

    The transport characters of non-uniform sediment before and after the reservoir operation are compared and analyzed. Field data from the Three Gorges Reservoir (TGR), Danjiangkou, and Sanmenxia reservoir indicate that the transport character of coarse particle is various in different reaches. Before the reservoir operation, the dramatic decrease of the hydraulic condition in some reaches is the main reason to cause the coarse particle deposited. After the reservoir operation,almost all grain sized sediment may be eroded, when the reach is eroded seriously. However, the transport character of the coarse particle will be consistent with what it was before, when the reach is not eroded seriously. The deposition amount will be less than its pre-dam value, and it will tend to decrease with the time going on. Erosion of fine particle results from its unsaturation. Long-distance erosion downstream from reservoir is caused by shortage of the supply from riverbed, es-pecially the shortage of fine particle.

  5. 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.

  6. Transcriptome complexity in a genome-reduced bacterium

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  7. 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

  8. Transcriptomic dissection of tongue squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    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.

  9. Transcriptome analysis of sika deer in China.

    Science.gov (United States)

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

    2016-10-01

    Sika deer is of great commercial value because their antlers are used in tonics and alternative medicine and their meat is healthy and delicious. The goal of this study was to generate transcript sequences from sika deer for functional genomic analyses and to identify the transcripts that demonstrate tissue-specific, age-dependent differential expression patterns. These sequences could enhance our understanding of the molecular mechanisms underlying sika deer growth and development. In the present study, we performed de novo transcriptome assembly and profiling analysis across ten tissue types and four developmental stages (juvenile, adolescent, adult, and aged) of sika deer, using Illumina paired-end tag (PET) sequencing technology. A total of 1,752,253 contigs with an average length of 799 bp were generated, from which 1,348,618 unigenes with an average length of 590 bp were defined. Approximately 33.2 % of these (447,931 unigenes) were then annotated in public protein databases. Many sika deer tissue-specific, age-dependent unigenes were identified. The testes have the largest number of tissue-enriched unigenes, and some of them were prone to develop new functions for other tissues. Additionally, our transcriptome revealed that the juvenile-adolescent transition was the most complex and important stage of the sika deer life cycle. The present work represents the first multiple tissue transcriptome analysis of sika deer across four developmental stages. The generated data not only provide a functional genomics resource for future biological research on sika deer but also guide the selection and manipulation of genes controlling growth and development. PMID:27423230

  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. Upstream plasticity and downstream robustness in evolution of molecular networks

    Directory of Open Access Journals (Sweden)

    Eriksen Kasper

    2004-03-01

    Full Text Available Abstract Background Gene duplication followed by the functional divergence of the resulting pair of paralogous proteins is a major force shaping molecular networks in living organisms. Recent species-wide data for protein-protein interactions and transcriptional regulations allow us to assess the effect of gene duplication on robustness and plasticity of these molecular networks. Results We demonstrate that the transcriptional regulation of duplicated genes in baker's yeast Saccharomyces cerevisiae diverges fast so that on average they lose 3% of common transcription factors for every 1% divergence of their amino acid sequences. The set of protein-protein interaction partners of their protein products changes at a slower rate exhibiting a broad plateau for amino acid sequence similarity above 70%. The stability of functional roles of duplicated genes at such relatively low sequence similarity is further corroborated by their ability to substitute for each other in single gene knockout experiments in yeast and RNAi experiments in a nematode worm Caenorhabditis elegans. We also quantified the divergence rate of physical interaction neighborhoods of paralogous proteins in a bacterium Helicobacter pylori and a fly Drosophila melanogaster. However, in the absence of system-wide data on transcription factors' binding in these organisms we could not compare this rate to that of transcriptional regulation of duplicated genes. Conclusions For all molecular networks studied in this work we found that even the most distantly related paralogous proteins with amino acid sequence identities around 20% on average have more similar positions within a network than a randomly selected pair of proteins. For yeast we also found that the upstream regulation of genes evolves more rapidly than downstream functions of their protein products. This is in accordance with a view which puts regulatory changes as one of the main driving forces of the evolution. In this

  13. A microelectrochemical scanning flow cell with downstream analytics

    International Nuclear Information System (INIS)

    Research highlights: → A flow type scanning droplet cell with in situ detection via UV-vis to investigate corrosion was constructed. → Dependency of OCP of Zn on pH between 6.6 and 9.0 was studied with passive active transition between pH 7.1 and 7.4. → Zinc concentration profiles revealed a steady etching process that is diffusion controlled at all pH values → Sulfate ions interfere with the passivity of zinc and increase the etching rate, they also influence the pitting potential. - Abstract: The combination of a capillary based microelectrochemical flow cell system and downstream UV-vis analytics allows obtaining synchronized electrochemical and spectroscopic data in a fully automated mode. This method combination can be generally applied to microelectrochemical studies in which an electrochemical species is released or consumed during the electrochemical reaction. For the example of pure zinc surfaces, the characterization of the integrated spectroscopic system is presented with a Zn2+ detection limit below 0.1 μmol l-1 using Zincon as complexing agent. A parameter screening of the effect of pH in the range of 6.6-9.0 in borate buffer reveals a linear increase in zinc dissolution with proton concentration but a distinct step in the open circuit potential from the active state (around -700 mV SHE, pH 6.6-7.1) to the passive state (around -300 mV SHE, pH 7.4-9.0) indicating the formation of a closed passive layer. This mechanism is strongly influenced by sulfate anions which increase the dissolution rate of the passive film and promote the active state as monitored by the dissolution profile and OCP (open circuit potential) values. Within the scope of this parameter variation, the congruency between OCP transients, potentiodynamic sweeps and time resolved dissolution profiles is discussed.

  14. 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.

  15. Estimation of Flood Warning Times for Flood Safety Management Downstream of Dams

    OpenAIRE

    Saqib Ehsan; Walter Marx; Silke Wieprecht

    2013-01-01

    Floods have always been a threat for people and property due to the extent of possible damages. The flooding could be catastrophic in case of possible dam failure and its impacts on downstream areas could also be very significant. Proper estimation of flood warning times plays a vital role in flood safety management of areas downstream of the dams. This research focuses on the realistic and precise estimation of flood warning times for the downstream areas in case of possible dam failure. As ...

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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. PMID:27387304

  4. 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.

  5. 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.

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

    Science.gov (United States)

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

    2016-01-01

    High-throughput RNA sequencing (RNA-seq) provides a comprehensive picture of the transcriptome, including the identity, structure, quantity, and variability of expressed transcripts in cells, through the assembly of sequenced short RNA-seq reads. Although the reference-based approach guarantees the high quality of the resulting transcriptome, this approach is only applicable when the relevant reference genome is present. Here, we developed a pseudo-reference-based assembly (PRA) that reconstructs a transcriptome based on a linear regression function of the optimized mapping parameters and genetic distances of the closest species. Using the linear model, we reconstructed transcriptomes of four different aves, the white leg horn, turkey, duck, and zebra finch, with the Gallus gallus genome as a pseudo-reference, and of three primates, the chimpanzee, gorilla, and macaque, with the human genome as a pseudo-reference. The resulting transcriptomes show that the PRAs outperformed the de novo approach for species with within about 10% mutation rate among orthologous transcriptomes, enough to cover distantly related species as far as chicken and duck. Taken together, we suggest that the PRA method can be used as a tool for reconstructing transcriptome maps of vertebrates whose genomes have not yet been sequenced. PMID:26927182

  7. Transfer of sediment-associated metals downstream of abandoned and active mining sites in the Quesnel River catchment, British Columbia

    NARCIS (Netherlands)

    Perk, M. van der; Lipzig, M.L.H.M. van; Karimlou, G.; Owens, P.N.; Petticrew, E.L.

    2011-01-01

    Metal mining may have considerable impact on downstream water and sediment composition. The rate and extent that metals move downstream determine the magnitude and time scale of downstream sediment contamination. Conversely, the downstream metal content of sediments provide important clues of sedime

  8. 17 CFR 270.57b-1 - Exemption for downstream affiliates of business development companies.

    Science.gov (United States)

    2010-04-01

    ... 17 Commodity and Securities Exchanges 3 2010-04-01 2010-04-01 false Exemption for downstream affiliates of business development companies. 270.57b-1 Section 270.57b-1 Commodity and Securities Exchanges....57b-1 Exemption for downstream affiliates of business development companies....

  9. DOWNSTREAM-WATER-LEVEL CONTROL TEST RESULTS ON THE WM LATERAL CANAL

    Science.gov (United States)

    On steep canals, distant downstream water-level control can be challenging. SacMan (Software for Automated Canal Management) was developed, in part, to test various distant downstream water level controllers. It was implemented on the WM canal of the Maricopa Stanfield Irrigation and Drainage Distri...

  10. Genome and Transcriptome Sequences Reveal the Specific Parasitism of the Nematophagous Purpureocillium lilacinum 36-1.

    Science.gov (United States)

    Xie, Jialian; Li, Shaojun; Mo, Chenmi; Xiao, Xueqiong; Peng, Deliang; Wang, Gaofeng; Xiao, Yannong

    2016-01-01

    Purpureocillium lilacinum is a promising nematophagous ascomycete able to adapt diverse environments and it is also an opportunistic fungus that infects humans. A microbial inoculant of P. lilacinum has been registered to control plant parasitic nematodes. However, the molecular mechanism of the toxicological processes is still unclear because of the relatively few reports on the subject. In this study, using Illumina paired-end sequencing, the draft genome sequence and the transcriptome of P. lilacinum strain 36-1 infecting nematode-eggs were determined. Whole genome alignment indicated that P. lilacinum 36-1 possessed a more dynamic genome in comparison with P. lilacinum India strain. Moreover, a phylogenetic analysis showed that the P. lilacinum 36-1 had a closer relation to entomophagous fungi. The protein-coding genes in P. lilacinum 36-1 occurred much more frequently than they did in other fungi, which was a result of the depletion of repeat-induced point mutations (RIP). Comparative genome and transcriptome analyses revealed the genes that were involved in pathogenicity, particularly in the recognition, adhesion of nematode-eggs, downstream signal transduction pathways and hydrolase genes. By contrast, certain numbers of cellulose and xylan degradation genes and a lack of polysaccharide lyase genes showed the potential of P. lilacinum 36-1 as an endophyte. Notably, the expression of appressorium-formation and antioxidants-related genes exhibited similar infection patterns in P. lilacinum strain 36-1 to those of the model entomophagous fungi Metarhizium spp. These results uncovered the specific parasitism of P. lilacinum and presented the genes responsible for the infection of nematode-eggs. PMID:27486440

  11. Genome and Transcriptome Sequences Reveal the Specific Parasitism of the Nematophagous Purpureocillium lilacinum 36-1

    Science.gov (United States)

    Xie, Jialian; Li, Shaojun; Mo, Chenmi; Xiao, Xueqiong; Peng, Deliang; Wang, Gaofeng; Xiao, Yannong

    2016-01-01

    Purpureocillium lilacinum is a promising nematophagous ascomycete able to adapt diverse environments and it is also an opportunistic fungus that infects humans. A microbial inoculant of P. lilacinum has been registered to control plant parasitic nematodes. However, the molecular mechanism of the toxicological processes is still unclear because of the relatively few reports on the subject. In this study, using Illumina paired-end sequencing, the draft genome sequence and the transcriptome of P. lilacinum strain 36-1 infecting nematode-eggs were determined. Whole genome alignment indicated that P. lilacinum 36-1 possessed a more dynamic genome in comparison with P. lilacinum India strain. Moreover, a phylogenetic analysis showed that the P. lilacinum 36-1 had a closer relation to entomophagous fungi. The protein-coding genes in P. lilacinum 36-1 occurred much more frequently than they did in other fungi, which was a result of the depletion of repeat-induced point mutations (RIP). Comparative genome and transcriptome analyses revealed the genes that were involved in pathogenicity, particularly in the recognition, adhesion of nematode-eggs, downstream signal transduction pathways and hydrolase genes. By contrast, certain numbers of cellulose and xylan degradation genes and a lack of polysaccharide lyase genes showed the potential of P. lilacinum 36-1 as an endophyte. Notably, the expression of appressorium-formation and antioxidants-related genes exhibited similar infection patterns in P. lilacinum strain 36-1 to those of the model entomophagous fungi Metarhizium spp. These results uncovered the specific parasitism of P. lilacinum and presented the genes responsible for the infection of nematode-eggs. PMID:27486440

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

    Science.gov (United States)

    Hsieh, T.; Coakley, T. J.

    1987-01-01

    An investigation of downstream boundary effects on the frequency of self-excited oscillations in two-dimensional, separated transonic diffuser flows has been conducted numerically by solving the compressible, Reynolds-averaged, thin-layer Navier-Stokes equation with a two-equation turbulence model. It was found that the unsteady diffuser flowfields 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. Computational results suggest that the mechanism causing the self-excited oscillation changes from viscous convective wave dominated oscillations to inviscid acoustic wave dominated oscillations when the location of downstream boundary varies from 8.66 to 134.7 throat height. The existence of a suction slot in the experimental setup obscures the physical downstream boundary and, therefore, presents a difficulty for quantitative comparisons between computation and experiment.

  13. Experimental and analytical investigation of fan flow interaction with downstream struts

    Science.gov (United States)

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

    1985-01-01

    An investigation which was designed to provide insight into the fundamental aspects of fan rotor-downstream strut interaction was undertaken. High response, miniature pressure transducers were embedded in the rotor blades of an experimental fan rig. Five downstream struts were placed at several downstream locations in the discharge flow annulus of the single-stage machine. Significant interaction of the rotor blade surface pressures with the flow disturbance produced by the downstream struts was measured. Several numerical procedures for calculating the quasi-steady rotor response due to downstream flow obstructions were developed. A preliminary comparison of experimental and calculated fluctuating blade pressures on the rotor blades shows general agreement between the experimental and calculated values.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. Comparative genomics and transcriptomics of Propionibacterium acnes.

    Directory of Open Access Journals (Sweden)

    Elzbieta Brzuszkiewicz

    Full Text Available The anaerobic gram-positive bacterium Propionibacterium acnes is a human skin commensal that is occasionally associated with inflammatory diseases. Recent work has indicated that evolutionary distinct lineages of P. acnes play etiologic roles in disease while others are associated with maintenance of skin homeostasis. To shed light on the molecular basis for differential strain properties, we carried out genomic and transcriptomic analysis of distinct P. acnes strains. We sequenced the genome of the P. acnes strain 266, a type I-1a strain. Comparative genome analysis of strain 266 and four other P. acnes strains revealed that overall genome plasticity is relatively low; however, a number of island-like genomic regions, encoding a variety of putative virulence-associated and fitness traits differ between phylotypes, as judged from PCR analysis of a collection of P. acnes strains. Comparative transcriptome analysis of strains KPA171202 (type I-2 and 266 during exponential growth revealed inter-strain differences in gene expression of transport systems and metabolic pathways. In addition, transcript levels of genes encoding possible virulence factors such as dermatan-sulphate adhesin, polyunsaturated fatty acid isomerase, iron acquisition protein HtaA and lipase GehA were upregulated in strain 266. We investigated differential gene expression during exponential and stationary growth phases. Genes encoding components of the energy-conserving respiratory chain as well as secreted and virulence-associated factors were transcribed during the exponential phase, while the stationary growth phase was characterized by upregulation of genes involved in stress responses and amino acid metabolism. Our data highlight the genomic basis for strain diversity and identify, for the first time, the actively transcribed part of the genome, underlining the important role growth status plays in the inflammation-inducing activity of P. acnes. We argue that the disease

  2. A transcriptome anatomy of human colorectal cancers

    International Nuclear Information System (INIS)

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

  3. A 3-methylcrotonyl-CoA carboxylase deficient human skin fibroblast transcriptome reveals underlying mitochondrial dysfunction and oxidative stress.

    Science.gov (United States)

    Zandberg, L; van Dyk, H C; van der Westhuizen, F H; van Dijk, A A

    2016-09-01

    Isolated 3-methylcrotonyl-CoA carboxylase (MCC) deficiency is an autosomal recessive inherited metabolic disease of leucine catabolism with a highly variable phenotype. Apart from extensive mutation analyses of the MCCC1 and MCCC2 genes encoding 3-methylcrotonyl-CoA carboxylase (EC 6.4.1.4), molecular data on MCC deficiency gene expression studies in human tissues is lacking. For IEMs, unbiased '-omics' approaches are starting to reveal the secondary cellular responses to defects in biochemical pathways. Here we present the first whole genome expression profile of immortalized cultured skin fibroblast cells of two clinically affected MCC deficient patients and two healthy individuals generated using Affymetrix(®)HuExST1.0 arrays. There were 16191 significantly differentially expressed transcript IDs of which 3591 were well annotated and present in the predefined knowledge database of Ingenuity Pathway Analysis software used for downstream functional analyses. The most noticeable feature of this MCCA deficient skin fibroblast transcriptome was the typical genetic hallmark of mitochondrial dysfunction, decreased antioxidant response and disruption of energy homeostasis, which was confirmed by mitochondrial functional analyses. The MCC deficient transcriptome seems to predict oxidative stress that could alter the complex secondary cellular response that involve genes of the glycolysis, the TCA cycle, OXPHOS, gluconeogenesis, β-oxidation and the branched-chain fatty acid metabolism. An important emerging insight from this human MCCA transcriptome in combination with previous reports is that chronic exposure to the primary and secondary metabolites of MCC deficiency and the resulting oxidative stress might impact adversely on the quality of life and energy levels, irrespective of whether MCC deficient individuals are clinically affected or asymptomatic. PMID:27417235

  4. Human transcriptome array for high-throughput clinical studies

    OpenAIRE

    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; Ronald V Maier; Tompkins, Ronald G.; Wong, Wing Hung

    2011-01-01

    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 ind...

