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Sample records for brassinosteroid upregulated1 encoding

  1. A semidwarf phenotype of barley uzu results from a nucleotide substitution in the gene encoding a putative brassinosteroid receptor.

    Science.gov (United States)

    Chono, Makiko; Honda, Ichiro; Zeniya, Haruko; Yoneyama, Koichi; Saisho, Daisuke; Takeda, Kazuyoshi; Takatsuto, Suguru; Hoshino, Tsuguhiro; Watanabe, Yoshiaki

    2003-11-01

    Brassinosteroids (BRs) play important roles throughout plant growth and development. Despite the importance of clarifying the mechanism of BR-related growth regulation in cereal crops, BR-related cereal mutants have been identified only in rice (Oryza sativa). We previously found that semidwarf barley (Hordeum vulgare) accessions carrying the "uzu" gene, called "uzu" barley in Japan, are non-responding for brassinolide (BL). We then performed chemical and molecular analyses to clarify the mechanisms of uzu dwarfism using isogenic line pairs of uzu gene. The response of the uzu line to BL was significantly lower than that of its corresponding normal line. Measurement of BRs showed that the uzu line accumulates BRs, similar to known BR-insensitive mutants. The marker synteny of rice and barley chromosomes suggests that the uzu gene may be homologous to rice D61, a rice homolog of Arabidopsis BR-insensitive 1 (BRI1), encoding a BR-receptor protein. A barley homolog of BRI1, HvBRI1, was isolated by using degenerate primers. A comparison of HvBRI1 sequences in uzu and normal barley varieties showed that the uzu phenotype is correlated with a single nucleotide substitution. This substitution results in an amino acid change at a highly conserved residue in the kinase domain of the BR-receptor protein. These results may indicate that uzu dwarfism is caused by the missense mutation in HvBRI1. The uzu gene is being introduced into all hull-less barley cultivars in Japan as an effective dwarf gene for practical use, and this is the first report about an agronomically important mutation related to BRs.

  2. nana plant2 Encodes a Maize Ortholog of the Arabidopsis Brassinosteroid Biosynthesis Gene DWARF1, Identifying Developmental Interactions between Brassinosteroids and Gibberellins.

    Science.gov (United States)

    Best, Norman B; Hartwig, Thomas; Budka, Josh; Fujioka, Shozo; Johal, Gurmukh; Schulz, Burkhard; Dilkes, Brian P

    2016-08-01

    A small number of phytohormones dictate the pattern of plant form affecting fitness via reproductive architecture and the plant's ability to forage for light, water, and nutrients. Individual phytohormone contributions to plant architecture have been studied extensively, often following a single component of plant architecture, such as plant height or branching. Both brassinosteroid (BR) and gibberellin (GA) affect plant height, branching, and sexual organ development in maize (Zea mays). We identified the molecular basis of the nana plant2 (na2) phenotype as a loss-of-function mutation in one of the two maize paralogs of the Arabidopsis (Arabidopsis thaliana) BR biosynthetic gene DWARF1 (DWF1). These mutants accumulate the DWF1 substrate 24-methylenecholesterol and exhibit decreased levels of downstream BR metabolites. We utilized this mutant and known GA biosynthetic mutants to investigate the genetic interactions between BR and GA. Double mutants exhibited additivity for some phenotypes and epistasis for others with no unifying pattern, indicating that BR and GA interact to affect development but in a context-dependent manner. Similar results were observed in double mutant analyses using additional BR and GA biosynthetic mutant loci. Thus, the BR and GA interactions were neither locus nor allele specific. Exogenous application of GA3 to na2 and d5, a GA biosynthetic mutant, also resulted in a diverse pattern of growth responses, including BR-dependent GA responses. These findings demonstrate that BR and GA do not interact via a single inclusive pathway in maize but rather suggest that differential signal transduction and downstream responses are affected dependent upon the developmental context.

  3. Brassinosteroid regulated kinases (BRKs) that mediate brassinosteroid signal transduction and uses thereof

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhi-Yong; Tang, Wenqiang

    2013-09-24

    The present invention identifies a novel family of kinases regulated by brassinosteroids, referred to as BRKs (brassinosteroid regulated kinases) or BSKs (brassinosteroid signaling kinases). The present invention provides methods for modulating the response of a plant cell to a brassinosteroid using BRKs.

  4. CYP72B1 Inactivates Brassinosteroid Hormones: An Intersection between Photomorphogenesis and Plant Steroid Signal Transduction1

    Science.gov (United States)

    Turk, Edward M.; Fujioka, Shozo; Seto, Hideharu; Shimada, Yukihisa; Takatsuto, Suguru; Yoshida, Shigeo; Denzel, Megan A.; Torres, Quetzal I.; Neff, Michael M.

    2003-01-01

    Active brassinosteroids, such as brassinolide (BL) and castasterone, are growth promoting plant hormones. An Arabidopsis cytochrome P450 monooxygenase encoded by CYP72B1 has been implicated in brassinosteroid catabolism as well as photomorphogenesis. We expressed CYP72B1 in yeast, coupled with brassinosteroid feeding, and established the biochemical function to be the hydroxylation of BL and castasterone, to give 26-hydroxybrassinolide and 26-hydroxycastasterone, respectively. Brassinosteroid feeding experiments with wild-type Arabidopsis, a CYP72B1 null mutant, and a CYP72B1 overexpression line demonstrated that carbon 26 hydroxylation of active brassinosteroids is an endogenous function of CYP72B1. Seedling growth assays demonstrated that 26-hydroxybrassinolide is an inactive brassinosteroid. Genetic and physiological analysis of the hypocotyl response to exogenous BL and varying intensities of white and monochromatic light suggested that CYP72B1 modulates photomorphogenesis primarily through far-red light and to a lesser extent through blue- and red-light pathways. CYP72B1 transcript accumulation in dark-grown seedlings was organ specific and down-regulated after 1 h of illumination in dim white, red, and blue light, but not far-red light. CYP72B1 translational fusions with the β-glucuronidase reporter gene demonstrated that protein levels increased in the hypocotyl elongation zone when shifted from the dark to far-red light, but not blue or red light. We propose a model in which Arabidopsis seedling development switches from dark-grown development (skotomorphogenesis) to light-grown development (photomorphogenesis) in part by rapid modulation of brassinosteroid sensitivity and levels. CYP72B1 provides an intersection between the light and brassinosteroid pathways mainly by far-red-light-dependent modulation of brassinosteroid levels. PMID:14605216

  5. Acceleration of cutaneous wound healing by brassinosteroids.

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    Esposito, Debora; Rathinasabapathy, Thirumurugan; Schmidt, Barbara; Shakarjian, Michael P; Komarnytsky, Slavko; Raskin, Ilya

    2013-01-01

    Brassinosteroids are plant growth hormones involved in cell growth, division, and differentiation. Their effects in animals are largely unknown, although recent studies showed that the anabolic properties of brassinosteroids are possibly mediated through the phosphoinositide 3-kinase/protein kinase B signaling pathway. Here, we examined biological activity of homobrassinolide (HB) and its synthetic analogues in in vitro proliferation and migration assays in murine fibroblast and primary keratinocyte cell culture. HB stimulated fibroblast proliferation and migration and weakly induced keratinocyte proliferation in vitro. The effects of topical HB administration on progression of wound closure were further tested in the mouse model of cutaneous wound healing. C57BL/6J mice were given a full-thickness dermal wound, and the rate of wound closure was assessed daily for 10 days, with adenosine receptor agonist CGS-21680 as a positive control. Topical application of brassinosteroid significantly reduced wound size and accelerated wound healing in treated animals. mRNA levels of transforming growth factor beta and intercellular adhesion molecule 1 were significantly lower, while tumor necrosis factor alpha was nearly suppressed in the wounds from treated mice. Our data suggest that topical application of brassinosteroids accelerates wound healing by positively modulating inflammatory and reepithelialization phases of the wound repair process, in part by enhancing Akt signaling in the skin at the edges of the wound and enhancing migration of fibroblasts in the wounded area. Targeting this signaling pathway with brassinosteroids may represent a promising approach to the therapy of delayed wound healing.