  5. 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...

  6. Pseudo-Reference-Based Assembly of Vertebrate Transcriptomes

    OpenAIRE

    Kyoungwoo Nam; Heesu Jeong; Jin-Wu Nam

    2016-01-01

    High-throughput RNA sequencing (RNA-seq) provides a comprehensive picture of the transcriptome, including the identity, structure, quantity, and variability of expressed transcripts in cells, through the assembly of sequenced short RNA-seq reads. Although the reference-based approach guarantees the high quality of the resulting transcriptome, this approach is only applicable when the relevant reference genome is present. Here, we developed a pseudo-reference-based assembly (PRA) that reconstr...

  7. CarrotDB: a genomic and transcriptomic database for carrot

    OpenAIRE

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

    2014-01-01

    Carrot (Daucus carota L.) is an economically important vegetable worldwide and is the largest source of carotenoids and provitamin A in the human diet. Given the importance of this vegetable to humans, research and breeding communities on carrot should obtain useful genomic and transcriptomic information. The first whole-genome sequences of ‘DC-27’ carrot were de novo assembled and analyzed. Transcriptomic sequences of 14 carrot genotypes were downloaded from the Sequence Read Archive (SRA) d...

  8. Functional Annotation and Comparative Analysis of a Zygopteran Transcriptome

    OpenAIRE

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

    2013-01-01

    In this paper we present a de novo assembly of the transcriptome of the damselfly (Enallagma hageni) through the use of 454 pyrosequencing. E. hageni is a member of the suborder Zygoptera, in the order Odonata, and Odonata organisms form the basal lineage of the winged insects (Pterygota). To date, sequence data used in phylogenetic analysis of Enallagma species have been derived from either mitochondrial DNA or ribosomal nuclear DNA. This Enallagma transcriptome contained 31,661 contigs that...

  9. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters

    Science.gov (United States)

    Lavender, Christopher A.; Hoffman, Jackson A.; Trotter, Kevin W.; Gilchrist, Daniel A.; Bennett, Brian D.; Burkholder, Adam B.; Fargo, David C.; Archer, Trevor K.

    2016-01-01

    Antisense transcription is a prevalent feature at mammalian promoters. Previous studies have primarily focused on antisense transcription initiating upstream of genes. Here, we characterize promoter-proximal antisense transcription downstream of gene transcription starts sites in human breast cancer cells, investigating the genomic context of downstream antisense transcription. We find extensive correlations between antisense transcription and features associated with the chromatin environment at gene promoters. Antisense transcription downstream of promoters is widespread, with antisense transcription initiation observed within 2 kb of 28% of gene transcription start sites. Antisense transcription initiates between nucleosomes regularly positioned downstream of these promoters. The nucleosomes between gene and downstream antisense transcription start sites carry histone modifications associated with active promoters, such as H3K4me3 and H3K27ac. This region is bound by chromatin remodeling and histone modifying complexes including SWI/SNF subunits and HDACs, suggesting that antisense transcription or resulting RNA transcripts contribute to the creation and maintenance of a promoter-associated chromatin environment. Downstream antisense transcription overlays additional regulatory features, such as transcription factor binding, DNA accessibility, and the downstream edge of promoter-associated CpG islands. These features suggest an important role for antisense transcription in the regulation of gene expression and the maintenance of a promoter-associated chromatin environment. PMID:27487356

  10. Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters.

    Science.gov (United States)

    Lavender, Christopher A; Cannady, Kimberly R; Hoffman, Jackson A; Trotter, Kevin W; Gilchrist, Daniel A; Bennett, Brian D; Burkholder, Adam B; Burd, Craig J; Fargo, David C; Archer, Trevor K

    2016-08-01

    Antisense transcription is a prevalent feature at mammalian promoters. Previous studies have primarily focused on antisense transcription initiating upstream of genes. Here, we characterize promoter-proximal antisense transcription downstream of gene transcription starts sites in human breast cancer cells, investigating the genomic context of downstream antisense transcription. We find extensive correlations between antisense transcription and features associated with the chromatin environment at gene promoters. Antisense transcription downstream of promoters is widespread, with antisense transcription initiation observed within 2 kb of 28% of gene transcription start sites. Antisense transcription initiates between nucleosomes regularly positioned downstream of these promoters. The nucleosomes between gene and downstream antisense transcription start sites carry histone modifications associated with active promoters, such as H3K4me3 and H3K27ac. This region is bound by chromatin remodeling and histone modifying complexes including SWI/SNF subunits and HDACs, suggesting that antisense transcription or resulting RNA transcripts contribute to the creation and maintenance of a promoter-associated chromatin environment. Downstream antisense transcription overlays additional regulatory features, such as transcription factor binding, DNA accessibility, and the downstream edge of promoter-associated CpG islands. These features suggest an important role for antisense transcription in the regulation of gene expression and the maintenance of a promoter-associated chromatin environment. PMID:27487356

  11. Downstream channel adjustment in a low-relief, glacially conditioned watershed

    Science.gov (United States)

    Thayer, James B.; Phillips, Roger T. J.; Desloges, Joseph R.

    2016-06-01

    River management practices are often informed by theoretical expectations of downstream channel adjustment, which may not be valid in low relief, glacially conditioned watersheds such as those in the lower North American Great Lakes region. Downstream trends in channel morphology and bed material size within a low-relief, glacially conditioned watershed are explored here and compared to a theoretical watershed model where slope and grain size are expected to decline exponentially. The observed channel morphology is then tested against a theoretical concept of reach-scale channel grade. The downstream hydraulic geometry relations wbf ∝ Qbf0.51S- 0.02 and dbf ∝ Qbf0.32S- 0.21 were found to best describe downstream changes in channel morphology and are consistent with some prior studies. Bed material size varies irregularly down the channel. Slope-controlled downstream fining trends are evident where inputs from glacial materials and tributaries are negligible but are masked by cobble/boulder lag deposits where the channel is cut into these glacial deposits. The asynchronous variability in slope and grain size produces downstream variations in graded and nongraded, understeepened conditions separated at τ*ex = 0. Graded reaches exist where τ*ex > 0, but an upper boundary with nongraded, oversteepened reaches is less clear. The results emphasize the geomorphic legacy of inherited slopes and sediment sources in dictating the modern downstream patterns of fluvial characteristics and morphologies in glacially conditioned, and similarly complex, watersheds.

  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. Measurement of velocity deficit at the downstream of a 1:10 axial hydrokinetic turbine model

    Energy Technology Data Exchange (ETDEWEB)

    Gunawan, Budi [ORNL; Neary, Vincent S [ORNL; Hill, Craig [St. Anthony Falls Laboratory, 2 Third Avenue SE, Minneapolis, MN 55414; Chamorro, Leonardo [St. Anthony Falls Laboratory, 2 Third Avenue SE, Minneapolis, MN 55414

    2012-01-01

    Wake recovery constrains the downstream spacing and density of turbines that can be deployed in turbine farms and limits the amount of energy that can be produced at a hydrokinetic energy site. This study investigates the wake recovery at the downstream of a 1:10 axial flow turbine model using a pulse-to-pulse coherent Acoustic Doppler Profiler (ADP). In addition, turbine inflow and outflow velocities were measured for calculating the thrust on the turbine. The result shows that the depth-averaged longitudinal velocity recovers to 97% of the inflow velocity at 35 turbine diameter (D) downstream of the turbine.

  14. 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.

  15. 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. PMID:23650531

  16. 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.

  17. 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

  18. SNP Discovery Using Next Generation Transcriptomic Sequencing.

    Science.gov (United States)

    De Wit, Pierre

    2016-01-01

    In this chapter, I will guide the user through methods to find new SNP markers from expressed sequence (RNA-Seq) data, focusing on the sample preparation and also on the bioinformatic analyses needed to sort through the immense flood of data from high-throughput sequencing machines. The general steps included are as follows: sample preparation, sequencing, quality control of data, assembly, mapping, SNP discovery, filtering, validation. The first few steps are traditional laboratory protocols, whereas steps following the sequencing are of bioinformatic nature. The bioinformatics described herein are by no means exhaustive, rather they serve as one example of a simple way of analyzing high-throughput sequence data to find SNP markers. Ideally, one would like to run through this protocol several times with a new dataset, while varying software parameters slightly, in order to determine the robustness of the results. The final validation step, although not described in much detail here, is also quite critical as that will be the final test of the accuracy of the assumptions made in silico.There is a plethora of downstream applications of a SNP dataset, not covered in this chapter. For an example of a more thorough protocol also including differential gene expression and functional enrichment analyses, BLAST annotation and downstream applications of SNP markers, a good starting point could be the "Simple Fool's Guide to population genomics via RNA-Seq," which is available at http://sfg.stanford.edu . PMID:27460371

  19. 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.

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

    OpenAIRE

    Guo, Hongyan; Zhang, Wei; Tian, Hainan; Zheng, Kaijie; Dai, Xuemei; Liu, Shanda; Hu, Qingnan; Wang, Xianling; Liu, Bao; Wang, Shucai

    2015-01-01

    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) CL...

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

    OpenAIRE

    Hongyan eGuo; Wei eZhang; Hainan eTian; Kaijie eZheng; Xuemei eDai; Shanda eLiu; Qingnan eHu; Xianling eWang; Bao eLiu; Shucai eWang

    2015-01-01

    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...

  2. Final Report [Function of the Arabidopsis TIR1 gene in auxin response

    Energy Technology Data Exchange (ETDEWEB)

    Estelle, Mark

    2000-12-18

    During this grant period substantial progress was made in the characterization of the TIR1 gene in Arabidopsis. Studies showed that the TIR1 protein is part of a protein complex that includes AtCUL1, ASK1 and RBX1. This complex, called SCF-TIR1, functions in the ubiquitin-mediated protein degradation pathway. Our work is the first report of an SCF complex in a plant system. The results of our studies are described in more detail in the report together with a publication resulting from this study.

  3. Auxin Response Factor%生长素反应因子

    Institute of Scientific and Technical Information of China (English)

    吴蓓; 吴建勇; 蔡刘体; 李运合; 黄学林

    2005-01-01

    生长素反应因子(ARF)是1997年发现的新一类转录因子家族,它们与生长素早期反应基因启动子中的生长素反应元件(AuxRE)TGTCTC特异性地结合,调节这类基因的转录活性.文章阐述生长素反应因子和其结构的特点、作用模式的设想的研究进展.

  4. Developmental anatomy and auxin response of lateral root formation in Ceratopteris richardii.

    Science.gov (United States)

    Hou, Guichuan; Hill, Jeffrey P; Blancaflor, Elison B

    2004-03-01

    The homosporous fern Ceratopteris richardii exhibits a homorhizic root system where roots originate from the shoot system. These shoot-borne roots form lateral roots (LRs) that arise from the endodermis adjacent to the xylem poles, which is in contrast to flowering plants where LR formation arises from cell division in the pericycle. A detailed study of the fifth shoot-borne root showed that one lateral root mother cell (LRMC) develops in each two out of three successive merophytes. As a result, LRs emerge alternately in two ranks from opposite positions on a parent root. From LRMC initiation to LR emergence, three developmental stages were identified based on anatomical criteria. The addition of auxins (either indole-3-acetic acid or indole-3-butyric acid) to the growth media did not induce additional LR formation, but exogenous applications of both auxins inhibited parent root growth rate. Application of the polar auxin-transport inhibitor N-(1-naphthyl)phthalamic acid (NPA) also inhibited parent root growth without changing the LR initiation pattern. The results suggest that LR formation does not depend on root growth rate per se. The result that exogenous auxins do not promote LR formation in C. richardii is similar to reports for certain species of flowering plants, in which there is an acropetal LR population and the formation of the LRs is insensitive to the application of auxins. It also may indicate that different mechanisms control LR development in non-seed vascular plants compared with angiosperms, taking into consideration the long and independent evolutionary history of the two groups. PMID:14754921

  5. Constitutive auxin response in Physcomitrella reveals complex interactions between Aux/IAA and ARF proteins.

    Science.gov (United States)

    Lavy, Meirav; Prigge, Michael J; Tao, Sibo; Shain, Stephanie; Kuo, April; Kirchsteiger, Kerstin; Estelle, Mark

    2016-01-01

    The coordinated action of the auxin-sensitive Aux/IAA transcriptional repressors and ARF transcription factors produces complex gene-regulatory networks in plants. Despite their importance, our knowledge of these two protein families is largely based on analysis of stabilized forms of the Aux/IAAs, and studies of a subgroup of ARFs that function as transcriptional activators. To understand how auxin regulates gene expression we generated a Physcomitrella patens line that completely lacks Aux/IAAs. Loss of the repressors causes massive changes in transcription with misregulation of over a third of the annotated genes. Further, we find that the aux/iaa mutant is blind to auxin indicating that auxin regulation of transcription occurs exclusively through Aux/IAA function. We used the aux/iaa mutant as a simplified platform for studies of ARF function and demonstrate that repressing ARFs regulate auxin-induced genes and fine-tune their expression. Further the repressing ARFs coordinate gene induction jointly with activating ARFs and the Aux/IAAs. PMID:27247276

  6. Downstream energetic proton and alpha particles during quasi-parallel interplanetary shock events

    Science.gov (United States)

    Tan, L. C.; Mason, G. M.; Gloeckler, G.; Ipavich, F. M.

    1988-01-01

    This paper considers the energetic particle populations in the downstream region of three quasi-parallel interplanetary shock events, which was explored using the ISEE 3 Ultra Low Energy Charge Analyzer sensor, which unambiguously identifies protons and alpha particles using the electrostatic deflection versus residual energy technique. The downstream particles were found to exhibit anisotropies due largely to convection in the solar wind. The spectral indices of the proton and the alpha-particle distribution functions were found to be remarkably constant during the downstream period, being generally insensitive to changes in particle flux levels, magnetic field direction, and solar wind densities. In two of the three events, the proton and the alpha spectra were the same throughout the entire downstream period, supporting the prediction of diffusive shock acceleration theory.

  7. Downstream movement of recently transformed sea lampreys, Petromyzon marinus, in Carp Lake River, Michigan

    Science.gov (United States)

    Applegate, Vernon C.; Brynildson, Clifford L.

    1951-01-01

    In order to obtain more precise information concerning the downstream movement of recently transformed sea lampreys, a trapping device was operated in the Carp Lake River, Emmet County, Michigan, from October, 1948, to July, 1951.

  8. 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

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    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

  9. A quantitative transcriptome reference map of the normal human hippocampus.

    Science.gov (United States)

    Caracausi, Maria; Rigon, Vania; Piovesan, Allison; Strippoli, Pierluigi; Vitale, Lorenza; Pelleri, Maria Chiara

    2016-01-01

    We performed an innovative systematic meta-analysis of 41 gene expression profiles of normal human hippocampus to provide a quantitative transcriptome reference map of it, i.e. a reference typical value of expression for each of the 30,739 known mapped and the 16,258 uncharacterized (unmapped) transcripts. For this aim, we used the software called TRAM (Transcriptome Mapper), which is able to generate transcriptome maps based on gene expression data from multiple sources. We also analyzed differential expression by comparing the hippocampus with the whole brain transcriptome map to identify a typical expression pattern of this subregion compared with the whole organ. Finally, due to the fact that the hippocampus is one of the main brain region to be severely affected in trisomy 21 (the best known genetic cause of intellectual disability), a particular attention was paid to the expression of chromosome 21 (chr21) genes. Data were downloaded from microarray databases, processed, and analyzed using TRAM software. Among the main findings, the most over-expressed loci in the hippocampus are the expressed sequence tag cluster Hs.732685 and the member of the calmodulin gene family CALM2. The tubulin folding cofactor B (TBCB) gene is the best gene at behaving like a housekeeping gene. The hippocampus vs. the whole brain differential transcriptome map shows the over-expression of LINC00114, a long non-coding RNA mapped on chr21. The hippocampus transcriptome map was validated in vitro by assaying gene expression through several magnitude orders by "Real-Time" reverse transcription polymerase chain reaction (RT-PCR). The highly significant agreement between in silico and experimental data suggested that our transcriptome map may be a useful quantitative reference benchmark for gene expression studies related to human hippocampus. Furthermore, our analysis yielded biological insights about those genes that have an intrinsic over-/under-expression in the hippocampus. PMID

  10. Particle acceleration by combined diffusive shock acceleration and downstream multiple magnetic island acceleration

    Science.gov (United States)

    Zank, G. P.; Hunana, P.; Mostafavi, P.; le Roux, J. A.; Li, Gang; Webb, G. M.; Khabarova, O.

    2015-09-01

    As a consequence of the evolutionary conditions [28; 29], shock waves can generate high levels of downstream vortical turbulence. Simulations [32-34] and observations [30; 31] support the idea that downstream magnetic islands (also called plasmoids or flux ropes) result from the interaction of shocks with upstream turbulence. Zank et al. [18] speculated that a combination of diffusive shock acceleration (DSA) and downstream reconnection-related effects associated with the dynamical evolution of a “sea of magnetic islands” would result in the energization of charged particles. Here, we utilize the transport theory [18; 19] for charged particles propagating diffusively in a turbulent region filled with contracting and reconnecting plasmoids and small-scale current sheets to investigate a combined DSA and downstream multiple magnetic island charged particle acceleration mechanism. We consider separately the effects of the anti-reconnection electric field that is a consequence of magnetic island merging [17], and magnetic island contraction [14]. For the merging plasmoid reconnection- induced electric field only, we find i) that the particle spectrum is a power law in particle speed, flatter than that derived from conventional DSA theory, and ii) that the solution is constant downstream of the shock. For downstream plasmoid contraction only, we find that i) the accelerated particle spectrum is a power law in particle speed, flatter than that derived from conventional DSA theory; ii) for a given energy, the particle intensity peaks downstream of the shock, and the peak location occurs further downstream of the shock with increasing particle energy, and iii) the particle intensity amplification for a particular particle energy, f(x, c/c0)/f(0, c/c0), is not 1, as predicted by DSA theory, but increases with increasing particle energy. These predictions can be tested against observations of electrons and ions accelerated at interplanetary shocks and the heliospheric

  11. Temporal progression in migratory status and sexual maturation in European silver eels during downstream migration

    OpenAIRE

    Arjan P Palstra; Guerrero, Ma Angeles; de Laak, Gerard; Klein Breteler, Jan P. G.; Guido E E J M van den Thillart

    2011-01-01

    The onset of downstream migration of European eels is accompanied by a cessation of feeding and the start of sexual maturation which stresses the link between metabolism and sexual maturation, also suggesting an important role for exercise. Exercise has been tested with eels in swim tunnels and was found to stimulate the onset of sexual maturation. In this study, we have investigated the interplay between migration and maturation in the field during the downstream migration of female silver e...

  12. Stable isotopes reveal food web modifications along the upstream-downstream gradient of a temperate stream

    OpenAIRE

    Hette-Tronquart, N.; Belliard, J.; Tales, E.; Oberdorff, Thierry

    2016-01-01

    The upstream-downstream gradient (UDG) is a key feature of streams. For instance food webs are assumed to change from upstream to downstream. We tested this hypothesis in a small European river catchment (937 km(2)), and examined whether food web modifications are related to structural (i.e. food web composition) or functional changes (i.e. alteration of linkages within the web). We adopted a double approach at two levels of organisation (assemblage and species levels) using two isotopic metr...

  13. 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

    2015-01-01

    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.

  14. 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.

  15. Entrepreneurial orientation and the threat of imitation: the influence of upstream and downstream capabilities

    OpenAIRE

    García-Villaverde, P.M.; Ruiz-Ortega, M.J.; Canales, J.I.

    2013-01-01

    This paper uncovers the complexity between Entrepreneurial Orientation (EO) and performance. The paper explores the effect of the threat of imitation, which is a key external factor to explain competitive dynamics, and hence highlights effectiveness of EO. Also the paper accounts for the role of upstream (technical) and downstream (marketing) capabilities as they influence effectiveness of EO. Our results show that, under threat of imitation, downstream marketing capabilities facilitate tapin...

  16. Photoperiod control of downstream movements of Atlantic salmon Salmo salar smolts.

    Science.gov (United States)

    Zydlewski, G B; Stich, D S; McCormick, S D

    2014-10-01

    This study provides the first direct observations that photoperiod controls the initiation of downstream movement in Atlantic salmon Salmo salar smolts. Under simulated natural day length (LDN) conditions and seasonal increases in temperature, smolts increased their downstream movements five-fold for a period of 1 month in late spring. Under the same conditions, parr did not show changes in downstream movement behaviour. When given a shortened day length (10L:14D) beginning in late winter, smolts did not increase the number of downstream movements. An early increase in day length (16L:8D) in late winter resulted in earlier initiation and termination of downstream movements compared to the LDN group. Physiological status and behaviour were related but not completely coincident: gill Na(+) /K(+) -ATPase activity increased in all treatments and thyroid hormone was elevated prior to movement in 16L:8D treatment. The most parsimonious model describing downstream movement of smolts included synergistic effects of photoperiod treatment and temperature, indicating that peak movements occurred at colder temperatures in the 16L:8D treatment than in LDN, and temperature did not influence movement of smolts in the 10L:14D treatment. The complicated interactions of photoperiod and temperature are not surprising since many organisms have evolved to rely on correlations among environmental cues and windows of opportunity to time behaviours associated with life-history transitions. These complicated interactions, however, have serious implications for phenological adjustments and persistence of S. salar populations in response to climate change. PMID:25263186

  17. 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

  18. 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.

  19. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  1. 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.

  2. 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

  3. 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.

  4. Transcriptome analysis of sarracenia, an insectivorous plant.

    Science.gov (United States)

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

    2011-08-01

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

  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. 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.

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

    Science.gov (United States)

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

    2013-03-11

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

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. Organic compounds downstream from a treated-wastewater discharge near Dallas, Texas, March 1987

    Science.gov (United States)

    Buszka, P.M.; Barber, L.B., II; Schroeder, M.P.; Becker, L.D.

    1994-01-01

    Water and streambed-sediment samples were collected on March 9 and 10,1987 from one site upstream and three sites downstream of the discharge from a municipal wastewater-treatment plant on Rowlett Creek near Dallas, Texas. To extract and separate organic compounds, purgeand-trap, closed-loop stripping, and pH-adjusted solvent extraction methods were used for water samples; and a Soxhlet-solvent extraction method was used for streambed sediment. These methods were combined with gas chromatography/mass spectrometry to identify organic compounds in Rowlett Creek. Results from this study confirm the persistence of many organic compounds in water as far as 13.5 kilometers downstream of the wastewater discharge. These include: (1) the volatile organic compounds chloroform, 1,2-dichlorobenzene, 1,4-dichlorobenzene, tetrachloroethene, and trichloroethene; (2) several linear alkylbenzene compounds, octyl phenol, and a tetramethylbutyl phenol isomer that are related to detergent use; (3) 9-phenyl-9H-carbazole, a compound related to coal tars and coal combustion residues; and (4) caffeine. The only compound present in water in concentrations greater than U.S. Environmental Protection Agency maximum contaminant levels for drinking water was tetrachloroethene (6.0 micrograms per liter) in a sample collected 13.5 kilometers downstream from the waste water discharge. Compounds identified from the streambed-sediment samples include a xylene isomer at 7.7 kilometers downstream and chrysene, fluoranthene, pyrene, and a xylene isomer at 13.5 kilometers downstream from the wastewater discharge.

  16. Analytical prediction of the unsteady lift on a rotor caused by downstream struts

    Science.gov (United States)

    Taylor, A. C., III; Ng, W. F.

    1987-01-01

    A two-dimensional, inviscid, incompressible procedure is presented for predicting the unsteady lift on turbomachinery blades caused by the upstream potential disturbance of downstream flow obstructions. Using the Douglas-Neumann singularity superposition potential flow computer program to model the downstream flow obstructions, classical equations of thin airfoil theory are then employed, to compute the unsteady lift on the upstream rotor blades. The method is applied to a particular geometry which consists of a rotor, a downstream stator, and downstream struts which support the engine casing. Very good agreement between the Douglas-Neumann program and experimental measurements was obtained for the downstream stator-strut flow field. The calculations for the unsteady lift due to the struts were in good agreement with the experiments in showing that the unsteady lift due to the struts decays exponentially with increased axial separation of the rotor and the struts. An application of the method showed that for a given axial spacing between the rotor and the strut, strut-induced unsteady lift is a very weak function of the axial or circumferential position of the stator.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. Flow Structure and Turbulence Characteristics downstream of a Spanwise Suspended Linear Canopy through Laboratory Experiments

    Science.gov (United States)

    Qiao, Jundong; Delavan, Sarah

    2014-11-01

    Laboratory experiments were conducted to explore the mean flow structure and turbulence properties downstream of a spanwise suspended linear canopy in a 2-D open channel flow using the Particle Tracking Velocimetry technique. This canopy simulated the effect of one long-line structure of a mussel farm. Four experimental scenarios with the approach velocities 50, 80, 110, and 140 mm s-1 were under investigation. Three sub-layers formed downstream of the canopy. An internal canopy layer, where the time-averaged velocity decreases linearly with increasing distance downstream, a canopy mixing layer increasing in vertical extent with increasing distance downstream of the canopy, and an external canopy layer with higher velocity under the canopy, which may bring nutrients from the local ambient environment into this layer. The canopy turbulence results in upward momentum transport downstream of the canopy within a distance of 0.60 of the canopy depth and downward momentum transport beyond 1.20 of it. In the scenarios with relatively lower approach velocities 50 and 80 mm s1 , the wake turbulence results in upward momentum transport. The broader goal of this study is to offer guidelines for the design and site selection of more productive mussel farms. The results suggest that distance interval between the parallel long-lines in a mussel farm should be less than 0.6 times the height of a long-line dropper. Also, potential farm locations that are characterized with current velocity from 50 to 80 mm s1 are suggested.

  19. 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.

  20. 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...

  1. Photoperiod control of downstream movements of Atlantic salmon Salmo salar smolts

    Science.gov (United States)

    Zydlewski, Gayle B.; Stich, Daniel S.; McCormick, Stephen D.

    2014-01-01

    This study provides the first direct observations that photoperiod controls the initiation of downstream movement in Atlantic salmon Salmo salar smolts. Under simulated natural day length (LDN) conditions and seasonal increases in temperature, smolts increased their downstream movements five-fold for a period of 1 month in late spring. Under the same conditions, parr did not show changes in downstream movement behaviour. When given a shortened day length (10L:14D) beginning in late winter, smolts did not increase the number of downstream movements. An early increase in day length (16L:8D) in late winter resulted in earlier initiation and termination of downstream movements compared to the LDN group. Physiological status and behaviour were related but not completely coincident: gill Na+/K+-ATPase activity increased in all treatments and thyroid hormone was elevated prior to movement in 16L:8D treatment. The most parsimonious model describing downstream movement of smolts included synergistic effects of photoperiod treatment and temperature, indicating that peak movements occurred at colder temperatures in the 16L:8D treatment than in LDN, and temperature did not influence movement of smolts in the 10L:14D treatment. The complicated interactions of photoperiod and temperature are not surprising since many organisms have evolved to rely on correlations among environmental cues and windows of opportunity to time behaviours associated with life-history transitions. These complicated interactions, however, have serious implications for phenological adjustments and persistence ofS. salar populations in response to climate change.

  2. A dulal-functional medium voltage level DVR to limit downstream fault currents

    DEFF Research Database (Denmark)

    Li, Yun Wei; Vilathgamuwa, D. Mahinda; Loh, Poh Chiang;

    2007-01-01

    , the DVR will therefore be tasked to mitigate even more faults involving downstream loads. Large fault currents would flow through the DVR during a downstream fault before the opening of a circuit breaker. This will cause the voltage at point of common coupling (PCC) to drop, which would affect the loads...... on the other parallel feeders connected to PCC. Furthermore, if not controlled properly, the DVR might also contribute to this PCC voltage sag in the process of compensating the missing voltage, thus further worsening the fault situation. To limit the flow of large line currents, and therefore restore the PCC...

  3. 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

    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......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 catchment and downstream runoff measurements to identify the runoff coefficients at subcatchment level....

  4. 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

  5. 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.

  6. 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.

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

    International Nuclear Information System (INIS)

    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

  8. Downstream-Conditioned Maximum Entropy Method for Exit Boundary Conditions in the Lattice Boltzmann Method

    Directory of Open Access Journals (Sweden)

    Javier A. Dottori

    2015-01-01

    Full Text Available A method for modeling outflow boundary conditions in the lattice Boltzmann method (LBM based on the maximization of the local entropy is presented. The maximization procedure is constrained by macroscopic values and downstream components. The method is applied to fully developed boundary conditions of the Navier-Stokes equations in rectangular channels. Comparisons are made with other alternative methods. In addition, the new downstream-conditioned entropy is studied and it was found that there is a correlation with the velocity gradient during the flow development.

  9. Estimating subcatchment runoff coefficients using weather radar and a downstream runoff sensor.

    Science.gov (United States)

    Ahm, Malte; Thorndahl, Søren; Rasmussen, Michael R; Bassø, Lene

    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 the catchment and downstream runoff measurements to identify the runoff coefficients at subcatchment level. PMID:24056426

  10. 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.

  11. 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

  12. De novo transcriptome assembly of two different Prunus salicina cultivars

    Directory of Open Access Journals (Sweden)

    Yeonhwa Jo

    2015-12-01

    Full Text Available Plum is a globally grown stone fruit and can be divided into several species. In particular, the Prunus salicina, which is native to China, is widely grown in many fruit orchards in Korea and Japan, as well as the United States and Australia. The transcriptome data for Prunus salicina has not been reported to our knowledge. In this study, we performed de novo transcriptome assembly for two selected P. salicina cultivars referred to as Akihime and Formosa (commercially important plum cultivars in Korea using next generation sequencing. We obtained a total of 9.04 GB and 8.68 GB raw data from Akihime and Formosa, respectively. De novo transcriptome assembly using Trinity revealed 155,169 and 160,186 transcripts for Akihime and Formosa. Next, we identified 121,278 and 116,544 proteins from Akihime and Formosa using TransDecoder. We performed BLASTP against the NCBI non-redundant (nr dataset to annotate proteins. Taken together, this is the first transcriptome data for P. salicina to our knowledge.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Transcriptome Analysis of Potato Tubers - Effects of Different Agricultural Practices

    NARCIS (Netherlands)

    Dijk, van J.P.; Cankar, K.; Scheffer, S.J.; Beenen, H.G.; Shepherd, L.V.T.; Stewart, D.; Davies, H.V.; Wilkockson, S.J.; Leifert, C.; Gruden, K.; Kok, E.J.

    2009-01-01

    The use of profiling techniques such as transcriptomics, proteomics, and metabolomics has been proposed to improve the detection of side effects of plant breeding processes. This paper describes the construction of a food safety-oriented potato cDNA microarray (FSPM). Microarray analysis was perform

  18. Transcriptome profiling of infectious diseases and cancer in zebrafish

    NARCIS (Netherlands)

    Ordas, Anita Katalin

    2010-01-01

    Analysis of the transcriptome, the total of all expressed RNA transcripts in a cell or an organism, contributes to our understanding of gene regulation during development and disease processes and is therefore of great importance in the field of genomic research. This thesis focuses on the analysis

  19. 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

  20. 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. PMID:27157132

  1. 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. PMID:25185649

  2. Transcriptome signature of the adult mouse choroid plexus

    Directory of Open Access Journals (Sweden)

    Marques Fernanda

    2011-01-01

    Full Text Available Abstract Background Although the gene expression profile of several tissues in humans and in rodent animal models has been explored, analysis of the complete choroid plexus (CP transcriptome is still lacking. A better characterization of the CP transcriptome can provide key insights into its functions as one of the barriers that separate the brain from the periphery and in the production of cerebrospinal fluid. Methods This work extends further what is known about the mouse CP transcriptome through a microarray analysis of CP tissue from normal mice under physiological conditions. Results We found that the genes most highly expressed are those implicated in energy metabolism (oxidative phosphorylation, glycolysis/gluconeogenesis and in ribosomal function, which is in agreement with the secretory nature of the CP. On the other hand, genes encoding for immune mediators are among those with lower expression in basal conditions. In addition, we found genes known to be relevant during brain development, and not previously identified to be expressed in the CP, including those encoding for various axonal guidance and angiogenesis molecules and for growth factors. Some of these are known to influence the neural stem cell niche in the subventricular zone, highlighting the involvement of the CP as a likely modulator of neurogenesis. Interestingly, our observations confirm that the CP transcriptome is unique, displaying low homology with that of other tissues. Of note, we describe here that the closest similarity is with the transcriptome of the endothelial cells of the blood-brain barrier. Conclusions Based on the data presented here, it will now be possible to further explore the function of particular proteins of the CP secretome in health and in disease.

  3. Characterisation of sewage wastewater and assessment of downstream pollution along Huluka River of Ambo, Ethiopia

    Directory of Open Access Journals (Sweden)

    Padanilly Chidambaram Prabu

    2008-04-01

    Full Text Available This study was conducted to assess the downstream pollution profiles of Huluka River due to sewage water contamination, and to provide the data on the physico-chemical properties and nutrient content of Huluka River in Ethiopia. The water quality indices, viz. temperature, pH, electrical conductivity, carbon dioxide content, total dissolved solids (TDS, hardness, dissolved oxygen (DO, biological oxygen demand (BOD, chemical oxygen demand (COD, calcium, magnesium, chloride, nitrate, sulphate, and phosphate were determined. Results reveal a worsening trend in the variations of most of these parameters from upstream to downstream areas of the river, which indicates an introduction of pollution load from domestic sewage and agricultural activities. For example, TDS and DO values for some downstream water samples do not conform to the accepted standards, and these samples also have eight to ten times higher values of BOD and COD compared to those for the upstream samples. Progressing downstream, the majority of the measured ions also show an increasing trend. All of these findings indicate that the quality of the water of Huluka River is declining.

  4. Subsequent to Suppression: Downstream Comprehension Consequences of Noun/Verb Ambiguity in Natural Reading

    Science.gov (United States)

    Stites, Mallory C.; Federmeier, Kara D.

    2015-01-01

    We used eye tracking to investigate the downstream processing consequences of encountering noun/verb (NV) homographs (i.e., park) in semantically neutral but syntactically constraining contexts. Target words were followed by a prepositional phrase containing a noun that was plausible for only 1 meaning of the homograph. Replicating previous work,…

  5. From Process Development to Manufacturing: Lab-Intensive Courses in Downstream Bioprocessing

    Science.gov (United States)

    Gilleskie, Gary L.; Reeves, Baley A.