  6. Hormone profiles in microalgae: gibberellins and brassinosteroids.

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    Stirk, W A; Bálint, P; Tarkowská, D; Novák, O; Strnad, M; Ördög, V; van Staden, J

    2013-09-01

    Endogenous gibberellins and brassinosteroids were quantified in 24 axenic microalgae strains from the Chlorophyceae, Trebouxiophyceae, Ulvophyceae and Charophyceae microalgae strains after 4 days in culture. This is the first report of endogenous gibberellins being successfully detected in microalgae. Between 18 and 20 gibberellins were quantified in all strains with concentrations ranging from 342.7 pg mg(-1) DW in Raphidocelis subcapitata MACC 317-4746.1 pg mg(-)(1) DW in Scotiellopsis terrestris MACC 44. Slower growing strains (S. terrestris MACC 44, Gyoerffyana humicola MACC 334, Nautococcus mamillatus MACC 716 and Chlorococcum ellipsoideum MACC 712) exhibited the highest gibberellin contents while lowest levels of gibberellins were found in faster growing strains (R. subcapitata MACC 317 and Coelastrum excentrica MACC 504). In all strains, the active gibberellin detected in the highest concentration was GA6, the predominant intermediates were GA15 and GA53 and the main biosynthetic end products were GA13 and GA51. Gibberellin profiles were similar in all strains except for the presence/absence of GA12 and GA12ald. To date this is the second report of endogenous brassinosteroids in microalgae. Brassinosteroids were detected in all 24 strains with concentrations ranging from 117.3 pg mg(-)(1) DW in R. subcapitata MACC 317-977.8 pg mg(-)(1) DW in Klebsormidium flaccidum MACC 692. Two brassinosteroids, brassinolide and castasterone were determined in all the strains. Generally, brassinolide occurred in higher concentrations than castasterone.

  7. A cytochrome P450 monooxygenase commonly used for negative selection in transgenic plants causes growth anomalies by disrupting brassinosteroid signaling

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    Manivasagam Sindhu

    2011-04-01

    Full Text Available Abstract Background Cytochrome P450 monooxygenases form a large superfamily of enzymes that catalyze diverse reactions. The P450SU1 gene from the soil bacteria Streptomyces griseolus encodes CYP105A1 which acts on various substrates including sulfonylurea herbicides, vitamin D, coumarins, and based on the work presented here, brassinosteroids. P450SU1 is used as a negative-selection marker in plants because CYP105A1 converts the relatively benign sulfonyl urea pro-herbicide R7402 into a highly phytotoxic product. Consistent with its use for negative selection, transgenic Arabidopsis plants were generated with P450SU1 situated between recognition sequences for FLP recombinase from yeast to select for recombinase-mediated excision. However, unexpected and prominent developmental aberrations resembling those described for mutants defective in brassinosteroid signaling were observed in many of the lines. Results The phenotypes of the most affected lines included severe stunting, leaf curling, darkened leaves characteristic of anthocyanin accumulation, delayed transition to flowering, low pollen and seed yields, and delayed senescence. Phenotype severity correlated with P450SU1 transcript abundance, but not with transcript abundance of other experimental genes, strongly implicating CYP105A1 as responsible for the defects. Germination and seedling growth of transgenic and control lines in the presence and absence of 24-epibrassinolide indicated that CYP105A1 disrupts brassinosteroid signaling, most likely by inactivating brassinosteroids. Conclusions Despite prior use of this gene as a genetic tool, deleterious growth in the absence of R7402 has not been elaborated. We show that this gene can cause aberrant growth by disrupting brassinosteroid signaling and affecting homeostasis.

  8. Proteomic Study of the Brassinosteroid Signalling Network

    Institute of Scientific and Technical Information of China (English)

    Zhiyong Wang

    2012-01-01

    Plant growth is controlled by multiple environmental signals and endogenous hormones.In particular,brassinosteroid (BR) regulates a wide range of developmental processes throughout the life cycle of plants.BR acts through a receptor kinase signalling pathway,and BR signalling crosstalk with many other signalling pathways including light and gibberellin pathways as well as other receptor kinase pathways.My lab uses a combination of genetic,proteomic,and genomic approaches to elucidate not only the BR signaling pathway but also the global organization of the signaling network.We have successfully used proteomics to identify new components of the BR signalling pathway and to elucidated the mechanisms of signal transduction from the BRI1 receptor kinase to the BZR1 transcription factor.We have further uncovered mechanisms of crosstalk between different receptor kinase pathways,and we are dissecting the molecular mechanisms underlying signalling crosstalk and specificity.Our recent proteomic analysis of BR-regulated nuclear proteins has identified a potential link for BR regulation of flowering through RNA splicing and epigenetic mechanisms.I will discuss strategies and potential pitfalls in using proteomics to study signal transduction in plants.

  9. Conjugates of abscisic acid, brassinosteroids, ethylene, gibberellins, and jasmonates.

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    Piotrowska, Alicja; Bajguz, Andrzej

    2011-12-01

    Phytohormones, including auxins, abscisic acid, brassinosteroids, cytokinins, ethylene, gibberellins, and jasmonates, are involved in all aspects of plant growth, and developmental processes as well as environmental responses. However, our understanding of hormonal homeostasis is far from complete. Phytohormone conjugation is considered as a part of the mechanism to control cellular levels of these compounds. Active phytohormones are changed into multiple forms by acylation, esterification or glycosylation, for example. It seems that conjugated compounds could serve as pool of inactive phytohormones that can be converted to active forms by de-conjugation reactions. Some conjugates are thought to be temporary storage forms, from which free active hormones can be released after hydrolysis. It is also believed that conjugation serves functions, such as irreversible inactivation, transport, compartmentalization, and protection against degradation. The nature of abscisic acid, brassinosteroid, ethylene, gibberellin, and jasmonate conjugates is discussed.

  10. Identification of brassinosteroid responsive genes in Arabidopsis by cDNA array

    Institute of Scientific and Technical Information of China (English)

    HU; Yuxin; (

    2001-01-01

    cdc5+ homolog of a higher plant, Arabidopsis thaliana, Proc. Natl. Acad. Sci. USA, 1996, 93: 13371-13376.[15]Javerzat, J. P., Cranston, G., Allshire, R. C., Fission yeast genes which disrupt mitotic chromosome segregation when overexpressed, Nucl. Acids Res., 1996, 24: 4676-4683.[16]Dhaubhadel, S., Chaudhary, S., Dobinson, K. F. et al., Treatment with 24-epibrassinolide, a brassinosteroid, increases the basic thermotolerance of Brassica napus and tomato seedlings, Plant Mol. Biol., 1999, 40: 333-342.[17]Beato, M., Herrlich, P., Schytz, G., Steroid hormone receptors: many actors in search of a plot, Cell, 1995, 83: 153-156.[18]Chou, I. T., Gasser, C. S., Characterization of the cyclophilin gene family of Arabidopsis thaliana and physiologenetic analysis of known cyclophilin proteins, Plant Mol. Biol., 1997, 35: 873-892.[19]Sykes, K., Gething, M. J., Sambrook, J., Proline isomerases function during heat shock, Proc. Natl. Acad. Sci. USA, 1993, 90: 5853-5857.[20]Marivet, J., Frendo, P., Burkard, G., DNA sequence analysis of a cyclophilin gene from maize: developmental expression and regulation by salicylic acid, Mol. Gen. Genet., 1995, 247: 222-228.[21]Kagaya, Y., Ohmiya, K., Hattori, T., RAV1, a novel DNA-binding protein, binds to bipartite recognition sequence through two distinct DNA-binding domains uniquely found in higher plant, Nucleic Acids Res., 1999, 27: 470-478.[22]Neff, M. M., Nguyen, S. M., Malancharuvil, E. J. et al., BAS1: a gene regulating brassinosteroid levels and light responsiveness in Arabidopsis, Proc. Natl. Acad. Sci. USA, 1999, 96: 15316-15323.[23]Chory, J., Nagpal, P., Peto, C. A., Phenotypic and genetic analysis of det2, a new mutant that affects light-regulated seedling development in Arabidopsis, Plant Cell, 1991, 3: 445-459.[24]Papenbrock, J., Grafe, S., Kruse, E. et al., Mg2+-chelatase of tobacco: identification of a ChlD cDNA sequence encoding a third subunit, analysis of the interaction of the three

  11. Heterodimerization and endocytosis of Arabidopsis brassinosteroid receptors BRI1 and AtSERK3 (BAK1)

    DEFF Research Database (Denmark)

    Russinova, Eugenia; Borst, Jan-Willem; Kwaaitaal, Mark Adrianus Cornelis J

    2004-01-01

    In Arabidopsis thaliana brassinosteroid (BR), perception is mediated by two Leu-rich repeat receptor-like kinases, BRASSINOSTEROID INSENSITIVE1 (BRI1) and BRI1-ASSOCIATED RECEPTOR KINASE1 (BAK1) (Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR-like KINASE3 [AtSERK3]). Genetic, biochemical, and yeast (...

  12. Brassinosteroids, gibberellins and light-mediated signalling are the three-way controls of plant sprouting.

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    Jaillais, Yvon; Vert, Grégory

    2012-08-01

    The steroid hormones found in plants, the brassinosteroids, were originally genetically identified about 15 years ago as critical regulators of seedling photomorphogenesis. Two studies now shed light on the molecular mechanisms behind this observation. Brassinosteroids control seedling morphogenesis through direct interaction with master transcriptional regulators downstream of growth-promoting hormones and light signalling.

  13. Brassinosteroids and Response of Plants to Heavy Metals Action

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    Rajewska, Iwona; Talarek, Marta; Bajguz, Andrzej

    2016-01-01

    Brassinosteroids (BRs) are a widespread group of plant hormones. These phytohormones play a crucial role in the regulation of growth and development of various plant species, and they demonstrate high biological activity. BRs are considered to demonstrate protective activity in the plants exposed to various stresses. Due to rapid industrialization and urbanization, heavy metals have become one of the most important plant stressors. In plants, accumulation of heavy metals beyond the critical levels leads to oxidative stress. However, BRs may inhibit the degradation of lipids, resulted from the overproduction of reactive oxygen species under stress conditions, and increase the activity of antioxidants. They also have the ability to promote phytochelatins synthesis. PMID:27242833

  14. Latest news on Arabidopsis brassinosteroid perception and signaling

    Directory of Open Access Journals (Sweden)

    Klaus eHarter

    2011-10-01

    Full Text Available Brassinosteroids (BR are plant hormones regulating growth and development. In interaction with other hormones, they are involved in environmental cue responses. The standard BR response pathway model in Arabidopsis includes the perception of the hormone by the plasma membrane receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1 and its hetero-oligomerisation with the co-receptor BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1, followed by the activation of a signaling cascade finally resulting in the expression of BR-responsive genes. Recent findings have shed new light on the molecular mechanism of BR perception, which includes the hormone-induced formation of a platform in BRI1 extracellular domain for interaction with BAK1, and on very early events of signaling at the plasma membrane-cytoplasm interface. In addition, a fast BR response pathway that modifies the membrane potential and the expansion of the cell wall – both crucial processes preceding cell elongation growth – was identified. In this review, these latest findings are summarized and discussed against the background of the standard model of BRI1-dependent signaling.

  15. Interaction of brassinosteroids and polyamines enhances copper stress tolerance in raphanus sativus.

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    Choudhary, Sikander Pal; Oral, H Volkan; Bhardwaj, Renu; Yu, Jing-Quan; Tran, Lam-Son Phan

    2012-09-01

    Brassinosteroids (BRs) and polyamines (PAs) regulate various responses to abiotic stress, but their involvement in the regulation of copper (Cu) homeostasis in plants exposed to toxic levels of Cu is poorly understood. This study provides an analysis of the effects of exogenously applied BRs and PAs on radish (Raphanus sativus) plants exposed to toxic concentrations of Cu. The interaction of 24-epibrassinolide (EBR, an active BR) and spermidine (Spd, an active PA) on gene expression and the physiology of radish plants resulted in enhanced tolerance to Cu stress. Results indicated that the combined application of EBR and Spd modulated the expression of genes encoding PA enzymes and genes that impact the metabolism of indole-3-acetic acid (IAA) and abscisic acid (ABA) resulting in enhanced Cu stress tolerance. Altered expression of genes implicated in Cu homeostasis appeared to be the main effect of EBR and Spd leading to Cu stress alleviation in radish. Ion leakage, in vivo imaging of H(2)O(2), comet assay, and improved tolerance of Cu-sensitive yeast strains provided further evidence for the ability of EBR and Spd to improve Cu tolerance significantly. The study indicates that co-application of EBR and Spd is an effective approach for Cu detoxification and the maintenance of Cu homeostasis in plants. Therefore, the use of these compounds in agricultural production systems should be explored.

  16. Barley Brassinosteroid Mutants Provide an Insight into Phytohormonal Homeostasis in Plant Reaction to Drought Stress

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    Gruszka, Damian; Janeczko, Anna; Dziurka, Michal; Pociecha, Ewa; Oklestkova, Jana; Szarejko, Iwona

    2016-01-01

    Brassinosteroids (BRs) are a class of steroid phytohormones, which regulate various processes of morphogenesis and physiology—from seed development to regulation of flowering and senescence. An accumulating body of evidence indicates that BRs take part in regulation of physiological reactions to various stress conditions, including drought. Many of the physiological functions of BRs are regulated by a complicated, and not fully elucidated network of interactions with metabolic pathways of other phytohormones. Therefore, the aim of this study was to characterize phytohormonal homeostasis in barley (Hordeum vulgare) in reaction to drought and validate role of BRs in regulation of this process. Material of this study included the barley cultivar “Bowman” and five Near-Isogenic Lines (NILs) representing characterized semi-dwarf mutants of several genes encoding enzymes participating in BR biosynthesis and signaling. Analysis of endogenous BRs concentrations in these NILs confirmed that their phenotypes result from abnormalities in BR metabolism. In general, concentrations of 18 compounds, representing various classes of phytohormones, including brassinosteroids, auxins, cytokinins, gibberellins, abscisic acid, salicylic acid and jasmonic acid were analyzed under control and drought conditions in the “Bowman” cultivar and the BR-deficient NILs. Drought induced a significant increase in accumulation of the biologically active form of BRs—castasterone in all analyzed genotypes. Another biologically active form of BRs—24-epi-brassinolide—was identified in one, BR-insensitive NIL under normal condition, but its accumulation was drought-induced in all analyzed genotypes. Analysis of concentration profiles of several compounds representing gibberellins allowed an insight into the BR-dependent regulation of gibberellin biosynthesis. The concentration of the gibberellic acid GA7 was significantly lower in all NILs when compared with the “Bowman” cultivar

  17. RD26 mediates crosstalk between drought and brassinosteroid signalling pathways

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    Ye, Huaxun; Liu, Sanzhen; Tang, Buyun; Chen, Jiani; Xie, Zhouli; Nolan, Trevor M.; Jiang, Hao; Guo, Hongqing; Lin, Hung-Ying; Li, Lei; Wang, Yanqun; Tong, Hongning; Zhang, Mingcai; Chu, Chengcai; Li, Zhaohu; Aluru, Maneesha; Aluru, Srinivas; Schnable, Patrick S.; Yin, Yanhai

    2017-01-01

    Brassinosteroids (BRs) regulate plant growth and stress responses via the BES1/BZR1 family of transcription factors, which regulate the expression of thousands of downstream genes. BRs are involved in the response to drought, however the mechanistic understanding of interactions between BR signalling and drought response remains to be established. Here we show that transcription factor RD26 mediates crosstalk between drought and BR signalling. When overexpressed, BES1 target gene RD26 can inhibit BR-regulated growth. Global gene expression studies suggest that RD26 can act antagonistically to BR to regulate the expression of a subset of BES1-regulated genes, thereby inhibiting BR function. We show that RD26 can interact with BES1 protein and antagonize BES1 transcriptional activity on BR-regulated genes and that BR signalling can also repress expression of RD26 and its homologues and inhibit drought responses. Our results thus reveal a mechanism coordinating plant growth and drought tolerance. PMID:28233777

  18. Brassinosteroids and response of plants to heavy metals action

    Directory of Open Access Journals (Sweden)

    Iwona eRajewska

    2016-05-01

    Full Text Available Brassinosteroids (BRs are a widespread group of plant hormones. These phytohormones play a crucial role in the regulation of growth and development of various plant species, and they demonstrate high biological activity. BRs are considered to demonstrate protective activity in the plants exposed to various stresses. Due to rapid industrialization and urbanization, heavy metals have become one of the most important plant stressors. In plants, accumulation of heavy metals beyond the critical levels leads to oxidative stress. However, BRs may inhibit the degradation of lipids, resulted from the overproduction of reactive oxygen species under stress conditions, and increase the activity of antioxidants. They also have the ability to promote phytochelatins synthesis.

  19. BAK1 Directly Regulates Brassinosteroid Perception and BRI1 Activation

    Institute of Scientific and Technical Information of China (English)

    Kai He; Shengbao Xu; Jia Li

    2013-01-01

    Plants utilize plasma membrane-localized receptor-like kinases (RLKs) to sense extracellular signals to coordinate growth, development, and innate immune responses. BAK1 regulates multiple signaling pathways acting as a co-receptor of several distinct ligand-binding RLKs. It has been debated whether BAK1 serves as an essential regulatory component or only a signal amplifier without pathway specificity. This issue has been clarified recently. Genetic and structural analyses indicated that BAK1 and its homologs play indispensible roles in mediating brassinosteroid (BR) signaling pathway by directly perceiving the ligand BR and activating the receptor of BR, BRI1. The mechanism revealed by these studies now serves as a paradigm for how a pair of RLKs can function together in ligand binding and subsequent initiation of signaling.

  20. Mechanisms of signaling crosstalk between brassinosteroids and gibberellins.

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    Li, Qian-Feng; He, Jun-Xian

    2013-07-01

    Brassinosteroids (BRs) and Gibberellins (GAs) are two principal groups of growth-promoting phytohormones. Accumulating evidence supports that there are crosstalks between BR and GA signaling pathways. However, a molecular mechanism for direct signaling crosstalk between BRs and GAs was not revealed until recently. Works from three different groups demonstrated that an interaction between BZR1/BES1 and DELLAs, two groups of key transcriptional regulators from the BR and GA signaling pathways, respectively, mediates the direct signaling crosstalk between BRs and GAs in controlling cell elongation in Arabidopsis. It was shown that DELLA proteins not only affect the protein stability but also inhibit the transcriptional activity of BZR1. Thus, GAs promote cell elongation, at least in part, through releasing DELLA-mediated inhibition of BZR1. This review aims to introduce these recent advances in our understanding of how BRs and GAs coordinate to regulate plant growth and development at the molecular level.