    2014-01-01

    Most chemical engineering graduates work in industry, a fact that underscores the need for courses to provide experiences that prepare them for industry. The Biomanufacturing Training and Education Center (BTEC) at North Carolina State University has addressed this need by developing and delivering a comprehensive downstream bioprocessing program…

  6. Concentration of radionuclides in fresh water fish downstream of Rancho Seco Nuclear Generating Plant

    International Nuclear Information System (INIS)

    Fish were collected for radionuclide analysis over a 5-month period in 1984 from creeks downstream of the Rancho Seco Nuclear Generating Plant, which has been discharging quantities of some fission and activation products to the waterway since 1981. Among the fish, the bluegill was selected for intensive study because it is very territorial and the radionuclide concentrations detected should be representative of the levels in the local environment at the downstream locations sampled. Among the gamma-emitting radionuclides routinely released, only 134Cs and 137Cs were detected in the edible flesh of fish. Concentrations in the flesh of fish decreased with distance from the plant. The relationship between concentration and distance was determined to be exponential. Exponential equations were generated to estimate concentrations in fish at downstream locations where no site-specific information was available. Mean concentrations of 137Cs in bluegill collected during April, May, July and August from specific downstream stations were not significantly different in spite of the release of 131 mCi to the creeks between April and August. The concentrations in fish are not responding to changes in water concentrations brought about by plant discharges. Diet appears to be a more significant factor than size or weight or water concentration in regulating body burdens of 137Cs in these fish

  7. 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)

  8. 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.

  9. 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.

  10. 40 CFR 80.219 - Designation and downstream requirements for GPA gasoline.

    Science.gov (United States)

    2010-07-01

    ... requirements for GPA gasoline. 80.219 Section 80.219 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY...-in Program § 80.219 Designation and downstream requirements for GPA gasoline. The requirements and... standards under § 80.216 as “GPA” gasoline. (b) Product transfer documents. (1) On each occasion that...

  11. 40 CFR 80.220 - What are the downstream standards for GPA gasoline?

    Science.gov (United States)

    2010-07-01

    ... GPA gasoline? 80.220 Section 80.220 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY...-in Program § 80.220 What are the downstream standards for GPA gasoline? (a) GPA gasoline. (1) During the period February 1, 2004 through January 31, 2005, the sulfur content of GPA gasoline at...

  12. 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

  13. Headwater effects on downstream waters: Legal perspectives, science needs, and assessment approaches

    Science.gov (United States)

    Headwater streams make up at least 53% of total stream length in the US. Although these systems are of interest for their own sake, there has recently been significant focus on how headwater streams contribute to downstream waters. This has resulted in part from recent legal op...

  14. 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 o...

  15. 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.

  16. 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.

  17. Modelling the role of transmission companies in the downstream European gas market

    International Nuclear Information System (INIS)

    This paper describes the empirical model GASTALE and shows several analyses of the European gas market using this model. These analyses are mainly focused on the role of the downstream transmission companies. Producers of natural gas are assumed to form an oligopoly throughout the paper. Considering an oligopolistic transmission structure our model results show that the level of transmitters' profits strongly depends on the possibilities of discrimination on the border prices. If price discrimination by producers is allowed, these producers collect the main part of the margins on end-use prices. Without price discrimination the transmission companies collect most of the margins. Assuming an oligopolistic downstream structure, end-use prices converge to prices corresponding to perfect competition when the number of transmitters increases. Given the oligopolistic structure of the upstream industry, it is of importance to prevent (or abolish) monopolistic structures in the downstream gas market. In the case where oligopolistic competition between downstream gas companies cannot be prevented, vertical integration should be supported (or at least not be discouraged). 14 refs

  18. Linking Three Gorges Dam and downstream hydrological regimes along the Yangtze River, China

    NARCIS (Netherlands)

    Mei, X.; Dai, Z.; Van Gelder, P.H.A.J.M.; Gao, J.

    2015-01-01

    The magnitude of anthropogenic influence, especially dam regulation, on hydrological system is of scientific and practical value for large river management. As the largest dam in the world by far, Three Gorges Dam (TGD) is expected to be a strong evidence on dam impacts on downstream hydrological re

  19. 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

  20. 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.

  1. Pharmacologic Treatment of Downstream of Tyrosine Kinase 7 Congenital Myasthenic Syndrome

    DEFF Research Database (Denmark)

    Witting, Nanna; Vissing, John

    2014-01-01

    of pharmacologic treatment of one of the most common subtypes of CMS, downstream of tyrosine kinase 7 (DOK7) CMS. EVIDENCE REVIEW: In a search of the PubMed database, we found 16 publications describing the response to medication in 122 individuals with DOK7 deficiency. The last search was performed August 15...

  2. 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

  3. Subthalamic, not striatal, activity correlates with basal ganglia downstream activity in normal and parkinsonian monkeys

    Science.gov (United States)

    Deffains, Marc; Iskhakova, Liliya; Katabi, Shiran; Haber, Suzanne N; Israel, Zvi; Bergman, Hagai

    2016-01-01

    The striatum and the subthalamic nucleus (STN) constitute the input stage of the basal ganglia (BG) network and together innervate BG downstream structures using GABA and glutamate, respectively. Comparison of the neuronal activity in BG input and downstream structures reveals that subthalamic, not striatal, activity fluctuations correlate with modulations in the increase/decrease discharge balance of BG downstream neurons during temporal discounting classical condition task. After induction of parkinsonism with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), abnormal low beta (8-15 Hz) spiking and local field potential (LFP) oscillations resonate across the BG network. Nevertheless, LFP beta oscillations entrain spiking activity of STN, striatal cholinergic interneurons and BG downstream structures, but do not entrain spiking activity of striatal projection neurons. Our results highlight the pivotal role of STN divergent projections in BG physiology and pathophysiology and may explain why STN is such an effective site for invasive treatment of advanced Parkinson's disease and other BG-related disorders. DOI: http://dx.doi.org/10.7554/eLife.16443.001 PMID:27552049

  4. 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.

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

    Science.gov (United States)

    Forestan, Cristian; Aiese Cigliano, Riccardo; Farinati, Silvia; Lunardon, Alice; Sanseverino, Walter; Varotto, Serena

    2016-01-01

    Plant’s response and adaptation to abiotic stresses involve sophisticated genetic and epigenetic regulatory systems. To obtain a global view of molecular response to osmotic stresses, including the non-coding portion of genome, we conducted a total leaf transcriptome analysis on maize plants subjected to prolonged drought and salt stresses. Stress application to both B73 wild type and the epiregulator mutant rpd1-1/rmr6 allowed dissection of the epigenetic component of stress response. Coupling total RNA-Seq and transcriptome re-assembly we annotated thousands of new maize transcripts, together with 13,387 lncRNAs that may play critical roles in regulating gene expression. Differential expression analysis revealed hundreds of genes modulated by long-term stress application, including also many lncRNAs and transposons specifically induced by stresses. The amplitude and dynamic of the stress-modulated gene sets are very different between B73 and rpd1-1/rmr6 mutant plants, as result of stress-like effect on genome regulation caused by the mutation itself, which activates many stress-related genes even in control condition. The analyzed extensive set of total RNA-Seq data, together with the improvement of the transcriptome and the identification of the non-coding portion of the transcriptome give a revealing insight into the genetic and epigenetic mechanism responsible for maize molecular response to abiotic stresses. PMID:27461139

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

    Science.gov (United States)

    Forestan, Cristian; Aiese Cigliano, Riccardo; Farinati, Silvia; Lunardon, Alice; Sanseverino, Walter; Varotto, Serena

    2016-01-01

    Plant's response and adaptation to abiotic stresses involve sophisticated genetic and epigenetic regulatory systems. To obtain a global view of molecular response to osmotic stresses, including the non-coding portion of genome, we conducted a total leaf transcriptome analysis on maize plants subjected to prolonged drought and salt stresses. Stress application to both B73 wild type and the epiregulator mutant rpd1-1/rmr6 allowed dissection of the epigenetic component of stress response. Coupling total RNA-Seq and transcriptome re-assembly we annotated thousands of new maize transcripts, together with 13,387 lncRNAs that may play critical roles in regulating gene expression. Differential expression analysis revealed hundreds of genes modulated by long-term stress application, including also many lncRNAs and transposons specifically induced by stresses. The amplitude and dynamic of the stress-modulated gene sets are very different between B73 and rpd1-1/rmr6 mutant plants, as result of stress-like effect on genome regulation caused by the mutation itself, which activates many stress-related genes even in control condition. The analyzed extensive set of total RNA-Seq data, together with the improvement of the transcriptome and the identification of the non-coding portion of the transcriptome give a revealing insight into the genetic and epigenetic mechanism responsible for maize molecular response to abiotic stresses. PMID:27461139

  7. Transcriptome profiling reveals higher vertebrate orthologous of intra-cytoplasmic pattern recognition receptors in grey bamboo shark.

    Directory of Open Access Journals (Sweden)

    Tirumurugaan Krishnaswamy Gopalan

    Full Text Available From an immunologist perspective, sharks are an important group of jawed cartilaginous fishes and survey of the public database revealed a great gap in availability of large-scale sequence data for the group of Chondrichthyans the elasmobranchs. In an attempt to bridge this deficit we generated the transcriptome from the spleen and kidney tissues (a total of 1,606,172 transcripts of the shark, Chiloscyllium griseum using the Illumina HiSeq2000 platform. With a cut off of > = 300 bp and an expression value of >1RPKM we used 43,385 transcripts for BLASTX analysis which revealed 17,548 transcripts matching to the NCBI nr database with an E-value of < = 10(-5 and similarity score of 40%. The longest transcript was 16,974 bases with matched to HECT domain containing E3 ubiqutin protein ligase. MEGAN4 annotation pipeline revealed immune and signalling pathways including cell adhesion molecules, cytokine-cytokine receptor interaction, T-cell receptor signalling pathway and chemokine signaling pathway to be highly expressed in spleen, while different metabolism pathways such as amino acid metabolism, carbohydrate metabolism, lipid metabolism and xenobiotic biodegradation were highly expressed in kidney. Few of the candidate genes were selected to analyze their expression levels in various tissues by real-time PCR and also localization of a receptor by in-situ PCR to validate the prediction. We also predicted the domains structures of some of the identified pattern recognition receptors, their phylogenetic relationship with lower and higher vertebrates and the complete downstream signaling mediators of classical dsRNA signaling pathway. The generated transcriptome will be a valuable resource to further genetic and genomic research in elasmobranchs.

  8. Salicylic acid modulates levels of phosphoinositide dependent-phospholipase C substrates and products to remodel the Arabidopsis suspension cell transcriptome

    Directory of Open Access Journals (Sweden)

    Eric eRuelland

    2014-11-01

    Full Text Available Basal phosphoinositide-dependent phospholipase C (PI-PLC activity controls gene expression in Arabidopsis suspension cells and seedlings. PI-PLC catalyzes the production of phosphorylated inositol and diacylglycerol (DAG from phosphoinositides. It is not known how PI-PLC regulates the transcriptome although the action of DAG-kinase (DGK on DAG immediately downstream from PI-PLC is responsible for some of the regulation. We previously established a list of genes whose expression is affected in the presence of PI-PLC inhibitors. Here this list of genes was used as a signature in similarity searches of curated plant hormone response transcriptome data. The strongest correlations obtained with the inhibited PI-PLC signature were with salicylic acid (SA treatments. We confirm here that in Arabidopsis suspension cells SA treatment leads to an increase in phosphoinositides, then demonstrate that SA leads to a significant 20% decrease in phosphatidic acid, indicative of a decrease in PI-PLC products. Previous sets of microarray data were re-assessed. The SA response of one set of genes was dependent on phosphoinositides. Alterations in the levels of a second set of genes, mostly SA-repressed genes, could be related to decreases in PI-PLC products that occur in response to SA action. Together, the two groups of genes comprise at least 40% of all SA-responsive genes. Overall these two groups of genes are distinct in the functional categories of the proteins they encode, their promoter cis-elements and their regulation by DGK or phospholipase D. SA-regulated genes dependent on phosphoinositides are typical SA response genes while those with an SA response that is possibly dependent on PI-PLC products are less SA-specific. We propose a model in which SA inhibits PI-PLC activity and alters levels of PI-PLC products and substrates, thereby regulating gene expression divergently.

  9. Assessing the impacts of Three Gorges Dam on lake inundation areas across the downstream Yangtze floodplain

    Science.gov (United States)

    Wang, J.; Sheng, Y.; Wada, Y.

    2013-12-01

    China's Three Gorges Dam (TGD) has received worldwide attention due to its profound impacts on the downstream hydraulic, morphological, and ecological systems. The TGD operation results in direct alternation of the discharge to the middle and lower Yangtze reach, manifested as regulated flow and reduced sediment load. TGD's flow regulation, typically described as water storage in fall while release in winter and spring, interferes with the natural seasonality of downstream Yangtze River levels which are essentially important to the inundation dynamics of surrounding lakes/wetlands in the Yangtze floodplain. Concurrent decrease of sediment load has caused chronic downstream channel erosion which lowers Yangtze level in relation to flow and further affects the sustainability of riparian lakes and the related ecosystems. By integrating satellite observations, in situ measurement, and hydrologic simulations, this study presents a systematic assessment of the TGD impacts on the inundation areas of six major freshwater lakes across the entire Yangtze basin downstream of the TGD, during the time period from TGD's initial impoundment in June 2003 to early 2012. Despite the small number, the six targeted lakes cover a total area of ~5,000 km2 accounting for ~25% of the freshwater lake area in China, and were identified as the only natural lakes that remain in open connection to the Yangtze River across the downstream floodplain. Using daily MODIS imagery from 2000 to 2012, we revealed a significant year-round decline in the aggregated inundation area of the studied lakes by an average of ~580 km2 or 17.7% from the pre-dam to post-dam period (i.e., before and after June, 2003). To diagnose TGD's contribution to such lake area decline, we followed a two-step procedure by first quantifying the TGD impacts on the seasonal level regime along the complete longitudinal range of the Yangtze River downstream from TGD to the estuary [Wang et al., 2013], and then estimating the

  10. The role of grazers and shredders in the retention and downstream transport of a PCB in lotic environments

    International Nuclear Information System (INIS)

    Field studies using flow-through artificial stream channels were conducted between May and October 1992 to study the role of the feeding activity of grazing and shredding invertebrates in promoting downstream transport of 2,2',4,4',5,5'-hexachlorobiphenyl (HCBP). Plant material was labeled with [14C]HCBP and fed to selected invertebrate species, and accrual of radioactivity by downstream collector species (Hydropsyche spp.) was measured. Downstream transport of HCBP was significantly increased by the presence of the grazer Elimia livescens in the upstream sections of the channels as demonstrated by significantly higher levels of radioactivity in hydropsychid larvae located downstream. Similarly, movement of HCBP downstream was significantly greater in channels containing the shredder Hydatophylax argus than in channels without shredders. These results suggest that the feeding processes of benthic invertebrates may play an important role in the downstream transport of particle-bound hydrophobic organic compounds

  11. The role of grazers and shredders in the retention and downstream transport of a PCB in lotic environments

    Energy Technology Data Exchange (ETDEWEB)

    Sallenave, R.M. (Univ. of Guelph, Ontario (Canada). Dept. of Environmental Biology); Day, K.E. (National Water Research Inst., Burlington, Ontario (Canada)); Kreutzweiser, D.P. (Forestry Canada, Sault Ste. Marie, Ontario (Canada). Forest Pest Management Inst.)

    1994-11-01

    Field studies using flow-through artificial stream channels were conducted between May and October 1992 to study the role of the feeding activity of grazing and shredding invertebrates in promoting downstream transport of 2,2[prime],4,4[prime],5,5[prime]-hexachlorobiphenyl (HCBP). Plant material was labeled with [[sup 14]C]HCBP and fed to selected invertebrate species, and accrual of radioactivity by downstream collector species (Hydropsyche spp.) was measured. Downstream transport of HCBP was significantly increased by the presence of the grazer Elimia livescens in the upstream sections of the channels as demonstrated by significantly higher levels of radioactivity in hydropsychid larvae located downstream. Similarly, movement of HCBP downstream was significantly greater in channels containing the shredder Hydatophylax argus than in channels without shredders. These results suggest that the feeding processes of benthic invertebrates may play an important role in the downstream transport of particle-bound hydrophobic organic compounds.

  12. 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

  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, 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.

  14. 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.

  15. 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

  16. 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.

  17. Assessment of the Possible Extent of Loss of Life (LOL) Downstream of Large Dams due to Dam Failure Flooding

    OpenAIRE

    Saqib Ehsan; Walter Marx

    2014-01-01

    High flooding downstream of a dam could cause severe damages to the people and property. The most important damage is the loss of life which does not have any substitute. In this study, the extent of loss of life (LOL) downstream of a large dam due to dam failure has been focused. The LOL extent has been considered in terms of downstream distance. For systematic hydraulic analysis, the Jhelum river valley, about 329 km long downstream of Mangla dam in Pakistan has been taken into consideratio...