  1. Two forward genetic screens for vein density mutants in sorghum converge on a cytochrome P450 gene in the brassinosteroid pathway.

    Science.gov (United States)

    Rizal, Govinda; Thakur, Vivek; Dionora, Jacqueline; Karki, Shanta; Wanchana, Samart; Acebron, Kelvin; Larazo, Nikki; Garcia, Richard; Mabilangan, Abigail; Montecillo, Florencia; Danila, Florence; Mogul, Reychelle; Pablico, Paquito; Leung, Hei; Langdale, Jane A; Sheehy, John; Kelly, Steven; Quick, William Paul

    2015-10-01

    The specification of vascular patterning in plants has interested plant biologists for many years. In the last decade a new context has emerged for this interest. Specifically, recent proposals to engineer C(4) traits into C(3) plants such as rice require an understanding of how the distinctive venation pattern in the leaves of C(4) plants is determined. High vein density with Kranz anatomy, whereby photosynthetic cells are arranged in encircling layers around vascular bundles, is one of the major traits that differentiate C(4) species from C(3) species. To identify genetic factors that specify C(4) leaf anatomy, we generated ethyl methanesulfonate- and γ-ray-mutagenized populations of the C(4) species sorghum (Sorghum bicolor), and screened for lines with reduced vein density. Two mutations were identified that conferred low vein density. Both mutations segregated in backcrossed F(2) populations as homozygous recessive alleles. Bulk segregant analysis using next-generation sequencing revealed that, in both cases, the mutant phenotype was associated with mutations in the CYP90D2 gene, which encodes an enzyme in the brassinosteroid biosynthesis pathway. Lack of complementation in allelism tests confirmed this result. These data indicate that the brassinosteroid pathway promotes high vein density in the sorghum leaf, and suggest that differences between C(4) and C(3) leaf anatomy may arise in part through differential activity of this pathway in the two leaf types.

  2. Brassinosteroids Are Master Regulators of Gibberellin Biosynthesis in Arabidopsis

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    Unterholzner, Simon J.; Rozhon, Wilfried; Papacek, Michael; Ciomas, Jennifer; Lange, Theo; Kugler, Karl G.; Mayer, Klaus F.; Sieberer, Tobias; Poppenberger, Brigitte

    2015-01-01

    Plant growth and development are highly regulated processes that are coordinated by hormones including the brassinosteroids (BRs), a group of steroids with structural similarity to steroid hormones of mammals. Although it is well understood how BRs are produced and how their signals are transduced, BR targets, which directly confer the hormone’s growth-promoting effects, have remained largely elusive. Here, we show that BRs regulate the biosynthesis of gibberellins (GAs), another class of growth-promoting hormones, in Arabidopsis thaliana. We reveal that Arabidopsis mutants deficient in BR signaling are severely impaired in the production of bioactive GA, which is correlated with defective GA biosynthetic gene expression. Expression of the key GA biosynthesis gene GA20ox1 in the BR signaling mutant bri1-301 rescues many of its developmental defects. We provide evidence that supports a model in which the BR-regulated transcription factor BES1 binds to a regulatory element in promoters of GA biosynthesis genes in a BR-induced manner to control their expression. In summary, our study underscores a role of BRs as master regulators of GA biosynthesis and shows that this function is of major relevance for the growth and development of vascular plants. PMID:26243314

  3. Chemical Genetic Dissection of Brassinosteroid-Ethylene Interaction

    Institute of Scientific and Technical Information of China (English)

    Joshua M.Gendron; Asif Haque; Nathan Gendron; Timothy Chang; Tadao Asami; Zhi-Yong Wang

    2008-01-01

    We undertook a chemical genetics screen to identify chemical inhibitors of brassinosteroid (BR) action.From a chemical library of 10,000 small molecules,one compound was found to inhibit hypocotyl length and activate the expression of a BR-repressed reporter gene (CPD::GUS) in Arabidopsis,and it was named brassinopride (BRP).These effects of BRP could be reversed by co-treatment with brassinolide,suggesting that BRP either directly or indirectly inhibits BR biosynthesis.Interestingly,the compound causes exaggerated apical hooks,similar to that caused by ethylene treatment.The BRP-induced apical hook phenotype can be blocked by a chemical inhibitor of ethylene perception or an ethylene-insensitive mutant,suggesting that,in addition to inhibiting BR,BRP activates ethylene response.Analysis of BRP analogs provided clues about structural features important for its effects on two separate targets in the BR and ethylene pathways.Analyses of the responses of various BR and ethylene mutants to BRP,ethylene,and BR treatments revealed modes of cross-talk between ethylene and BR in dark-grown seedlings.Our results suggest that active downstream BR signaling,but not BR synthesis or a BR gradient,is required for ethylene-induced apical hook formation.The BRP-related compounds can be useful tools for manipulating plant growth and studying hormone interactions.

  4. Induction of systemic stress tolerance by brassinosteroid in Cucumis sativus.

    Science.gov (United States)

    Xia, Xiao-Jian; Zhou, Yan-Hong; Ding, Ju; Shi, Kai; Asami, Tadao; Chen, Zhixiang; Yu, Jing-Quan

    2011-08-01

    Brassinosteroids (BRs) are a new class of plant hormones that are essential for plant growth and development. Here, the involvement of BRs in plant systemic tolerance to biotic and abiotic stresses was studied. • The effects of 24-epibrassinolide (EBR) on plant stress tolerance were studied through the assessment of symptoms of photooxidative stress by chlorophyll fluorescence imaging pulse amplitude modulation, the analysis of gene expression using quantitative real-time PCR and the measurement of hydrogen peroxide (H₂O₂) production using a spectrophotometric assay or confocal laser scanning microscopy. • Treatment of primary leaves with EBR induced systemic tolerance to photooxidative stress in untreated upper and lower leaves. This was accompanied by the systemic accumulation of H₂O₂ and the systemic induction of genes associated with stress responses. Foliar treatment of EBR also enhanced root resistance to Fusarium wilt pathogen. Pharmacological study showed that EBR-induced systemic tolerance was dependent on local and systemic H₂O₂ accumulation. The expression of BR biosynthetic genes was repressed in EBR-treated leaves, but elevated significantly in untreated systemic leaves. Further analysis indicated that EBR-induced systemic induction of BR biosynthetic genes was mediated by systemically elevated H₂O₂. • These results strongly argue that local EBR treatment can activate the continuous production of H₂O₂, and the autopropagative nature of the reactive oxygen species signal, in turn, mediates EBR-induced systemic tolerance.

  5. The Role of Brassinosteroids in the Development of Sorghum

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    William Sutherlin

    2012-01-01

    Full Text Available Current day seed sorghum stocks contain up to fourdwarf genes that minimize the size of vegetative partsand increase harvest index. To date, only the d3 dwarfgene has been characterized molecularly. The geneencodes a homolog of the Arabidopsis and maize ABCtransporter ABCB1, which is associated with polartransport of the plant growth hormone auxin. Themechanism behind the other dwarf mutations is currentlyunknown. Brassinosteroids (BRs have a profound effect ondevelopment of monocot species, as they are involved in celldivision, cell elongation, and sex determination. Mutationsin the biosynthesis or the reception of BRs result in shorter,stunted plants (dwarf. This project aims to determine therole of BRs in growth and development of sorghum.We developed a strategy to phenocopy a BR mutantby treating sorghum plants (Tx623 with the potentbrassinosteroid inhibitor propiconazole (PCZ. PCZis a chemical inhibitor of the rate-limiting step of BRbiosynthesis in plants. The compound is also usedcommercially as fungicide to treat turf grass diseases.After analyzing the growth retardation effect of PCZ, weperformed a phenotypic screen in a mutagenized sorghumcollection provided by Professors Clifford Weil andMitchell Tuinstra (Department of Agronomy.The results showed that the PCZ-treated plants hadreduced height (61% and 33% of control for 100μM PCZand 500μM PCZ, respectively and tiller number (control= 4.6, 100μM PCZ = 3.3, 500μM PCZ = 1.4. Surprisingly,yield (8.5g = control, 19.3g = 100μM PCZ, 20.7g = 500μMPCZ and harvest indices (seed yield/total biomass(control = 0.09, 100μM PCZ = 0.31, 500μM PCZ = 0.38were significantly greater in PCZ-treated plants.

  6. Arabidopsis PIZZA has the capacity to acylate brassinosteroids.

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    Schneider, Katja; Breuer, Christian; Kawamura, Ayako; Jikumaru, Yusuke; Hanada, Atsushi; Fujioka, Shozo; Ichikawa, Takanari; Kondou, Youichi; Matsui, Minami; Kamiya, Yuji; Yamaguchi, Shinjiro; Sugimoto, Keiko

    2012-01-01

    Brassinosteroids (BRs) affect a wide range of developmental processes in plants and compromised production or signalling of BRs causes severe growth defects. To identify new regulators of plant organ growth, we searched the Arabidopsis FOX (Full-length cDNA Over-eXpressor gene) collection for mutants with altered organ size and isolated two overexpression lines that display typical BR deficient dwarf phenotypes. The phenotype of these lines, caused by an overexpression of a putative acyltransferase gene PIZZA (PIZ), was partly rescued by supplying exogenous brassinolide (BL) and castasterone (CS), indicating that endogenous BR levels are rate-limiting for the growth of PIZ overexpression lines. Our transcript analysis further showed that PIZ overexpression leads to an elevated expression of genes involved in BR biosynthesis and a reduced expression of BR inactivating hydroxylases, a transcriptional response typical to low BR levels. Taking the advantage of relatively high endogenous BR accumulation in a mild bri1-301 background, we found that overexpression of PIZ results in moderately reduced levels of BL and CS and a strong reduction of typhasterol (TY) and 6-deoxocastasterone (6-deoxoCS), suggesting a role of PIZ in BR metabolism. We tested a set of potential substrates in vitro for heterologously expressed PIZ and confirmed its acyltransferase activity with BL, CS and TY. The PIZ gene is expressed in various tissues but as reported for other genes involved in BR metabolism, the loss-of-function mutants did not display obvious growth phenotypes under standard growth conditions. Together, our data suggest that PIZ can modify BRs by acylation and that these properties might help modulating endogenous BR levels in Arabidopsis.

  7. Arabidopsis PIZZA has the capacity to acylate brassinosteroids.

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    Katja Schneider

    Full Text Available Brassinosteroids (BRs affect a wide range of developmental processes in plants and compromised production or signalling of BRs causes severe growth defects. To identify new regulators of plant organ growth, we searched the Arabidopsis FOX (Full-length cDNA Over-eXpressor gene collection for mutants with altered organ size and isolated two overexpression lines that display typical BR deficient dwarf phenotypes. The phenotype of these lines, caused by an overexpression of a putative acyltransferase gene PIZZA (PIZ, was partly rescued by supplying exogenous brassinolide (BL and castasterone (CS, indicating that endogenous BR levels are rate-limiting for the growth of PIZ overexpression lines. Our transcript analysis further showed that PIZ overexpression leads to an elevated expression of genes involved in BR biosynthesis and a reduced expression of BR inactivating hydroxylases, a transcriptional response typical to low BR levels. Taking the advantage of relatively high endogenous BR accumulation in a mild bri1-301 background, we found that overexpression of PIZ results in moderately reduced levels of BL and CS and a strong reduction of typhasterol (TY and 6-deoxocastasterone (6-deoxoCS, suggesting a role of PIZ in BR metabolism. We tested a set of potential substrates in vitro for heterologously expressed PIZ and confirmed its acyltransferase activity with BL, CS and TY. The PIZ gene is expressed in various tissues but as reported for other genes involved in BR metabolism, the loss-of-function mutants did not display obvious growth phenotypes under standard growth conditions. Together, our data suggest that PIZ can modify BRs by acylation and that these properties might help modulating endogenous BR levels in Arabidopsis.

  8. Genetic analyses of interactions among gibberellin, abscisic acid, and brassinosteroids in the control of flowering time in Arabidopsis thaliana.

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    Malgorzata A Domagalska

    Full Text Available BACKGROUND: Genetic interactions between phytohormones in the control of flowering time in Arabidopsis thaliana have not been extensively studied. Three phytohormones have been individually connected to the floral-timing program. The inductive function of gibberellins (GAs is the most documented. Abscisic acid (ABA has been demonstrated to delay flowering. Finally, the promotive role of brassinosteroids (BRs has been established. It has been reported that for many physiological processes, hormone pathways interact to ensure an appropriate biological response. METHODOLOGY: We tested possible genetic interactions between GA-, ABA-, and BR-dependent pathways in the control of the transition to flowering. For this, single and double mutants deficient in the biosynthesis of GAs, ABA, and BRs were used to assess the effect of hormone deficiency on the timing of floral transition. Also, plants that over-express genes encoding rate-limiting enzymes in each biosynthetic pathway were generated and the flowering time of these lines was investigated. CONCLUSIONS: Loss-of-function studies revealed a complex relationship between GAs and ABA, and between ABA and BRs, and suggested a cross-regulatory relation between GAs to BRs. Gain-of-function studies revealed that GAs were clearly limiting in their sufficiency of action, whereas increases in BRs and ABA led to a more modest phenotypic effect on floral timing. We conclude from our genetic tests that the effects of GA, ABA, and BR on timing of floral induction are only in partially coordinated action.

  9. An interaction between BZR1 and DELLAs mediates direct signaling crosstalk between brassinosteroids and gibberellins in Arabidopsis.

    Science.gov (United States)

    Li, Qian-Feng; Wang, Chunming; Jiang, Lei; Li, Shuo; Sun, Samuel S M; He, Jun-Xian

    2012-10-02

    Plant growth and development are coordinated by several groups of small-molecule hormones, including brassinosteroids (BRs) and gibberellins (GAs). Physiological and molecular studies have suggested the existence of crosstalk between BR and GA signaling. We report that BZR1, a key transcription factor activated by BR signaling, interacts in vitro and in vivo with REPRESSOR OF ga1-3 (RGA), a member of the DELLA family of transcriptional regulators that inhibits the GA signaling pathway in Arabidopsis thaliana. Genetic analyses of plants with mutations in the genes encoding RGA and BZR1 revealed that RGA suppressed root and hypocotyl elongation of the gain-of-function mutant bzr1-1D. Ectopic expression of proteins of the DELLA family reduced the abundance and transcriptional activity of BZR1. Reporter gene analyses further indicated that BZR1 and RGA antagonize each other's transcriptional activity. Our data indicated that BZR1 and RGA served as positive and negative regulators, respectively, of both the BR and the GA signaling pathways and establish DELLAs as mediators of signaling crosstalk between BRs and GAs in controlling cell elongation and regulation of plant growth.

  10. Functional Characterization of Soybean Glyma04g39610 as a Brassinosteroid Receptor Gene and Evolutionary Analysis of Soybean Brassinosteroid Receptors

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    Suna Peng

    2016-06-01

    Full Text Available Brassinosteroids (BR play important roles in plant growth and development. Although BR receptors have been intensively studied in Arabidopsis, the BR receptors in soybean remain largely unknown. Here, in addition to the known receptor gene Glyma06g15270 (GmBRI1a, we identified five putative BR receptor genes in the soybean genome: GmBRI1b, GmBRL1a, GmBRL1b, GmBRL2a, and GmBRL2b. Analysis of their expression patterns by quantitative real-time PCR showed that they are ubiquitously expressed in primary roots, lateral roots, stems, leaves, and hypocotyls. We used rapid amplification of cDNA ends (RACE to clone GmBRI1b (Glyma04g39160, and found that the predicted amino acid sequence of GmBRI1b showed high similarity to those of AtBRI1 and pea PsBRI1. Structural modeling of the ectodomain also demonstrated similarities between the BR receptors of soybean and Arabidopsis. GFP-fusion experiments verified that GmBRI1b localizes to the cell membrane. We also explored GmBRI1b function in Arabidopsis through complementation experiments. Ectopic over-expression of GmBRI1b in Arabidopsis BR receptor loss-of-function mutant (bri1-5 bak1-1D restored hypocotyl growth in etiolated seedlings; increased the growth of stems, leaves, and siliques in light; and rescued the developmental defects in leaves of the bri1-6 mutant, and complemented the responses of BR biosynthesis-related genes in the bri1-5 bak1-D mutant grown in light. Bioinformatics analysis demonstrated that the six BR receptor genes in soybean resulted from three gene duplication events during evolution. Phylogenetic analysis classified the BR receptors in dicots and monocots into three subclades. Estimation of the synonymous (Ks and the nonsynonymous substitution rate (Ka and selection pressure (Ka/Ks revealed that the Ka/Ks of BR receptor genes from dicots and monocots were less than 1.0, indicating that BR receptor genes in plants experienced purifying selection during evolution.

  11. Brassinosteroids can regulate cellulose biosynthesis by controlling the expression of CESA genes in Arabidopsis

    OpenAIRE

    Xie, Liqiong; Yang, Cangjing; Wang, Xuelu

    2011-01-01

    The phytohormones, brassinosteroids (BRs), play important roles in regulating cell elongation and cell size, and BR-related mutants in Arabidopsis display significant dwarf phenotypes. Cellulose is a biopolymer which has a major contribution to cell wall formation during cell expansion and elongation. However, whether BRs regulate cellulose synthesis, and if so, what the underlying mechanism of cell elongation induced by BRs is, is unknown. The content of cellulose and the expression levels o...