  18. Transcriptome analysis of monocyte-HIV interactions

    Directory of Open Access Journals (Sweden)

    Tran Huyen

    2010-06-01

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

  19. Transcriptome and Biochemical Analyses of Fungal Degradation of Wood

    Energy Technology Data Exchange (ETDEWEB)

    Tien, Ming

    2009-03-14

    Lignocellulosic accounts for a large percentage of material that can be utilized for biofuels. The most costly part of lignocellulosic material processing is the initial hydrolysis of the wood which is needed to circumvent the lignin barrier and the crystallinity of cellulose. Enzymes will play an increased role in this conversion in that they potentially provide an alternative to costly and caustic high temperature and acid treatment. The increasing use of enzymes in biotechnology is facilitated by both continued improvements in enzyme technology but also in the discovery of new and novel enzymes. The present proposal is aimed at identifying the enzymes which are known to depolymerize woody biomass. Fundamental understanding of how nature gains access to cellulose and hemicellulose will impact all applications. Because fungi are the only known microbes capable of circumventing the lignin barrier, knowledge of the enzyme they use is of great potential for biofuel processing. Nature has evolved different fungal mechanisms for enzymatic hydrolysis of wood. Most notable are the white-rot fungi (wrf) and the brown-rot fungi (brf). This proposed research aims at determining the complete transcriptome of three wrf and two brf to determine the enzymes involved in lignocellulose degradation. The transcriptome work will be supported by enzyme characterization (and zymograms) and finally analysis of the lignin component to determine the mode of lignin modification. In this proposed research, we hypothesize that: 1) Determination of the complete transcriptome of closely related white and brown rot fungi will lead to knowledge of the relevant enzymes involved in wood degradation. 2) Knowledge of the extracellular transcriptome and the mechanism of wood decay can only be obtained if the products of the decay are known. As such, characterization of the lignin oxidation products will correlate the enzymes involved (obtained from the transcriptome) to the lignin oxidation products

  20. 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

  1. 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

  2. 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

  3. The effect of CD4 receptor downregulation and its downstream signaling molecules on HIV-1 latency

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Kyung-Chang [National Institute of Health, Chungbuk (Korea, Republic of); School of Life Science and Biotechnology, Korea University, Seoul (Korea, Republic of); Kim, Hyeon Guk [National Institute of Health, Chungbuk (Korea, Republic of); Roh, Tae-Young [Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Gyeongbuk (Korea, Republic of); Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk (Korea, Republic of); Park, Jihwan [Division of Molecular and Life Science, Pohang University of Science and Technology, Pohang, Gyeongbuk (Korea, Republic of); Jung, Kyung-Min; Lee, Joo-Shil [National Institute of Health, Chungbuk (Korea, Republic of); Choi, Sang-Yun [School of Life Science and Biotechnology, Korea University, Seoul (Korea, Republic of); Kim, Sung Soon [National Institute of Health, Chungbuk (Korea, Republic of); Choi, Byeong-Sun, E-mail: byeongsun@korea.kr [National Institute of Health, Chungbuk (Korea, Republic of)

    2011-01-14

    Research highlights: {yields} CD4 receptors were downregulated on the surface of HIV-1 latently infected cells. {yields} CD4 downstream signaling molecules were suppressed in HIV-1 latently infected cells. {yields} HIV-1 progeny can be reactivated by induction of T-cell activation signal molecules. {yields} H3K4me3 and H3K9ac were highly enriched in CD4 downstream signaling molecules. {yields} HIV-1 latency can be maintained by the reduction of downstream signaling molecules. -- Abstract: HIV-1 can establish a latent infection in memory CD4 + T cells to evade the host immune response. CD4 molecules can act not only as the HIV-1 receptor for entry but also as the trigger in an intracellular signaling cascade for T-cell activation and proliferation via protein tyrosine kinases. Novel chronic HIV-1-infected A3.01-derived (NCHA) cells were used to examine the involvement of CD4 downstream signaling in HIV-1 latency. CD4 receptors in NCHA cells were dramatically downregulated on its surface but were slightly decreased in whole-cell lysates. The expression levels of CD4 downstream signaling molecules, including P56{sup Lck}, ZAP-70, LAT, and c-Jun, were sharply decreased in NCHA cells. The lowered histone modifications of H3K4me3 and H3K9ac correlated with the downregulation of P56{sup Lck}, ZAP-70, and LAT in NCHA cells. AP-1 binding activity was also reduced in NCHA cells. LAT and c-Jun suppressed in NCHA cells were highly induced after PMA treatment. In epigenetic analysis, other signal transduction molecules which are associated with active and/or latent HIV-1 infection showed normal states in HIV-1 latently infected cells compared to A3.01 cells. In conclusion, we demonstrated that the HIV-1 latent state is sustained by the reduction of downstream signaling molecules via the downregulation of CD4 and the attenuated activity of transcription factor as AP-1. The HIV-1 latency model via T-cell deactivation may provide some clues for the development of the new

  4. Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis.

    Science.gov (United States)

    Woo, Hye Ryun; Koo, Hee Jung; Kim, Jeongsik; Jeong, Hyobin; Yang, Jin Ok; Lee, Il Hwan; Jun, Ji Hyung; Choi, Seung Hee; Park, Su Jin; Kang, Byeongsoo; Kim, You Wang; Phee, Bong-Kwan; Kim, Jin Hee; Seo, Chaehwa; Park, Charny; Kim, Sang Cheol; Park, Seongjin; Lee, Byungwook; Lee, Sanghyuk; Hwang, Daehee; Nam, Hong Gil; Lim, Pyung Ok

    2016-05-01

    Plant leaves, harvesting light energy and fixing CO2, are a major source of foods on the earth. Leaves undergo developmental and physiological shifts during their lifespan, ending with senescence and death. We characterized the key regulatory features of the leaf transcriptome during aging by analyzing total- and small-RNA transcriptomes throughout the lifespan of Arabidopsis (Arabidopsis thaliana) leaves at multidimensions, including age, RNA-type, and organelle. Intriguingly, senescing leaves showed more coordinated temporal changes in transcriptomes than growing leaves, with sophisticated regulatory networks comprising transcription factors and diverse small regulatory RNAs. The chloroplast transcriptome, but not the mitochondrial transcriptome, showed major changes during leaf aging, with a strongly shared expression pattern of nuclear transcripts encoding chloroplast-targeted proteins. Thus, unlike animal aging, leaf senescence proceeds with tight temporal and distinct interorganellar coordination of various transcriptomes that would be critical for the highly regulated degeneration and nutrient recycling contributing to plant fitness and productivity. PMID:26966169

  5. Transcriptome data - Air-drying stress - DGBY | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us DGBY Tran...scriptome data - Air-drying stress Data detail Data name Transcriptome data - Air-drying stress Des...suggested that the genes involved in protein folding were transiently upregulated at early stages, and that ... License Update History of This Database Site Policy | Contact Us Transcriptome data - Air-drying stress - DGBY | LSDB Archive ...

  6. Up- and downstream sheaths in an ion-beam-plasma system

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Zi-an; Ma, J. X., E-mail: jxma@ustc.edu.cn [CAS Key Laboratory of Geospace Environment and Department of Modern Physics, University of Science and Technology of China, Hefei, Anhui 230026 (China)

    2016-02-15

    Ion sheaths formed in the up- and downstream sides of a negatively biased metal plate/mesh in an ion-beam-background-plasma system were experimentally investigated in a double plasma device. Measured potential profiles near the plate exhibit asymmetric structure, showing thicker sheath in the downstream side. The presence of the ion beam causes the shrink of the sheaths on both sides. The sheath thickness decreases with the increase of beam energy and density. Furthermore, the sheaths near the mesh are substantially thinner than that near the plate because of the partial transmission of the mesh to the ions. In addition, the increase of neutral gas pressure leads to the reduction of the beam energy and density, resulting in the increase of the sheath thickness.

  7. 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.

  8. Downstream evolution of proper orthogonal decomposition eigenfunctions in a lobed mixer

    Science.gov (United States)

    Ukeiley, L.; Glauser, M.; Wick, D.

    1993-01-01

    A two-dimensional (one space and time) scalar adaptation of the proper orthogonal decomposition was applied to streamwise velocity data obtained in a lobed mixer flowfield, using a rake of 15 single-component hot wires. Through the application of the proper orthogonal decomposition, the amount of streamwise turbulent kinetic energy contained in the various proper orthogonal modes was examined for two different downstream locations (z/h = 2.6 and 3.9). The large eddy or dominant mode was shown to have a measurable decrease in the relative streamwise component of the kinetic energy between these two downstream locations. This indicates that the large eddy, as defined by the proper orthogonal decomposition, breaks down, and the flow becomes more homogeneous. A pseudoflow visualization technique was then employed to help visualize this process.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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

    2016-01-01

    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. PMID:27561246

  15. 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.

  16. 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.

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

    Science.gov (United States)

    Sahoo, Ambika; Kar, Basudeba; Sahoo, Suprava; Ray, Asit; Nayak, Sanghamitra

    2016-12-01

    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. PMID:27668184

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

    Science.gov (United States)

    Thompson, Andrew W; Ortí, Guillermo

    2016-09-01

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

  19. Transcriptomes of the desiccation- tolerant resurrection plant Craterostigma plantagineum

    DEFF Research Database (Denmark)

    Rodriguez, M. C.; Edsgard, Stefan Daniel; Hussain, S. S.;

    2010-01-01

    Studies of the resurrection plant Craterostigma plantagineum have revealed some of the mechanisms which these desiccation-tolerant plants use to survive environments with extreme dehydration and restricted seasonal water. Most resurrection plants are polyploid with large genomes, which has hindered...... efforts to obtain whole genome sequences and perform mutational analysis. However, the application of deep sequencing technologies to transcriptomics now permits large-scale analyses of gene expression patterns despite the lack of a reference genome. Here we use pyro-sequencing to characterize...... the transcriptomes of C. plantagineum leaves at four stages of dehydration and rehydration. This reveals that genes involved in several pathways, such as those required for vitamin K and thiamin biosynthesis, are tightly regulated at the level of gene expression. Our analysis also provides a comprehensive picture...

  20. Candidate olfaction genes identified within the Helicoverpa armigera Antennal Transcriptome.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    Full Text Available Antennal olfaction is extremely important for insect survival, mediating key behaviors such as host preference, mate choice, and oviposition site selection. Multiple antennal proteins are involved in olfactory signal transduction pathways. Of these, odorant receptors (ORs and ionotropic receptors (IRs confer specificity on olfactory sensory neuron responses. In this study, we identified the olfactory gene repertoire of the economically important agricultural pest moth, Helicoverpa armigera, by assembling the adult male and female antennal transcriptomes. Within the male and female antennal transcriptomes we identified a total of 47 OR candidate genes containing 6 pheromone receptor candidates. Additionally, 12 IR genes as well as 26 odorant-binding proteins and 12 chemosensory proteins were annotated. Our results allow a systematic functional analysis across much of conventional ORs repertoire and newly reported IRs mediating the key olfaction-mediated behaviors of H. armigera.

  1. 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.

  2. Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1.

    Directory of Open Access Journals (Sweden)

    Mikael Brosché

    2014-02-01

    Full Text Available Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1 has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS. Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR.

  3. Transcriptomics and functional genomics of ROS-induced cell death regulation by RADICAL-INDUCED CELL DEATH1.

    Science.gov (United States)

    Brosché, Mikael; Blomster, Tiina; Salojärvi, Jarkko; Cui, Fuqiang; Sipari, Nina; Leppälä, Johanna; Lamminmäki, Airi; Tomai, Gloria; Narayanasamy, Shaman; Reddy, Ramesha A; Keinänen, Markku; Overmyer, Kirk; Kangasjärvi, Jaakko

    2014-02-01

    Plant responses to changes in environmental conditions are mediated by a network of signaling events leading to downstream responses, including changes in gene expression and activation of cell death programs. Arabidopsis thaliana RADICAL-INDUCED CELL DEATH1 (RCD1) has been proposed to regulate plant stress responses by protein-protein interactions with transcription factors. Furthermore, the rcd1 mutant has defective control of cell death in response to apoplastic reactive oxygen species (ROS). Combining transcriptomic and functional genomics approaches we first used microarray analysis in a time series to study changes in gene expression after apoplastic ROS treatment in rcd1. To identify a core set of cell death regulated genes, RCD1-regulated genes were clustered together with other array experiments from plants undergoing cell death or treated with various pathogens, plant hormones or other chemicals. Subsequently, selected rcd1 double mutants were constructed to further define the genetic requirements for the execution of apoplastic ROS induced cell death. Through the genetic analysis we identified WRKY70 and SGT1b as cell death regulators functioning downstream of RCD1 and show that quantitative rather than qualitative differences in gene expression related to cell death appeared to better explain the outcome. Allocation of plant energy to defenses diverts resources from growth. Recently, a plant response termed stress-induced morphogenic response (SIMR) was proposed to regulate the balance between defense and growth. Using a rcd1 double mutant collection we show that SIMR is mostly independent of the classical plant defense signaling pathways and that the redox balance is involved in development of SIMR. PMID:24550736

  4. Location Specificity and the Transferability of Downstream Assets to Foreign Subsidiaries

    OpenAIRE

    Jaideep Anand; Andrew Delios

    1997-01-01

    We investigate the effect of firm-specific advantages being ‘local’ in scope, and the influence of subsequent location-specific disadvantages, on the choice of foreign entry mode and subsidiary performance. To look into this issue, we examine Japanese FDI data from the wholesale and retail industries – two sectors that have productive activity concentrated in downstream processes and location-bound resources. Our theoretical and empirical analyses demonstrate that, in situations where require...

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

    OpenAIRE

    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 and phone repair, the paper analyses the micro-enterprises providing them and their contribution to income and employment creation. It shows that majority of the enterprises providing the services ar...

  6. Downstream effect of ramping neural activity through synapses with short-term plasticity

    Science.gov (United States)

    Wei, Wei; Wang, Xiao-Jing

    2016-01-01

    Ramping neuronal activity has been observed in multiple cortical areas correlated with evidence accumulation processes or timing. In this work we investigate the downstream effect of ramping neuronal activity through synapses that display short-term facilitation (STF) or depression (STD). We obtain an analytical result for a synapse driven by deterministic linear ramping input that exhibits pure STF or STD, and investigate the general case when both STF and STD exist numerically. In neural circuits, the ramping inputs usually have strong fluctuation and each downstream neuron receives converging inputs from many presynaptic neurons. We show that the analytical deterministic solution gives an accurate description of the averaging synaptic activation that a postsynaptic neuron receives in a neural circuit, even when the fluctuation in ramping input is strong. Therefore our work provides insights on the impact of ramping neuronal activity on downstream neurons through synapses displaying short-term plasticity. Specifically, activation of a synapse with STF shows a sublinear increase with time and is insensitive to the slopes of ramping inputs during the initial period, followed by a linear ramping similar to a synapse without STF. Activation of a synapse with STD, on the other hand, develops a local maximum before reaching a steady state, which is independent of the slope of ramping input. For a synapse displaying both STF and STD, increase of the depression time constant from a value much smaller than the facilitation time constant τF to a value much larger than τF leads to a transition from facilitation domination to depression domination. By utilizing STD in the corticostriatal synapses, our work provides an understanding of the saturation of striatal activity as observed for monkeys performing evidence accumulation. Our work also predicts that in the fixed duration version of motion discrimination tasks the stationary state of neuronal activity downstream to the

  7. Wash functions downstream of Rho1 GTPase in a subset of Drosophila immune cell developmental migrations

    OpenAIRE

    Verboon, Jeffrey M; Travis K Rahe; Rodriguez-Mesa, Evelyn; Parkhurst, Susan M.

    2015-01-01

    Drosophila immune cells, the hemocytes, undergo four stereotypical developmental migrations to populate the embryo, where they provide immune reconnoitering, as well as a number of non–immune-related functions necessary for proper embryogenesis. Here, we describe a role for Rho1 in one of these developmental migrations in which posteriorly located hemocytes migrate toward the head. This migration requires the interaction of Rho1 with its downstream effector Wash, a Wiskott–Aldrich syndrome fa...

  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. Regulating water extraction in a river basin with upstream-downstream communities

    DEFF Research Database (Denmark)

    Graversen, Mette Kildegaard

    This paper proposes a tax mechanism modelled for water extraction in a river system with upstream and downstream farmers. The tax mechanism is based on the regulator’s own estimation of aggregate extraction and for that reason the tax addresses the problem of asymmetric information....... It is demonstrated that the tax mechanism ensures approximately correct marginal extraction incentives for the individual farmer. Consequently, it is concluded that the tax mechanism proposed here has a practical application....

  10. Evaluating lignocellulosic biomass, its derivatives, and downstream products with Raman spectroscopy

    OpenAIRE

    Jason S. Lupoi; Erica eGjersing; 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 gauge the recalcitrance of the plants, and develop efficient deconstruction strategi...

  11. Downstream changes in spring-fed stream invertebrate communities: the effect of increased temperature range?

    OpenAIRE

    Russell G. DEATH; José BARQU��N

    2011-01-01

    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 characteristic...

  12. 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....

  13. 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...

  14. Pressure Fluctuation in a Vaned Diffuser Downstream from a Centrifugal Pump Impeller

    OpenAIRE

    Akinori Furukawa; Hisasada Takahara; Takahiro Nakagawa; Yusuke Ono

    2003-01-01

    Periodic flows downstream from a centrifugal pump impeller in vaneless and vaned diffusers were measured by using a single hole yawmeter and a phase-locked sampling method. The flows were also calculated by an inviscid flow analysis using the blade-surface singularity method. The periodic variations in calculated static pressure with the impeller rotating quantitatively agree well with the measured ones. The flow behaviors in the vaned diffuser are discussed, citing measured and calculated re...

  15. 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.

  16. 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

  17. 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.

  18. Comprehensive analysis of circadian periodic pattern in plant transcriptome

    OpenAIRE

    Ptitsyn Andrey

    2008-01-01

    Abstract Background Circadian rhythm is a crucial factor in orchestration of plant physiology, keeping it in synchrony with the daylight cycle. Previous studies have reported that up to 16% of plant transcriptome are circadially expressed. Results Our studies of mammalian gene expression revealed circadian baseline oscillation in nearly 100% of genes. Here we present a comprehensive analysis of periodicity in two independent data sets. Application of the advanced algorithms and analytic appro...