  12. Brassinosteroids protect photosynthetic machinery against the cadmium induced oxidative stress in two tomato cultivars.

    Science.gov (United States)

    Hasan, Syed Aiman; Hayat, Shamsul; Ahmad, Aqil

    2011-09-01

    The present study was conducted with an aim to gain better insight of brassinosteroid generated response on the effects of cadmium on photosynthetic machinery and active oxygen metabolism in two tomato cultivars (K-25 and Sarvodya). These tomato cultivars were subjected to graded cadmium levels in soil (0, 3, 6, 9 or 12 mg kg(-1) soil) with their foliage being sprayed with 0 or 10(-8) M of 28-homobrassinolide/24-epibrassinolide (HBL/EBL) at 59 d stage. The results suggested that photosynthetic parameters, leaf water potential and activity of several enzymes (nitrate reductase and carbonic anhydrase) decreased significantly in both the cultivars, to a lesser extent in K-25 than Sarvodya with the increasing levels of cadmium in the soil. However, the activity of antioxidant enzymes and proline content increased in response to metal treatment as well as the application of brassinosteroids (HBL/EBL). Overall, exogenous application of brassinosteroids improved the activity of photosynthetic machinery and that of antioxidant defense system in both the cultivars, and also nullified the damaging effect of metal on these parameters.

  13. Arabidopsis brassinosteroid biosynthetic mutant dwarf7-1 exhibits slower rates of cell division and shoot induction

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    Schulz Burkhard

    2010-12-01

    Full Text Available Abstract Background Plant growth depends on both cell division and cell expansion. Plant hormones, including brassinosteroids (BRs, are central to the control of these two cellular processes. Despite clear evidence that BRs regulate cell elongation, their roles in cell division have remained elusive. Results Here, we report results emphasizing the importance of BRs in cell division. An Arabidopsis BR biosynthetic mutant, dwarf7-1, displayed various characteristics attributable to slower cell division rates. We found that the DWARF4 gene which encodes for an enzyme catalyzing a rate-determining step in the BR biosynthetic pathways, is highly expressed in the actively dividing callus, suggesting that BR biosynthesis is necessary for dividing cells. Furthermore, dwf7-1 showed noticeably slower rates of callus growth and shoot induction relative to wild-type control. Flow cytometric analyses of the nuclei derived from either calli or intact roots revealed that the cell division index, which was represented as the ratio of cells at the G2/M vs. G1 phases, was smaller in dwf7-1 plants. Finally, we found that the expression levels of the genes involved in cell division and shoot induction, such as PROLIFERATING CELL NUCLEAR ANTIGEN2 (PCNA2 and ENHANCER OF SHOOT REGENERATION2 (ESR2, were also lower in dwf7-1 as compared with wild type. Conclusions Taken together, results of callus induction, shoot regeneration, flow cytometry, and semi-quantitative RT-PCR analysis suggest that BRs play important roles in both cell division and cell differentiation in Arabidopsis.

  14. Isolation and Characterization of the Brassinosteroid Receptor Gene (GmBRI1 from Glycine max

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    Miao Wang

    2014-03-01

    Full Text Available Brassinosteroids (BRs constitute a group of steroidal phytohormones that contribute to a wide range of plant growth and development functions. The genetic modulation of BR receptor genes, which play major roles in the BR signaling pathway, can create semi-dwarf plants that have great advantages in crop production. In this study, a brassinosteroid insensitive gene homologous with AtBRI1 and other BRIs was isolated from Glycine max and designated as GmBRI1. A bioinformatic analysis revealed that GmBRI1 shares a conserved kinase domain and 25 tandem leucine-rich repeats (LRRs that are characteristic of a BR receptor for BR reception and reaction and bear a striking similarity in protein tertiary structure to AtBRI1. GmBRI1 transcripts were more abundant in soybean hypocotyls and could be upregulated in response to exogenous BR treatment. The transformation of GmBRI1 into the Arabidopsis dwarf mutant bri1-5 restored the phenotype, especially regarding pod size and plant height. Additionally, this complementation is a consequence of a restored BR signaling pathway demonstrated in the light/dark analysis, root inhibition assay and BR-response gene expression. Therefore, GmBRI1 functions as a BR receptor to alter BR-mediated signaling and is valuable for improving plant architecture and enhancing the yield of soybean.

  15. Brassinosteroids Denigrate the Seasonal Stress through Antioxidant Defense System in Seedlings of Brassica juncea L.

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    Sandeep Kumar

    2014-05-01

    Full Text Available The present work has been undertaken to study the effect of exogenously application of 24-epiBL and 28-homoBL on soluble protein, proline contents and antioxidant defense system of Brassica juncea L. RLM 619 under the influence of seasonal stress. It was observed that 24-epiBL and 28-homoBL treatment enhance the soluble protein, dry weight and shoot length of B. juncea seedlings under seasonal stress. If seeds treated with the different concentrations (10-6, 10-8 and 10-10 M of 24-epiBL and 28-homoBL revealed batter growth, protein and proline contents as compare to untreated seedlings. Similarly the activities of antioxidant enzymes SOD, CAT, APOX, DHAR, PPO and Auxinases were enhanced by the application of different concentration of both brassinosteroids, whereas MDA content was decrease with both brassinosteroids treatments. Then we have concluded that both brassinolides have the seasonal stress ameliorative properties in B. juncea seedlings grown under the influence of seasonal stress. This study culminates to the role of brassinolides as an anti-stress property for protection of plant from various types of stresses.

  16. Interactions between ethylene, gibberellins, and brassinosteroids in the development of rhizobial and mycorrhizal symbioses of pea.

    Science.gov (United States)

    Foo, Eloise; McAdam, Erin L; Weller, James L; Reid, James B

    2016-04-01

    The regulation of arbuscular mycorrhizal development and nodulation involves complex interactions between the plant and its microbial symbionts. In this study, we use the recently identified ethylene-insensitive ein2 mutant in pea (Pisum sativum L.) to explore the role of ethylene in the development of these symbioses. We show that ethylene acts as a strong negative regulator of nodulation, confirming reports in other legumes. Minor changes in gibberellin1 and indole-3-acetic acid levels in ein2 roots appear insufficient to explain the differences in nodulation. Double mutants produced by crosses between ein2 and the severely gibberellin-deficient na and brassinosteroid-deficient lk mutants showed increased nodule numbers and reduced nodule spacing compared with the na and lk single mutants, but nodule numbers and spacing were typical of ein2 plants, suggesting that the reduced number of nodules innaandlkplants is largely due to the elevated ethylene levels previously reported in these mutants. We show that ethylene can also negatively regulate mycorrhizae development when ethylene levels are elevated above basal levels, consistent with a role for ethylene in reducing symbiotic development under stressful conditions. In contrast to the hormone interactions in nodulation, ein2 does not override the effect of lk or na on the development of arbuscular mycorrhizae, suggesting that brassinosteroids and gibberellins influence this process largely independently of ethylene.

  17. Proteomic Study Identifies Proteins Involved in Brassinosteroid Regulation of Rice Growth

    Institute of Scientific and Technical Information of China (English)

    Fengru Wang; Ming-Yi Bai; Zhiping Deng; Juan A. Oses-Prieto; Alma L. Burlingame; Tiegang Lu; Kang Chong; Zhi-Yong Wang

    2010-01-01

    Brassinosteroids (BRs) are essential hormones for growth and development of plant. In rice, BRs regulate multiple developmental processes and affect many important traits such as height, leaf angle, fertility and seed filling. We identified brassinosteroid-regulated proteins in rice using proteomic approaches and performed functional analysis of some BR-regulated proteins by overexpression experiments. Using two-dimensional difference gel electrophoresis (2-D DIGE) followed by protein identification by mass spectrometry, we compared proteomic differences in the shoots and roots of the BR-insensitive mutant d61-4 and BR-deficient mutant brd1-3. We identified a large number of proteins differentially expressed in the mutants compared with wild type control. These include a glycine-rich RNA-binding protein (OsGRP1)and a DREPP2 protein, which showed reduced levels in the BR mutants. Overexpression of these two proteins partially suppressed the dwarf phenotype of the Arabidopsis BR-insensitive mutant bri1-5. In contrast to the reduced protein level, the RNA level of OsGRP1 was not significantly affected in the BR mutants or by BR treatment, suggesting BR regulation of OsGRP1 at the posttranslational level. This study identifies many BR-regulated proteins and demonstrates that OsGRP1 functions downstream in the BR signal transduction pathway to promote cell expansion.

  18. Diurnal Regulation of the Brassinosteroid-Biosynthetic CPD Gene in Arabidopsis1[W

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    Bancos, Simona; Szatmári, Anna-Mária; Castle, Julie; Kozma-Bognár, László; Shibata, Kyomi; Yokota, Takao; Bishop, Gerard J.; Nagy, Ferenc; Szekeres, Miklós

    2006-01-01

    Plant steroid hormones, brassinosteroids (BRs), are essential for normal photomorphogenesis. However, the mechanism by which light controls physiological functions via BRs is not well understood. Using transgenic plants carrying promoter-luciferase reporter gene fusions, we show that in Arabidopsis (Arabidopsis thaliana) the BR-biosynthetic CPD and CYP85A2 genes are under diurnal regulation. The complex diurnal expression profile of CPD is determined by dual, light-dependent, and circadian control. The severely decreased expression level of CPD in phytochrome-deficient background and the red light-specific induction in wild-type plants suggest that light regulation of CPD is primarily mediated by phytochrome signaling. The diurnal rhythmicity of CPD expression is maintained in brassinosteroid insensitive 1 transgenic seedlings, indicating that its transcriptional control is independent of hormonal feedback regulation. Diurnal changes in the expression of CPD and CYP85A2 are accompanied by changes of the endogenous BR content during the day, leading to brassinolide accumulation at the middle of the light phase. We also show that CPD expression is repressed in extended darkness in a BR feedback-dependent manner. In the dark the level of the bioactive hormone did not increase; therefore, our data strongly suggest that light also influences the sensitivity of plants to BRs. PMID:16531479

  19. Diurnal regulation of the brassinosteroid-biosynthetic CPD gene in Arabidopsis.

    Science.gov (United States)

    Bancos, Simona; Szatmári, Anna-Mária; Castle, Julie; Kozma-Bognár, László; Shibata, Kyomi; Yokota, Takao; Bishop, Gerard J; Nagy, Ferenc; Szekeres, Miklós

    2006-05-01

    Plant steroid hormones, brassinosteroids (BRs), are essential for normal photomorphogenesis. However, the mechanism by which light controls physiological functions via BRs is not well understood. Using transgenic plants carrying promoter-luciferase reporter gene fusions, we show that in Arabidopsis (Arabidopsis thaliana) the BR-biosynthetic CPD and CYP85A2 genes are under diurnal regulation. The complex diurnal expression profile of CPD is determined by dual, light-dependent, and circadian control. The severely decreased expression level of CPD in phytochrome-deficient background and the red light-specific induction in wild-type plants suggest that light regulation of CPD is primarily mediated by phytochrome signaling. The diurnal rhythmicity of CPD expression is maintained in brassinosteroid insensitive 1 transgenic seedlings, indicating that its transcriptional control is independent of hormonal feedback regulation. Diurnal changes in the expression of CPD and CYP85A2 are accompanied by changes of the endogenous BR content during the day, leading to brassinolide accumulation at the middle of the light phase. We also show that CPD expression is repressed in extended darkness in a BR feedback-dependent manner. In the dark the level of the bioactive hormone did not increase; therefore, our data strongly suggest that light also influences the sensitivity of plants to BRs.

  20. Identification and Characterization of Multiple Intermediate Alleles of the Key Genes Regulating Brassinosteroid Biosynthesis Pathways

    Science.gov (United States)

    Du, Junbo; Zhao, Baolin; Sun, Xin; Sun, Mengyuan; Zhang, Dongzhi; Zhang, Shasha; Yang, Wenyu

    2017-01-01

    Most of the early identified brassinosteroid signaling and biosynthetic mutants are null mutants, exhibiting extremely dwarfed phenotypes and male sterility. These null mutants are usually unable to be directly transformed via a routinely used Agrobacterium-mediated gene transformation system and therefore are less useful for genetic characterization of the brassinosteroid (BR)-related pathways. Identification of intermediate signaling mutants such as bri1–5 and bri1–9 has contributed drastically to the elucidation of BR signaling pathway using both genetic and biochemical approaches. However, intermediate mutants of key genes regulating BR biosynthesis have seldom been reported. Here we report identification of several intermediate BR biosynthesis mutants mainly resulted from leaky transcriptions due to the insertions of T-DNAs in the introns. These mutants are semi-dwarfed and fertile and capable to be transformed. These intermediate mutants could be useful tools for future discovery and analyses of novel components regulating BR biosynthesis and catabolism via genetic modifier screen. PMID:28138331

  1. Ligand Perception, Activation, and Early Signaling of Plant Steroid Receptor Brassinosteroid Insensitive 1

    Institute of Scientific and Technical Information of China (English)

    Jianjun Jiang; Chi Zhang; Xuelu Wang

    2013-01-01

    Leucine-rich repeat receptor-like kinases (LRR-RLKs) belong to a large group of cell surface proteins involved in many aspects of plant development and environmental responses in both monocots and dicots. Brassinosteroid insensitive 1 (BRI1), a member of the LRR X subfamily, was first identified through several forward genetic screenings for mutants insensitive to brassinosteroids (BRs), which are a class of plant-specific steroid hormones. Since its identification, BRI1 and its homologs had been proved as receptors perceiving BRs and initiating BR signaling. The co-receptor BRI1-associated kinase 1 and its homologs, and other BRI1 interacting proteins such as its inhibitor BRI1 kinase inhibitor 1 (BKI1) were identified by genetic and biochemical approaches. The detailed mechanisms of BR perception by BRI1 and the activation of BRI1 receptor complex have also been elucidated. Moreover, several mechanisms for termination of the activated BRI1 signaling were also discovered. In this review, we will focus on the recent advances on the mechanism of BRI1 phosphorylation and activation, the regulation of its receptor complex, the structure basis of BRI1 ectodomain and BR recognition, its direct substrates, and the termination of the activated BRI1 receptor complex.

  2. XIAO is involved in the control of organ size by contributing to the regulation of signaling and homeostasis of brassinosteroids and cell cycling in rice.

    Science.gov (United States)

    Jiang, Yunhe; Bao, Liang; Jeong, So-Yoon; Kim, Seong-Ki; Xu, Caiguo; Li, Xianghua; Zhang, Qifa

    2012-05-01

    Organ size is determined by cell number and size, and involves two fundamental processes: cell proliferation and cell expansion. Although several plant hormones are known to play critical roles in shaping organ size by regulating the cell cycle, it is not known whether brassinosteroids (BRs) are also involved in regulating cell division. Here we identified a rice T-DNA insertion mutant for organ size, referred to as xiao, that displays dwarfism and erect leaves, typical BR-related phenotypes, together with reduced seed setting. XIAO is predicted to encode an LRR kinase. The small stature of the xiao mutant resulted from reduced organ sizes due to decreased cell numbers resulting from reduced cell division rate, as supported by the observed co-expression of XIAO with a number of genes involved in cell cycling. The xiao mutant displayed a tissue-specific enhanced BR response and greatly reduced BR contents at the whole-plant level. These results indicated that XIAO is a regulator of BR signaling and cell division. Thus, XIAO may provide a possible connection between BRs and cell-cycle regulation in controlling organ growth.

  3. ‘Candidatus Liberibacter asiaticus’, Causal Agent of Citrus Huanglongbing, Is Reduced by Treatment with Brassinosteroids

    Science.gov (United States)

    Hernández, Ingrid; Portieles, Roxana; Rodríguez García, Mayra; López, Yunior; Aranguren, Miguel; Alonso, Eugenio; Delgado, Roger; Luis, Maritza; Batista, Lochy; Paredes, Camilo; Rodríguez, Meilyn; Pujol, Merardo; Ochagavia, María Elena; Falcón, Viviana; Terauchi, Ryohei; Matsumura, Hideo; Ayra-Pardo, Camilo; Llauger, Raixa; Pérez, María del Carmen; Núñez, Mirian; Borrusch, Melissa S.; Walton, Jonathan D.; Silva, Yussuan; Pimentel, Eulogio; Borroto, Carlos; Borrás-Hidalgo, Orlando

    2016-01-01

    Huanglongbing (HLB) constitutes the most destructive disease of citrus worldwide, yet no established efficient management measures exist for it. Brassinosteroids, a family of plant steroidal compounds, are essential for plant growth, development and stress tolerance. As a possible control strategy for HLB, epibrassinolide was applied to as a foliar spray to citrus plants infected with the causal agent of HLB, ‘Candidatus Liberibacter asiaticus’. The bacterial titers were reduced after treatment with epibrassinolide under both greenhouse and field conditions but were stronger in the greenhouse. Known defense genes were induced in leaves by epibrassinolide. With the SuperSAGE technology combined with next generation sequencing, induction of genes known to be associated with defense response to bacteria and hormone transduction pathways were identified. The results demonstrate that epibrassinolide may provide a useful tool for the management of HLB. PMID:26731660

  4. 'Candidatus Liberibacter asiaticus', Causal Agent of Citrus Huanglongbing, Is Reduced by Treatment with Brassinosteroids.