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

    OpenAIRE

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

    2014-01-01

    Background Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, e...

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

    Directory of Open Access Journals (Sweden)

    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.

  1. From single-cell transcriptomics to single-molecule counting

    OpenAIRE

    Islam, Saiful

    2013-01-01

    RNA-sequencing (RNA-seq) technology has been progressing so fast in the last few years and made it possible to perform transcriptome analysis at single-cell level that was even unimaginable a few years before. Nowadays, the importance of gene expression analysis at the single-cell level is increasingly appreciated for the study of complex heterogeneous tissue. Also, in order to solve the obscure and no consensus definition of cell types, the single-cell gene expression analysis ap...

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

    Directory of Open Access Journals (Sweden)

    Zi Long Wang

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

  3. Whole Genome and Transcriptome Sequencing of a B3 Thymoma

    OpenAIRE

    Iacopo Petrini; Arun Rajan; Trung Pham; Donna Voeller; Sean Davis; James Gao; Yisong Wang; Giuseppe Giaccone

    2013-01-01

    Molecular pathology of thymomas is poorly understood. Genomic aberrations are frequently identified in tumors but no extensive sequencing has been reported in thymomas. Here we present the first comprehensive view of a B3 thymoma at whole genome and transcriptome levels. A 55-year-old Caucasian female underwent complete resection of a stage IVA B3 thymoma. RNA and DNA were extracted from a snap frozen tumor sample with a fraction of cancer cells over 80%. We performed array comparative genomi...

  4. The effect of listening to music on human transcriptome

    OpenAIRE

    Chakravarthi Kanduri; Pirre Raijas; Minna Ahvenainen; Philips, Anju K.; Liisa Ukkola-Vuoti; Harri Lähdesmäki; Irma Järvelä

    2015-01-01

    Although brain imaging studies have demonstrated that listening to music alters human brain structure and function, the molecular mechanisms mediating those effects remain unknown. With the advent of genomics and bioinformatics approaches, these effects of music can now be studied in a more detailed fashion. To verify whether listening to classical music has any effect on human transcriptome, we performed genome-wide transcriptional profiling from the peripheral blood of participants after li...

  5. INsPeCT: INtegrative Platform for Cancer Transcriptomics

    OpenAIRE

    Madhamshettiwar, Piyush B; Maetschke, Stefan R; Davis, Melissa J; Antonio Reverter; Ragan, Mark A

    2014-01-01

    The emergence of transcriptomics, fuelled by high-throughput sequencing technologies, has changed the nature of cancer research and resulted in a massive accumulation of data. Computational analysis, integration, and data visualization are now major bottlenecks in cancer biology and translational research. Although many tools have been brought to bear on these problems, their use remains unnecessarily restricted to computational biologists, as many tools require scripting skills, data infrast...

  6. Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation

    OpenAIRE

    Hawdon John; Wilson Richard K; Martin John; Abubucker Sahar; Wang Zhengyuan; Mitreva Makedonka

    2010-01-01

    Abstract Background Hookworm infection is one of the most important neglected diseases in developing countries, with approximately 1 billion people infected worldwide. To better understand hookworm biology and nematode parasitism, the present study generated a near complete transcriptome of the canine hookworm Ancylostoma caninum to a very high coverage using high throughput technology, and compared it to those of the free-living nematode Caenorhabditis elegans and the parasite Brugia malayi....

  7. 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

  8. Global transcriptome analysis of developing chickpea (Cicer arietinum L. seeds

    Directory of Open Access Journals (Sweden)

    Seema ePradhan

    2014-12-01

    Full Text Available Understanding developmental processes, especially in non-model crop plants, is extremely important in order to unravel unique mechanisms regulating development. Chickpea (C. arietinum L. seeds are especially valued for their high carbohydrate and protein content. Therefore, in order to elucidate the mechanisms underlying seed development in chickpea, deep sequencing of transcriptomes from four developmental stages was undertaken. In this study, next generation sequencing platform was utilised to sequence the transcriptome of four distinct stages of seed development in chickpea. About 1.3 million reads were generated which were assembled into 51,099 unigenes by merging the de novo and reference assemblies. Functional annotation of the unigenes was carried out using the Uniprot, COG and KEGG databases. RPKM based digital expression analysis revealed specific gene activities at different stages of development which was validated using Real time PCR analysis. More than 90% of the unigenes were found to be expressed in at least one of the four seed tissues. DEGseq was used to determine differentially expressing genes which revealed that only 6.75% of the unigenes were differentially expressed at various stages. Homology based comparison revealed 17.5% of the unigenes to be putatively seed specific. Transcription factors were predicted based on HMM profiles built using TF sequences from five legume plants and analysed for their differential expression during progression of seed development. Expression analysis of genes involved in biosynthesis of important secondary metabolites suggested that chickpea seeds can serve as a good source of antioxidants. Since transcriptomes are a valuable source of molecular markers like simple sequence repeats (SSRs, about 12,000 SSRs were mined in chickpea seed transcriptome and few of them were validated. In conclusion, this study will serve as a valuable resource for improved chickpea breeding.

  9. Evolution of alternative splicing in primate brain transcriptomes

    OpenAIRE

    Lin, Lan; Shen, Shihao; Jiang, Peng; Sato, Seiko; Davidson, Beverly L.; Xing, Yi

    2010-01-01

    Alternative splicing is a predominant form of gene regulation in higher eukaryotes. The evolution of alternative splicing provides an important mechanism for the acquisition of novel gene functions. In this work, we carried out a genome-wide phylogenetic survey of lineage-specific splicing patterns in the primate brain, via high-density exon junction array profiling of brain transcriptomes of humans, chimpanzees and rhesus macaques. We identified 509 genes showing splicing differences among t...

  10. On the downstream boundary conditions for the vorticity-stream function formulation of two-dimensional incompressible flows

    Science.gov (United States)

    Tezduyar, T. E.; Liou, J.

    1991-01-01

    Downstream boundary conditions equivalent to the homogeneous form of the natural boundary conditions associated with the velocity-pressure formulation of the Navier-Stokes equations are derived for the vorticity-stream function formulation of two-dimensional incompressible flows. Of particular interest are the zero normal and shear stress conditions at a downstream boundary.

  11. 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

  12. Downstream effects of reservoir releases to the Potomac River from Luke, Maryland, to Washington, DC

    Science.gov (United States)

    Trombley, T.J.

    1982-01-01

    A digital computer flow-routing model was developed for the Potomac River in order to determine the downstream effects of flow releases from the Bloomington and Savage River Reservoirs. Both reservoirs are located above Luke, Maryland approximately 230 miles upstream from Washington, D. C. The downstream effects of reservoir releases were determined by using the unit-response method of flow routing implemented by a diffusion analogy. Results are in the form of unit response coefficients which are used to route flows downstream from Luke. A 24-hour sustained reservoir release input at Luke will result in 35 percent of the flow arriving at Washington, D.C., during the 4th day after the beginning of the release, followed by 61 percent and 4 percent arriving on the 5th and 6th days, respectively. For a 7-day sustained reservoir release, 47 percent of the flow will arrive during the 1st week, and 53 percent will arrive the 2d week. Two methods were used to estimate the amount of water that goes into channel storage between Luke and Washington, D.C., during sustained reservoir releases. Analysis of the flow-routing results indicates channel storage is equivalent to the volume of water releases over a 3.7-day period. Using channel geometry relationships, that volume is equal to 3.2 days ' release. (USGS)

  13. Downstream movement of mature eels in a hydroelectric reservoir in New Zealand

    Science.gov (United States)

    Watene, E.M.; Boubee, J.A.T.; Haro, A.

    2003-01-01

    This study investigates the behavior of migrant eels as they approached the Patea hydroelectric dam on the West Coast of the North Island, New Zealand. Seventeen mature migrant eels (870-1,240 mm; 2,000-6,380 g) were implanted with coded acoustic transmitters and released. Their movements in the reservoir were monitored for 14 months with stationary data logging and manual tracking receivers. The downstream migration of sexually maturing eels was found to occur mainly at night, usually during, or immediately after, rainfall events. Eels tended to travel at the surface, within the upper 4 m of the water column, at speeds ranging from 16 to 89 cm/s. Upon reaching the headrace, eels typically spent time searching, presumably for an unobstructed downstream route. In order to aid downstream passage of eels at the Patea Dam, power station operators began spillway opening trials during peak migration periods. Although this allowed some migrant eels to safely pass over the dam, information on the relative effectiveness and cost of this method over other possible mitigation methods is still required. ?? Copyright by the American Fisheries Society 2003.

  14. Environmental radiological studies downstream from the Rancho Seco Nuclear Power Generating Station, 1985

    International Nuclear Information System (INIS)

    Information compiled in 1985 while assessing the environmental impact of radionuclides previously discharged with aqueous releases from the Rancho Seco Nuclear Power Generating Plant is presented. In October 1984, the quantities of gamma-emitting radionuclides in water discharged to Clay Creek from the plant were reduced below operationally defined detection limits for liquid effluents. However, radionuclides previously discharged persist in the downstream environment and are found in many aquatic dietary components. 134Cs and 137Cs are the primary gamma-emitting radionuclides detected in the edible flesh of different fish, crayfish, and frogs. Coefficients for exponential equations are generated, from a least square analysis, that relate the change in concentration of 137Cs in fish to distance downstream and time between March and October 1985. Concentrations of 137Cs in surface creek sediments also decreased in the downstream direction much in the same manner as concentrations decreased in fish. However, there was no significant difference in the radiocesium concentrations in surface sediements collected from comparable locations during both 1984 and 1985

  15. 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.

  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. Evidence of Mercurial Contamination and Denundation Downstream of New Idria Mercury Mine, San Benito County, California

    Science.gov (United States)

    Letsinger, H. E.; Sharma, R. K.; Weinman, B.

    2014-12-01

    California's Central Valley water quality and soils are essential to the survival of the valley's communities and agriculture. Therefore, detection of possible contaminants within the valley streams and soils are paramount to the protection of this land and the people that depend upon it. Here we explore the impact of the contaminated stream beds near the New Idria Mercury Mine site, San Benito County, California. Previous work by Ganguli et al. (2000) has been done in this area to determine the mercury levels associated with the water that flows near the ghost town of New Idria. We performed geochemical analyses on the finer bed sediments from channels draining the area, as well as the coarser sediments taken from along the channel banks, to determine mercury transport downriver from the source. Using a novel application of tau, a mass transfer coefficient typically used in critical zone studies or soil production and weathering rates, we determine downstream weathering, accumulation, and transport of mercury. Our initial geochemical data showed higher tau values upstream as well as within the banks of the contaminated streambed and a greater accumulation of mercury near the pollution source (i.e., mine tailings, (τ ~ 103)). Tau results also show elevated mercurial levels existing downstream, with accumulations in mid- (τ ~ 102) and down-stream (τ ~ 10) reaches. Combining tau results with more traditional indices of chemical weathering (CIA) support consistent overall Hg-weathering processes with low levels of chemical weathering and higher dominance of coupled physical-anthropogenic weathering.

  18. Optimization of Upstream Detention Reservoir Facilities for Downstream Flood Mitigation in Urban Areas

    Directory of Open Access Journals (Sweden)

    Thi Thuy Ngo

    2016-07-01

    Full Text Available A detention reservoir is one of the most effective engineered solutions for flood damage mitigation in urban areas. Detention facilities are constructed to temporarily store storm water and then slowly drain when the peak period has passed. This delayed drainage may coincide with upstream floods and aggravate the flood risk downstream. Optimal operation and design are needed to improve the performance of detention reservoirs for flood reduction. This study couples hydrologic simulation software (EPA-SWMM with an evolutional optimizer (extraordinary particle swarm optimization, EPSO to minimize flood damage downstream while considering the inundation risk at the detention reservoir. The optimum design and operation are applied to an urban case study in Seoul, Korea, for historical severe flooding events and designed rainfall scenarios. The optimal facilities outperform the present facilities in terms of flood damage reduction both downstream and in the detention reservoir area. Specifically, the peak water level at the detention pond under optimal conditions is significantly smaller than that of the current conditions. The comparison of the total flooded volume in the whole watershed shows a dramatic reduction of 79% in a severe flooding event in 2010 and around 20% in 2011 and in 180 min designed rainfall scenarios.

  19. Experimental tsunami deposits: Linking hydrodynamics to sediment entrainment, advection lengths and downstream fining

    Science.gov (United States)

    Johnson, Joel P. L.; Delbecq, Katie; Kim, Wonsuck; Mohrig, David

    2016-01-01

    A goal of paleotsunami research is to quantitatively reconstruct wave hydraulics from sediment deposits in order to better understand coastal hazards. Simple models have been proposed to predict wave heights and velocities, based largely on deposit grain size distributions (GSDs). Although seemingly consistent with some recent tsunamis, little independent data exist to test these equations. We conducted laboratory experiments to evaluate inversion assumptions and uncertainties. A computer-controlled lift gate instantaneously released ~ 6.5 m3 of water into a 32 m flume with shallow ponded water, creating a hydraulic bore that transported sand from an upstream source dune. Differences in initial GSDs and ponded water depths influenced entrainment, transport, and deposition. While the source dune sand was fully suspendable based on size alone, experimental tsunamis produced deposits dominated by bed load sand transport in the upstream ~ 1/3 of the flume and suspension-dominated transport downstream. The suspension deposits exhibited downstream fining and thinning. At 95% confidence, a published advection-settling model predicts time-averaged flow depths to approximately a factor of two, and time-averaged downstream flow velocities to within a factor of 1.5. Finally, reasonable scaling is found between flume and field cases by comparing flow depths, inundation distances, Froude numbers, Rouse numbers and grain size trends in suspension-dominated tsunami deposits, justifying laboratory study of sediment transport and deposition by tsunamis.

  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. 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.

  2. Sluiceway Operations for Adult Steelhead Downstream Passage at The Dalles Dam, Columbia River, USA

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Fenton; Royer, Ida M.; Johnson, Gary E.; Tackley, Sean C.

    2013-10-01

    This study evaluated adult steelhead (Oncorhynchus mykiss; fallbacks and kelts) downstream passage at The Dalles Dam in the Columbia River, USA, during the late fall, winter, and early spring months between 2008 and 2011. The purpose of the study was to determine the efficacy of operating the dam’s ice-and-trash sluiceway during non-spill months to provide a relatively safe, non-turbine, surface outlet for overwintering steelhead fallbacks and downstream migrating steelhead kelts. We applied the fixed-location hydroacoustic technique to estimate fish passage rates at the sluiceway and turbines of the dam. The spillway was closed during our sampling periods, which generally occurred in late fall, winter, and early spring. The sluiceway was highly used by adult steelhead (91–99% of total fish sampled passing the dam) during all sampling periods. Turbine passage was low when the sluiceway was not operated. This implies that lack of a sluiceway route did not result in increased turbine passage. However, when the sluiceway was open, adult steelhead used it to pass through the dam. The sluiceway may be operated during late fall, winter, and early spring to provide an optimal, non-turbine route for adult steelhead (fallbacks and kelts) downstream passage at The Dalles Dam.

  3. Microdistribution patterns of macroinvertebrate communities upstream and downstream of organic effluents.

    Science.gov (United States)

    Alvarez-Cabria, Mario; Barquín, José; Juanes, José Antonio

    2011-01-01

    The present study analyses the distribution patterns of macroinvertebrate communities in four microhabitats (riffles, glides, leaf litter and bank roots) upstream and downstream of two waste water treatment plant (WWTP) effluents in northern Spain rivers. Macroinvertebrate communities were analysed in November 2006 by taking 5 samples from each of the microhabitats under unaffected (upstream WWTP) and affected (downstream WWTP) conditions, respectively. Water velocity, depth, substrate coarseness and hydraulic stress by means of the Froude number were also estimated at all sampling locations. Under unaffected conditions, the abundance and presence/absence of certain macroinvertebrate taxa were mainly determined by hydraulic characteristics (water velocity and Froude number) and feeding resource availability. However, neither macroinvertebrate richness nor abundance were neither significantly correlated with hydraulic stress nor substrate coarseness, although the number of macroinvertebrate taxa increased in microhabitats with high structural complexity. Macroinvertebrate abundance increased downstream of both WWTPs, while macroinvertebrate richness was not adversely affected by the organic enrichment of water. The structure and composition of macroinvertebrate communities occurring in riffles was similar under unaffected and affected conditions, while communities from leaf litter and submerged bank roots showed important changes above and below the WWTPs, indicating that they are probably the most appropriate communities for water quality assessment. PMID:21168894

  4. 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).

  5. A ROBUST COMBINATORIAL APPROACH BASED ON P-GRAPH FOR SUPERSTRUCTURE GENERATION IN DOWNSTREAM BIOPROCESSES

    Directory of Open Access Journals (Sweden)

    Xiaohui Xu

    2015-03-01

    Full Text Available Abstract In the production of chemicals from fermentation, the cost of downstream purification constitutes the major portion of the total production cost. Since the bioprocess generally contains a large amount of biochemical separation units, its flowsheets are complex. How to generate the rigorous superstructure of the downstream bioprocess is a primary problem and key step. In this work, a robust combined approach based on the P-graph was proposed to generate the rigorous superstructure of the downstream process of fermentation. This method integrates the hierarchical decomposition of the heuristics with P-graph-based algorithm MSG with the advantages including: (1 Different design flowsheets could be evaluated simultaneously; (2 An unique bipartite graph, P-graph, was introduced, which could represent the maximum structure clearly and intuitively; (3 The rigorous superstructure could be automatically generated. The validity of the present method was verified with two practical bioprocesses. Results show that the effective processes and the adequate operation units could be determined in the beginning stage of the design, and the tedious reforming steps during process synthesis could be avoided.

  6. DNA Source Selection for Downstream Applications Based on DNA Quality Indicators Analysis.

    Science.gov (United States)

    Lucena-Aguilar, Gema; Sánchez-López, Ana María; Barberán-Aceituno, Cristina; Carrillo-Ávila, José Antonio; López-Guerrero, José Antonio; Aguilar-Quesada, Rocío

    2016-08-01

    High-quality human DNA samples and associated information of individuals are necessary for biomedical research. Biobanks act as a support infrastructure for the scientific community by providing a large number of high-quality biological samples for specific downstream applications. For this purpose, biobank methods for sample preparation must ensure the usefulness and long-term functionality of the products obtained. Quality indicators are the tool to measure these parameters, the purity and integrity determination being those specifically used for DNA. This study analyzes the quality indicators in DNA samples derived from 118 frozen human tissues in optimal cutting temperature (OCT) reactive, 68 formalin-fixed paraffin-embedded (FFPE) tissues, 119 frozen blood samples, and 26 saliva samples. The results obtained for DNA quality are discussed in association with the usefulness for downstream applications and availability of the DNA source in the target study. In brief, if any material is valid, blood is the most approachable option of prospective collection of samples providing high-quality DNA. However, if diseased tissue is a requisite or samples are available, the recommended source of DNA would be frozen tissue. These conclusions will determine the best source of DNA, according to the planned downstream application. Furthermore our results support the conclusion that a complete procedure of DNA quantification and qualification is necessary to guarantee the appropriate management of the samples, avoiding low confidence results, high costs, and a waste of samples. PMID:27158753

  7. 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.)

  8. 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; Toner, Mehmet; Warren, H. Shaw; Schoenfeld, David A.; Rahme, Laurence; McDonald-Smith, Grace P.; Hayden, Douglas; Mason, Philip; Fagan, Shawn; Yu, Yong-Ming; Cobb, J. Perren; Remick, Daniel G.; Mannick, John A.; Lederer, James A.; Gamelli, Richard L.; Silver, Geoffrey M.; West, Michael A.; Shapiro, Michael B.; Smith, Richard; Camp, David G.; Qian, Weijun; Tibshirani, Rob; Lowry, Stephen; Calvano, Steven; Chaudry, Irshad; Cohen, Mitchell; Moore, Ernest E.; Johnson, Jeffrey; Baker, Henry V.; Efron, Philip A.; Balis, Ulysses G. J.; Billiar, Timothy R.; Ochoa, Juan B.; Sperry, Jason L.; Miller-Graziano, Carol L.; De, Asit K.; Bankey, Paul E.; Herndon, David N.; Finnerty, Celeste C.; Jeschke, Marc G.; Minei, Joseph P.; Arnoldo, Brett D.; Hunt, John L.; Horton, Jureta; Cobb, J. Perren; Brownstein, Bernard; Freeman, Bradley; Nathens, Avery B.; Cuschieri, Joseph; Gibran, Nicole; Klein, Matthew; O'Keefe, Grant

    2011-01-01

    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. PMID:21317363

  9. 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.

  10. 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.

  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. Chromosomal clustering of a human transcriptome reveals regulatory background

    Directory of Open Access Journals (Sweden)

    Purmann Antje

    2005-09-01

    Full Text Available Abstract Background There has been much evidence recently for a link between transcriptional regulation and chromosomal gene order, but the relationship between genomic organization, regulation and gene function in higher eukaryotes remains to be precisely defined. Results Here, we present evidence for organization of a large proportion of a human transcriptome into gene clusters throughout the genome, which are partly regulated by the same transcription factors, share biological functions and are characterized by non-housekeeping genes. This analysis was based on the cardiac transcriptome identified by our genome-wide array analysis of 55 human heart samples. We found 37% of these genes to be arranged mainly in adjacent pairs or triplets. A significant number of pairs of adjacent genes are putatively regulated by common transcription factors (p = 0.02. Furthermore, these gene pairs share a significant number of GO functional classification terms. We show that the human cardiac transcriptome is organized into many small clusters across the whole genome, rather than being concentrated in a few larger clusters. Conclusion Our findings suggest that genes expressed in concert are organized in a linear arrangement for coordinated regulation. Determining the relationship between gene arrangement, regulation and nuclear organization as well as gene function will have broad biological implications.

  15. Comparative transcriptomic analysis of streptococcus pseudopneumoniae with viridans group streptococci

    Directory of Open Access Journals (Sweden)

    Park Hee

    2012-07-01

    Full Text Available Abstract Background Streptococcus pseudopneumoniae, is a novel member of the genus Streptococcus, falling close to related members like S. pneumoniae, S. mitis, and S. oralis. Its recent appearance has shed light on streptococcal infections, which has been unclear till recently. In this study, the transcriptome of S. pseudopneumoniae CCUG 49455T was analyzed using the S. pneumoniae R6 microarray platform and compared with those of S. pneumoniae KCTC 5080T, S. mitis KCTC 3556T, and S. oralis KCTC 13048T strains. Results Comparative transcriptome analysis revealed the extent of genetic relatedness among the species, and implies that S. pseudopneumoniae is the most closely related to S. pneumoniae. A total of 489, 444 and 470 genes were upregulated while 347, 484 and 443 were downregulated relative to S. pneumoniae in S. pseudopneumoniae, S. oralis and S. mitis respectively. Important findings were the up-regulation of TCS (two component systems and transposase which were found to be specific to S. pseudopneumoniae. Conclusions This study provides insight to the current understanding of the genomic content of S. pseudopneumoniae. The comparative transcriptome analysis showed hierarchical clustering of expression data of S. pseudopneumoniae with S. pneumoniae and S. mitis with S. oralis. This proves that transcriptional profiling can facilitate in elucidating the genetic distance between closely related strains.

  16. 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. PMID:26981408

  17. Transcriptomic landscape of prophase I sunflower male meiocytes

    Directory of Open Access Journals (Sweden)

    Nathalia M.V. Flórez-Zapata

    2014-06-01

    Full Text Available Meiosis is a form of specialized cell division that generates gametes, allowing recombination of alleles and halving the chromosome number. Arabidopsis and maize are the plant models that have been most extensively studied to determine the genes involved in meiosis. Here we present an RNA-seq study in which gene expression in male meiocytes isolated during prophase I was compared to that in somatic tissues of the sunflower HA89 line. We sampled more than 490 million gene tags from these libraries, assembled them de novo into a sunflower transcriptome. We obtained expression data for 36,304 sunflower genes, of which 19,574 (54% were differentially expressed between meiocytes and somatic tissue. We also determined the functional categories and metabolic pathways that are differentially expressed in these libraries. As expected, we found large differences between the meiotic and somatic transcriptomes, which is in accordance with previous studies in Arabidopsis and maize. Furthermore, most of the previously implicated meiotic genes were abundantly and differentially expressed in meiocytes and a large repertoire of transcription factors and genes related to silencing are expressed in the sunflower meiocytes. We detected transcription factors which appear to be exclusively expressed in meiocytes. Our results allow for a better understanding of the conservation and differences in the meiotic transcriptome of plants.

  18. 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.

  19. De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle.

    Science.gov (United States)

    Jo, Yeonhwa; Chu, Hyosub; Cho, Jin Kyong; Choi, Hoseong; Lian, Sen; Cho, Won Kyong

    2015-12-01

    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. PMID:26697395

  20. Transcriptome Analysis of Spartina pectinata in Response to Freezing Stress.

    Science.gov (United States)

    Nah, Gyoungju; Lee, Moonsub; Kim, Do-Soon; Rayburn, A Lane; Voigt, Thomas; Lee, D K

    2016-01-01

    Prairie cordgrass (Spartina pectinata), a perennial C4 grass native to the North American prairie, has several distinctive characteristics that potentially make it a model crop for production in stressful environments. However, little is known about the transcriptome dynamics of prairie cordgrass despite its unique freezing stress tolerance. Therefore, the purpose of this work was to explore the transcriptome dynamics of prairie cordgrass in response to freezing stress at -5°C for 5 min and 30 min. We used a RNA-sequencing method to assemble the S. pectinata leaf transcriptome and performed gene-expression profiling of the transcripts under freezing treatment. Six differentially expressed gene (DEG) groups were categorized from the profiling. In addition, two major consecutive orders of gene expression were observed in response to freezing; the first being the acute up-regulation of genes involved in plasma membrane modification, calcium-mediated signaling, proteasome-related proteins, and transcription regulators (e.g., MYB and WRKY). The follow-up and second response was of genes involved in encoding the putative anti-freezing protein and the previously known DNA and cell-damage-repair proteins. Moreover, we identified the genes involved in epigenetic regulation and circadian-clock expression. Our results indicate that freezing response in S. pectinata reflects dynamic changes in rapid-time duration, as well as in metabolic, transcriptional, post-translational, and epigenetic regulation. PMID:27032112

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Shedding light on an extremophile lifestyle through transcriptomics.

    Science.gov (United States)

    Dassanayake, M; Haas, J S; Bohnert, H J; Cheeseman, J M

    2009-08-01

    The tropical intertidal ecosystem is defined by trees - mangroves - which are adapted to an extreme and extremely variable environment. The genetic basis underlying these adaptations is, however, virtually unknown. Based on advances in pyrosequencing, we present here the first transcriptome analysis for plants for which no prior genomic information was available. We selected the mangroves Rhizophora mangle (Rhizophoraceae) and Heritiera littoralis (Malvaceae) as ecologically important extremophiles employing markedly different physiological and life-history strategies for survival and dominance in this extreme environment. For maximal representation of conditional transcripts, mRNA was obtained from a variety of developmental stages, tissues types, and habitats. For each species, a normalized cDNA library of pooled mRNAs was analysed using GSFLX pyrosequencing. A total of 537,635 sequences were assembled de novo and annotated as > 13,000 distinct gene models for each species. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology annotations highlighted remarkable similarities in the mangrove transcriptome profiles, which differed substantially from the model plants Arabidopsis and Populus. Similarities in the two species suggest a unique mangrove lifestyle overarching the effects of transcriptome size, habitat, tissue type, developmental stage, and biogeographic and phylogenetic differences between them. PMID:19549131

  7. Low methane (CH4) emissions downstream of a monomictic subtropical hydroelectric reservoir (Nam Theun 2, Lao PDR)

    Science.gov (United States)

    Deshmukh, Chandrashekhar; Guérin, Frédéric; Labat, David; Pighini, Sylvie; Vongkhamsao, Axay; Guédant, Pierre; Rode, Wanidaporn; Godon, Arnaud; Chanudet, Vincent; Descloux, Stéphane; Serça, Dominique

    2016-03-01

    Methane (CH4) emissions from hydroelectric reservoirs could represent a significant fraction of global CH4 emissions from inland waters and wetlands. Although CH4 emissions downstream of hydroelectric reservoirs are known to be potentially significant, these emissions are poorly documented in recent studies. We report the first quantification of emissions downstream of a subtropical monomictic reservoir. The Nam Theun 2 Reservoir (NT2R), located in the Lao People's Democratic Republic, was flooded in 2008 and commissioned in April 2010. This reservoir is a trans-basin diversion reservoir which releases water into two downstream streams: the Nam Theun River below the dam and an artificial channel downstream of the powerhouse and a regulating pond that diverts the water from the Nam Theun watershed to the Xe Bangfai watershed. We quantified downstream emissions during the first 4 years after impoundment (2009-2012) on the basis of a high temporal (weekly to fortnightly) and spatial (23 stations) resolution of the monitoring of CH4 concentration. Before the commissioning of NT2R, downstream emissions were dominated by a very significant degassing at the dam site resulting from the occasional spillway discharge for controlling the water level in the reservoir. After the commissioning, downstream emissions were dominated by degassing which occurred mostly below the powerhouse. Overall, downstream emissions decreased from 10 GgCH4 yr-1 after the commissioning to 2 GgCH4 yr-1 4 years after impoundment. The downstream emissions contributed only 10 to 30 % of total CH4 emissions from the reservoir during the study. Most of the downstream emissions (80 %) occurred within 2-4 months during the transition between the warm dry season (WD) and the warm wet season (WW) when the CH4 concentration in hypolimnic water is maximum (up to 1000 µmol L-1) and downstream emissions are negligible for the rest of the year. Emissions downstream of NT2R are also lower than expected because

  8. European high-impact weather caused by the downstream response to the extratropical transition of North Atlantic Hurricane Katia (2011)

    Science.gov (United States)

    Blumer, Sandro R.; Grams, Christian M.

    2016-04-01

    Tropical cyclones undergoing extratropical transition (ET) are thought to cause high-impact weather (HIW) close to the transitioning tropical cyclone and in remote regions. However, no study so far clearly attributed European HIW to the downstream impact of North Atlantic ET. When Hurricane Katia underwent ET in September 2011, severe thunderstorms occurred downstream in Central Europe. We quantify the role of Katia in the European HIW, using numerical sensitivity experiments. Results show that Katia was crucial for the evolution of a narrow downstream trough. Large-scale forcing for ascent ahead of this trough triggered deep convection. In the absence of ET, no trough was present over Europe and no HIW occurred. This study is the first unambiguous documentation that European HIW is caused by the downstream impact of North Atlantic ET and would not occur otherwise. It likewise corroborates the crucial role of ET in altering the large-scale midlatitude flow in downstream regions.

  9. 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

  10. 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

  11. 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

  12. Transcriptomic signatures of transfer cells in early developing nematode feeding cells of Arabidopsis focused on auxin and ethylene signalling.

    Directory of Open Access Journals (Sweden)

    Javier eCabrera

    2014-03-01

    Full Text Available Phyto-endoparasitic nematodes induce specialized feeding cells (NFCs in their hosts, termed syncytia and giant cells (GCs for cyst and root-knot nematodes, respectively. They differ in their ontogeny and global transcriptional signatures, but both develop cell wall ingrowths to facilitate high rates of apoplastic/symplastic solute exchange showing transfer cell (TC characteristics. Regulatory signals for TC differentiation are not still well known. The two-component signalling system (2CS and reactive oxygen species are proposed as inductors of TC identity, while, 2CSs-related genes are not major contributors to differential gene expression in early developing NFCs. Additionally, transcriptomic and functional studies have assigned a major role to auxin and ethylene as regulatory signals on early developing TCs. Genes encoding proteins with similar functions expressed in both early developing NFCs and typical TCs are putatively involved in upstream or downstream responses mediated by auxin and ethylene. Yet, no function directly associated to the TCs identity of NFCs, such as the formation of cell wall ingrowths is described for most of them. Thus we reviewed similarities between transcriptional changes observed during the early stages of NFCs formation and those described during differentiation of TCs to hypothesize about putative signals leading to TC-like differentiation of NFCs with particular emphasis on auxin an ethylene.

  13. Dissecting the pre-placodal transcriptome to reveal presumptive direct targets of Six1 and Eya1 in cranial placodes

    Science.gov (United States)

    Riddiford, Nick; Schlosser, Gerhard

    2016-01-01

    The pre-placodal ectoderm, marked by the expression of the transcription factor Six1 and its co-activator Eya1, develops into placodes and ultimately into many cranial sensory organs and ganglia. Using RNA-Seq in Xenopus laevis we screened for presumptive direct placodal target genes of Six1 and Eya1 by overexpressing hormone-inducible constructs of Six1 and Eya1 in pre-placodal explants, and blocking protein synthesis before hormone-inducing nuclear translocation of Six1 or Eya1. Comparing the transcriptome of explants with non-induced controls, we identified hundreds of novel Six1/Eya1 target genes with potentially important roles for placode development. Loss-of-function studies confirmed that target genes encoding known transcriptional regulators of progenitor fates (e.g. Sox2, Hes8) and neuronal/sensory differentiation (e.g. Ngn1, Atoh1, Pou4f1, Gfi1) require Six1 and Eya1 for their placodal expression. Our findings provide insights into the gene regulatory network regulating placodal neurogenesis downstream of Six1 and Eya1 suggesting new avenues of research into placode development and disease. DOI: http://dx.doi.org/10.7554/eLife.17666.001 PMID:27576864

  14. 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.

  15. Analysis of receptor tyrosine kinases (RTKs) and downstream pathways in chordomas†

    Science.gov (United States)

    Tamborini, Elena; Virdis, Emanuela; Negri, Tiziana; Orsenigo, Marta; Brich, Silvia; Conca, Elena; Gronchi, Alessandro; Stacchiotti, Silvia; Manenti, Giacomo; Casali, Paolo G.; Pierotti, Marco A.; Pilotti, Silvana

    2010-01-01

    We have previously demonstrated that chordomas express activated platelet-derived growth factor receptor (PDGFRB) and that treatment with imatinib, which is capable of switching off the activation of various receptor tyrosine kinases (RTKs) including PDGFRB, benefits a number of patients. The aim of this study was to identify the possible presence of other activated RTKs and their downstream signaling effectors. Cryopreserved material from 22 naïve sporadic chordomas was investigated for the presence of activated RTKs and their cognate ligands and downstream signaling effectors by means of human phospho-RTK antibody arrays, Western blotting, and molecular analysis; immunohistochemistry and fluorescence in situ hybridization were used to analyze the corresponding formalin-fixed and paraffin-embedded samples. We detected activated PDGFRB, FLT3, and colony stimulating factor 1 receptor (CSF1R) of the PDGFR family and highly phosphorylated EGFR, HER2/neu, and (to a lesser extent) HER4 of the EGFR family. The detection of PDGFRB/PDGFB confirmed our previous data. The presence of activated EGFR was paralleled by the finding of high levels of epidermal growth factor (EGF) and transforming growth factor α (TGFα) and PDGFB co-expression and PDGFRB co-immunoprecipitation. Of the downstream effectors, the PI3K/AKT and RAS/MAPK pathways were both activated, thus leading to the phosphorylation of mammalian target of rapamycin (mTOR) and 4E-BP1 among the regulators involved in translational control. Taken together, our results (i) provide a rationale for tailored treatments targeting upstream activated receptors, including the PDGFR and EGFR families; (ii) support the idea that a combination of upstream antagonists and mTOR inhibitors enhances the control of tumor growth; and (iii) indicate that the 4E-BP1/eIF4E pathway is a major regulator of protein synthesis in chordoma. PMID:20164240

  16. 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.

  17. 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.

  18. 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.

  19. Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis

    DEFF Research Database (Denmark)

    Nicolas, Pierre; Mäder, Ulrike; Dervyn, Etienne;

    2012-01-01

    Bacteria adapt to environmental stimuli by adjusting their transcriptomes in a complex manner, the full potential of which has yet to be established for any individual bacterial species. Here, we report the transcriptomes of Bacillus subtilis exposed to a wide range of environmental and nutrition...

  20. Conditions at the downstream boundary for simulations of viscous incompressible flow

    Science.gov (United States)

    Hagstrom, Thomas

    1990-01-01

    The proper specification of boundary conditions at artificial boundaries for the simulation of time-dependent fluid flows has long been a matter of controversy. A general theory of asymptotic boundary conditions for dissipative waves is applied to the design of simple, accurate conditions at downstream boundary for incompressible flows. For Reynolds numbers far enough below the critical value for linear stability, a scaling is introduced which greatly simplifies the construction of the asymptotic conditions. Numerical experiments with the nonlinear dynamics of vortical disturbances to plane Poiseuille flow are presented which illustrate the accuracy of our approach. The consequences of directly applying the scalings to the equations are also considered.

  1. Downstream dilution of a lahar: transition from debris flow to hyperconcentrated streamflow.

    Science.gov (United States)

    Pierson, T.C.; Scott, K.M.

    1985-01-01

    Nearly instantaneous melting of snow and ice by the March 19, 1982, eruption of Mount St. Helens, released a 4 X 106 m3 flood of water from the crater that was converted to a lahar (volcanic debris flow) through erosion and incorporation of sediment by the time it reached the base of the volcano. Over the next 81 km that it traveled down the Toutle River, the flood wave was progressively diluted through several mechanisms. A transformation from debris flow to hyperconcentrated streamflow began to occur about 27 km downstream from the crater, when the total sediment concentration had decreased to about 78% by weight (57% by volume).-from Authors

  2. Groundwater contamination downstream of a contaminant penetration site. II. Horizontal penetration of the contaminant plume

    Science.gov (United States)

    Rubin, H.; Buddemeier, R.W.

    2002-01-01

    Part I of this study (Rubin, H.; Buddemeier, R.W. Groundwater Contamination Downstream of a Contaminant Penetration Site Part 1: Extension-Expansion of the Contaminant Plume. J. of Environmental Science and Health Part A (in press).) addressed cases, in which a comparatively thin contaminated region represented by boundary layers (BLs) developed within the freshwater aquifer close to contaminant penetration site. However, at some distance downstream from the penetration site, the top of the contaminant plume reaches the top or bottom of the aquifer. This is the location of the "attachment point," which comprises the entrance cross section of the domain evaluated by the present part of the study. It is shown that downstream from the entrance cross section, a set of two BLs develop in the aquifer, termed inner and outer BLs. It is assumed that the evaluated domain, in which the contaminant distribution gradually becomes uniform, can be divided into two sections, designated: (a) the restructuring section, and (b) the establishment section. In the restructuring section, the vertical concentration gradient leads to expansion of the inner BL at the expense of the outer BL, and there is almost no transfer of contaminant mass between the two layers. In the establishment section, each of the BLs occupies half of the aquifer thickness, and the vertical concentration gradient leads to transfer of contaminant mass from the inner to the outer BL. By use of BL approximations, changes of salinity distribution in the aquifer are calculated and evaluated. The establishment section ends at the uniformity point, downstream from which the contaminant concentration profile is practically uniform. The length of the restructuring section, as well as that of the establishment section, is approximately proportional to the aquifer thickness squared, and is inversely proportional to the transverse dispersivity. The study provides a convenient set of definitions and terminology that are

  3. An all-season trap for downstream-migrating fish and other aquatic organisms

    Science.gov (United States)

    McLain, Alberton; Manion, Patrick J.

    1967-01-01

    AN INVESTIGATION OF THE LARVAL STAGES OF THE SEA LAMPREY (Petromyzon marinus), which started in 1960, required a trap that could capture lamprey larvae moving downstream, and that would operate efficiently throughout the year. Sub zero temperatures in the winter and flooding during the spring were the most critical operational problems. Part of the trap was based on the principles of an inclined-plane trap described by Wolf (1951), but the design also incorporated features to prevent ice formation during the winter and to and to strain high flows during the spring runoff.

  4. 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

  5. Brf1 posttranscriptionally regulates pluripotency and differentiation responses downstream of Erk MAP kinase

    OpenAIRE

    Tan, Frederick E.; Elowitz, Michael B.

    2014-01-01

    AU-rich element mRNA-binding proteins (AUBPs) are key regulators of development, but how they are controlled and what functional roles they play depends on cellular context. Here, we show that Brf1 (zfp36l1), an AUBP from the Zfp36 protein family, operates downstream of FGF/Erk MAP kinase signaling to regulate pluripotency and cell fate decision making in mouse embryonic stem cells (mESCs). FGF/Erk MAP kinase signaling up-regulates Brf1, which disrupts the expression of core pluripotency-asso...

  6. Chemical effects and the impact to insulation debris filter cakes at ECCS upstream and downstream components

    International Nuclear Information System (INIS)

    Investigations regarding release, solution, transportation and deposit of corrosion products become important to reactor safety research for PWR, when considering the long-term behaviour of emergency core cooling systems (ECCS) during loss of coolant accidents (LOCA). The knowledge of corrosion processes in boric acid is necessary to evaluate the impact on insulation debris filter cakes in upstream (sump strainers) and downstream (reactor core) components and their influence on head loss and heat removal out of the core. Generic complex experiments determined the quantity of flow-induced, released corrosion products and their influences on head losses at filter cakes. (author)

  7. 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.

  8. Event-based approach of downstream Rhône River flood regimes variability since 1982

    Science.gov (United States)

    Hénaff, Quentin; Arnaud-Fassetta, Gilles; Beltrando, Gérard

    2015-04-01

    Numerous downstream Rhône River floods have been recorded as catastrophic by French inter-ministerial order since the creation of natural disaster state recognition in 1982. Downstream Rhône River flood regimes, influenced by Mediterranean climate, are fundamentally affected by the spatio-temporal variability of rainfall events, especially in case of widespread flooding. Event-based analysis of cumulative rainfall data should allow us to characterise downstream Rhône River flood regimes variability by applying data mining methods to a spatio-temporal hydro-meteorological database. The first objective of this study is to determine if extreme rainfall events could be considered as geographical events, in other words if rainfall distribution is related to spatial processes. The proposed method is based on the measure of rainfall distribution spatial auto-correlation through the calculation of (i) Global Moran's index and (ii) the significance evaluation of that index with a z-score statistical test and its associated p-value. Secondly, cumulative rainfall data are integrated into a geo-event two-dimensional matrix: (i) cumulative rainfall per sub-catchment in row (spatial base unit) and (ii) cumulative rainfall per catastrophic event in column (temporal base unit). This matrix was co-clustered which allows simultaneous clustering of the rows (sub-catchment) and columns (events) by hierarchical clustering on principal components (HCPC) using Ward's method applying Euclidean Distance as similarity measure. Computing the Global Moran's index demonstrated a spatial aggregation tendency of rainfall distribution and the associated statistical test (z-core and p-value) noted the improbability of statistical evidence of random spatial pattern. Spatial variability of rainfall distribution is the result of two factors: rainfall event structure and rainfall event scale. The co-clustering geo-event matrix provided two co-clustering maps on two different cumulative rainfall

  9. 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).

  10. Corrosion mechanisms downstream the nuclear cycle: from processing-recycling to transmutation

    International Nuclear Information System (INIS)

    The author gives a detailed overview of his scientific and research activities in the field of material behaviour in environments met during the downstream part of the nuclear cycle. In the first part, he presents his works on material corrosion in concentrated and high temperature nitric acid, and more particularly on the phenomenon which governs this corrosion: the nitric acid reduction mechanism. In the second part, he reports researches performed within the frame of hybrid reactor development for the processing of future fuels. In both parts, he also discusses the perspectives for new researches and developments

  11. Reptilian-transcriptome v1.0, a glimpse in the brain transcriptome of five divergent Sauropsida lineages and the phylogenetic position of turtles

    OpenAIRE

    Tzika Athanasia C; Helaers Raphaël; Schramm Gerrit; Milinkovitch Michel C

    2011-01-01

    Abstract Background Reptiles are largely under-represented in comparative genomics despite the fact that they are substantially more diverse in many respects than mammals. Given the high divergence of reptiles from classical model species, next-generation sequencing of their transcriptomes is an approach of choice for gene identification and annotation. Results Here, we use 454 technology to sequence the brain transcriptome of four divergent reptilian and one reference avian species: the Nile...

  12. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata

    2016-01-01

    A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea. PMID:27348121

  13. 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

  14. 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.

  15. Transcriptomic analysis of murine embryos lacking endogenous retinoic acid signaling.

    Directory of Open Access Journals (Sweden)

    Marie Paschaki

    Full Text Available Retinoic acid (RA, an active derivative of the liposoluble vitamin A (retinol, acts as an important signaling molecule during embryonic development, regulating phenomenons as diverse as anterior-posterior axial patterning, forebrain and optic vesicle development, specification of hindbrain rhombomeres, pharyngeal arches and second heart field, somitogenesis, and differentiation of spinal cord neurons. This small molecule directly triggers gene activation by binding to nuclear receptors (RARs, switching them from potential repressors to transcriptional activators. The repertoire of RA-regulated genes in embryonic tissues is poorly characterized. We performed a comparative analysis of the transcriptomes of murine wild-type and Retinaldehyde Dehydrogenase 2 null-mutant (Raldh2 (-/- embryos - unable to synthesize RA from maternally-derived retinol - using Affymetrix DNA microarrays. Transcriptomic changes were analyzed in two embryonic regions: anterior tissues including forebrain and optic vesicle, and posterior (trunk tissues, at early stages preceding the appearance of overt phenotypic abnormalities. Several genes expected to be downregulated under RA deficiency appeared in the transcriptome data (e.g. Emx2, Foxg1 anteriorly, Cdx1, Hoxa1, Rarb posteriorly, whereas reverse-transcriptase-PCR and in situ hybridization performed for additional selected genes validated the changes identified through microarray analysis. Altogether, the affected genes belonged to numerous molecular pathways and cellular/organismal functions, demonstrating the pleiotropic nature of RA-dependent events. In both tissue samples, genes upregulated were more numerous than those downregulated, probably due to feedback regulatory loops. Bioinformatic analyses highlighted groups (clusters of genes displaying similar behaviors in mutant tissues, and biological functions most significantly affected (e.g. mTOR, VEGF, ILK signaling in forebrain tissues; pyrimidine and purine

  16. 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

  17. Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.)

    Science.gov (United States)

    Kant, Chandra; Pradhan, Seema; Bhatia, Sabhyata

    2016-01-01

    A hallmark trait of chickpea (Cicer arietinum L.), like other legumes, is the capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri. However, the complexity of molecular networks associated with the dynamics of nodule development in chickpea need to be analyzed in depth. Hence, in order to gain insights into the chickpea nodule development, the transcriptomes of nodules at early, middle and late stages of development were sequenced using the Roche 454 platform. This generated 490.84 Mb sequence data comprising 1,360,251 reads which were assembled into 83,405 unigenes. Transcripts were annotated using Gene Ontology (GO), Cluster of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways analysis. Differential expression analysis revealed that a total of 3760 transcripts were differentially expressed in at least one of three stages, whereas 935, 117 and 2707 transcripts were found to be differentially expressed in the early, middle and late stages of nodule development respectively. MapMan analysis revealed enrichment of metabolic pathways such as transport, protein synthesis, signaling and carbohydrate metabolism during root nodulation. Transcription factors were predicted and analyzed for their differential expression during nodule development. Putative nodule specific transcripts were identified and enriched for GO categories using BiNGO which revealed many categories to be enriched during nodule development, including transcription regulators and transporters. Further, the assembled transcriptome was also used to mine for genic SSR markers. In conclusion, this study will help in enriching the transcriptomic resources implicated in understanding of root nodulation events in chickpea. PMID:27348121

  18. Transcriptome analysis of the oriental fruit fly (Bactrocera dorsalis.

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    Guang-Mao Shen

    Full Text Available BACKGROUND: The oriental fruit fly, Bactrocera dorsalis (Hendel, is one of the most economically important pests in the world, causing serious damage to fruit production. However, lack of genetic information on this organism is an obstacle to understanding the mechanisms behind its development and its ability to resist insecticides. Analysis of the B. dorsalis transcriptome and its expression profile data is essential to extending the genetic information resources on this species, providing a shortcut that will support studies on B. dorsalis. METHODOLOGY/PRINCIPAL FINDINGS: We performed de novo assembly of a transcriptome using short read sequencing technology (Illumina. The results generated 484,628 contigs, 70,640 scaffolds, and 49,804 unigenes. Of those unigenes, 27,455 (55.13% matched known proteins in the NCBI database, as determined by BLAST search. Clusters of orthologous groups (COG, gene orthology (GO, and the Kyoto Encyclopedia of Genes and Genomes (KEGG annotations were performed to better understand the functions of these unigenes. Genes related to insecticide resistance were analyzed in additional detail. Digital gene expression (DGE libraries showed differences in gene expression profiles at different developmental stages (eggs, third-instar larvae, pupae, and adults. To confirm the DGE results, the expression profiles of six randomly selected genes were analyzed. CONCLUSION/SIGNIFICANCE: This transcriptome greatly improves our genetic understanding of B. dorsalis and makes a huge number of gene sequences available for further study, including both genes of known importance and genes of unknown function. The DGE data provide comprehensive insight into gene expression profiles at different developmental stages. This facilitates the study of the role of each gene in the developmental process and in insecticide resistance.

  19. Microarray-based sketches of the HERV transcriptome landscape.

    Science.gov (United States)

    Pérot, Philippe; Mugnier, Nathalie; Montgiraud, Cécile; Gimenez, Juliette; Jaillard, Magali; Bonnaud, Bertrand; Mallet, François

    2012-01-01

    Human endogenous retroviruses (HERVs) are spread throughout the genome and their long terminal repeats (LTRs) constitute a wide collection of putative regulatory sequences. Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. Herein, we have introduced a generic method aiming to optimally characterize individual loci associated with 25-mer probes by minimizing cross-hybridization risks. We therefore set up a microarray dedicated to a collection of 5,573 HERVs that can reasonably be assigned to a unique genomic position. We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment showed that almost one third of the HERV repertoire is indeed transcribed. The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. The probeset definition within the U3 and U5 regions was used to assign a function to some LTRs (i.e. promoter or polyA) and revealed that (i) autonomous active LTRs are broadly subjected to operational determinism (ii) the cellular gene density is substantially higher in the surrounding environment of active LTRs compared to silent LTRs and (iii) the configuration of neighboring cellular genes differs between active and silent LTRs, showing an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects.

  20. Microarray-based sketches of the HERV transcriptome landscape.

    Directory of Open Access Journals (Sweden)

    Philippe Pérot

    Full Text Available Human endogenous retroviruses (HERVs are spread throughout the genome and their long terminal repeats (LTRs constitute a wide collection of putative regulatory sequences. Phylogenetic similarities and the profusion of integration sites, two inherent characteristics of transposable elements, make it difficult to study individual locus expression in a large-scale approach, and historically apart from some placental and testis-regulated elements, it was generally accepted that HERVs are silent due to epigenetic control. Herein, we have introduced a generic method aiming to optimally characterize individual loci associated with 25-mer probes by minimizing cross-hybridization risks. We therefore set up a microarray dedicated to a collection of 5,573 HERVs that can reasonably be assigned to a unique genomic position. We obtained a first view of the HERV transcriptome by using a composite panel of 40 normal and 39 tumor samples. The experiment showed that almost one third of the HERV repertoire is indeed transcribed. The HERV transcriptome follows tropism rules, is sensitive to the state of differentiation and, unexpectedly, seems not to correlate with the age of the HERV families. The probeset definition within the U3 and U5 regions was used to assign a function to some LTRs (i.e. promoter or polyA and revealed that (i autonomous active LTRs are broadly subjected to operational determinism (ii the cellular gene density is substantially higher in the surrounding environment of active LTRs compared to silent LTRs and (iii the configuration of neighboring cellular genes differs between active and silent LTRs, showing an approximately 8 kb zone upstream of promoter LTRs characterized by a drastic reduction in sense cellular genes. These gathered observations are discussed in terms of virus/host adaptive strategies, and together with the methods and tools developed for this purpose, this work paves the way for further HERV transcriptome projects.