    Directory of Open Access Journals (Sweden)

    Eduardo Canales

    Full Text Available Huanglongbing (HLB constitutes the most destructive disease of citrus worldwide, yet no established efficient management measures exist for it. Brassinosteroids, a family of plant steroidal compounds, are essential for plant growth, development and stress tolerance. As a possible control strategy for HLB, epibrassinolide was applied to as a foliar spray to citrus plants infected with the causal agent of HLB, 'Candidatus Liberibacter asiaticus'. The bacterial titers were reduced after treatment with epibrassinolide under both greenhouse and field conditions but were stronger in the greenhouse. Known defense genes were induced in leaves by epibrassinolide. With the SuperSAGE technology combined with next generation sequencing, induction of genes known to be associated with defense response to bacteria and hormone transduction pathways were identified. The results demonstrate that epibrassinolide may provide a useful tool for the management of HLB.

  5. Identification of brassinosteroid responsive genes in Arabidopsis by cDNA array

    Institute of Scientific and Technical Information of China (English)

    胡玉欣; 汪政科; 王永红; 包方; 李凝; 彭镇华; 李家洋

    2001-01-01

    We have systematically monitored brassinosteroid (BR) responsive genes in a BR-deficient mutant det2 suspension culture of Arabidopsis by using a cDNA array approach. Among 13000 cDNA clones arrayed on filters, 53 BR responsive clones were identified and designated BRR1-BRR53. Sequence analysis of 43 clones showed that 19 clones are novel genes, 3 clones are genes involved in the control of cell division, 4 clones are genes related to plant stress responses, 4 clones are transcriptional factor or signal transduction component genes, and 3 clones are genes involved in RNA splicing or structure forming. In addition, we also found that BR regulated the transcription of genes related to many physiological processes, such as photoreaction, ion transportation and some metabolic processes. These findings present molecular evidence that BR plays an essential role in plant growth and development.

  6. Microarray and Proteomic Analysis of Brassinosteroid- and Gibberellin-Regulated Gene and Protein Expression in Rice

    Institute of Scientific and Technical Information of China (English)

    Guangxiao Yang; Setsuko Komatsu

    2004-01-01

    Brassinosteroid (BR) and gibberellin (GA) are two groups of plant growth regulators essential for normal plant growth and development. To gain insight into the molecular mechanism by which BR and GA regulate the growth and development of plants, especially the monocot plant rice, it is necessary to identify and analyze more genes and proteins that are regulated by them. With the availability of draft sequences of two major types, japonica and indica rice, it has become possible to analyze expression changes of genes and proteins at genome scale. In this review, we summarize rice functional genomic research by using microarray and proteomic approaches and our recent research results focusing on the comparison of cDNA microarray and proteomic analyses of BR- and GA-regulated gene and protein expression in rice. We believe our findings have important implications for understanding the mechanism by which BR and GA regulate the growth and development of rice.

  7. Phosphatidic Acid Regulates BZR1 Activity andBrassinosteroid Signal of Arabidopsis

    Institute of Scientific and Technical Information of China (English)

    2014-01-01

    Dear Editor, Brassinosteroid (BR) is an important hormone and playscrucial roles in plant growth and development (Kim andWang, 2010). Genetics studies identify many componentsinvolving in BR signaling, including transcript factor BZR1(BRASSINAZOLE RESISTANT 1). BZR1 is dephosphorylated (Heet al., 2005) to regulate expression of target genes. A sin-gle amino acid mutation in BZR1 PEST domain results inenhanced binding and dephosphorylation by PP2A (PROTEINPHOSPHATASE 2A; Tang et al., 2011), leading to constitutivelyactivated BZR1 and enhanced BR signal in gain-of-functionmutant bzr1-1D. Although BR signal is well characterized inArabidopsis, how the components of BR signaling transduc-tion pathway are reclulated needs further illustrations.

  8. Visualization of BRI1 and BAK1(SERK3) membrane receptor heterooligomers during brassinosteroid signaling.

    Science.gov (United States)

    Bücherl, Christoph A; van Esse, G Wilma; Kruis, Alex; Luchtenberg, Jeroen; Westphal, Adrie H; Aker, José; van Hoek, Arie; Albrecht, Catherine; Borst, Jan Willem; de Vries, Sacco C

    2013-08-01

    The leucine-rich repeat receptor-like kinase BRASSINOSTEROID-INSENSITIVE1 (BRI1) is the main ligand-perceiving receptor for brassinosteroids (BRs) in Arabidopsis (Arabidopsis thaliana). Binding of BRs to the ectodomain of plasma membrane (PM)-located BRI1 receptors initiates an intracellular signal transduction cascade that influences various aspects of plant growth and development. Even though the major components of BR signaling have been revealed and the PM was identified as the main site of BRI1 signaling activity, the very first steps of signal transmission are still elusive. Recently, it was shown that the initiation of BR signal transduction requires the interaction of BRI1 with its SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK) coreceptors. In addition, the resolved structure of the BRI1 ectodomain suggested that BRI1-ASSOCIATED KINASE1 [BAK1](SERK3) may constitute a component of the ligand-perceiving receptor complex. Therefore, we investigated the spatial correlation between BRI1 and BAK1(SERK3) in the natural habitat of both leucine-rich repeat receptor-like kinases using comparative colocalization analysis and fluorescence lifetime imaging microscopy. We show that activation of BR signaling by exogenous ligand application resulted in both elevated colocalization between BRI1 and BAK1(SERK3) and an about 50% increase of receptor heterooligomerization in the PM of live Arabidopsis root epidermal cells. However, large populations of BRI1 and BAK1(SERK3) colocalized independently of BRs. Moreover, we could visualize that approximately 7% of the BRI1 PM pool constitutively heterooligomerizes with BAK1(SERK3) in live root cells. We propose that only small populations of PM-located BRI1 and BAK1(SERK3) receptors participate in active BR signaling and that the initiation of downstream signal transduction involves preassembled BRI1-BAK1(SERK3) heterooligomers.

  9. A Small G Protein as a Novel Component of the Rice Brassinosteroid Signal Transduction.

    Science.gov (United States)

    Zhang, Ge; Song, Xiaoguang; Guo, Hongyan; Wu, Yao; Chen, Xiaoying; Fang, Rongxiang

    2016-09-01

    Brassinosteroids (BRs) are a class of steroid hormones that are essential for plant growth and development. The BR signal transduction pathway in the dicot model plant Arabidopsis is well established, but the components connecting the BR signaling steps in rice have not been fully explored. For example, how the BR signaling is fine-tuned in rice, especially at the BR receptor level, is largely unknown. Here we show that OsPRA2, a rice small G protein, plays a repressive role in the BR signaling pathway. Lamina inclination, coleoptile elongation, and root inhibition assays indicated that rice plants with suppressed expression of OsPRA2 were more sensitive to exogenously applied brassinolide than the wild-type plants. Conversely, rice overexpressing OsPRA2 was less sensitive to exogenous brassinolide. Further study uncovered that OsPRA2 inhibited the dephosphorylation of, and thus inactivated the transcription factor BRASSINAZOLE-RESISTANT 1 (OsBZR1). More importantly, OsPRA2 was found to co-localize with and directly bind to rice BR receptor BRASSINOSTEROID-INSENSITIVE 1 (OsBRI1) at the plasma membrane. Additionally, the in vitro assays showed that OsPRA2 inhibits its autophosphorylation. This OsPRA2-OsBRI1 interaction led to the dissociation of OsBRI1 from its co-receptor OsBAK1, and abolished OsBRI1-mediated phosphorylation of OsBAK1. Together, these results reveal a possible working mechanism of OsPRA2 as a novel negative regulator on OsBRI1 and OsBZR1 and extend the knowledge about the regulatory mechanism of rice BR signaling.

  10. Brassinosteroids-Induced Systemic Stress Tolerance was Associated with Increased Transcripts of Several Defence-Related Genes in the Phloem in Cucumis sativus.

    Directory of Open Access Journals (Sweden)

    Pingfang Li

    Full Text Available Brassinosteroids (BRs, a group of naturally occurring plant steroidal compounds, are essential for plant growth, development and stress tolerance. Recent studies showed that BRs could induce systemic tolerance to biotic and abiotic stresses; however, the molecular mechanisms by which BRs signals lead to responses in the whole plant are largely unknown. In this study, 24-epibrassinosteroid (EBR-induced systemic tolerance in Cucumis sativus L. cv. Jinyan No. 4 was analyzed through the assessment of symptoms of photooxidative stress by chlorophyll fluorescence imaging pulse amplitude modulation. Expression of defense/stress related genes were induced in both treated local leaves and untreated systemic leaves by local EBR application. With the suppressive subtractive hybridization (SSH library using cDNA from the phloem sap of EBR-treated plants as the tester and distilled water (DW-treated plants as the driver, 14 transcripts out of 260 clones were identified. Quantitative Real Time-Polymerase Chain Reaction (RT-qPCR validated the specific up-regulation of these transcripts. Of the differentially expressed transcripts with known functions, transcripts for the selected four cDNAs, which encode an auxin-responsive protein (IAA14, a putative ankyrin-repeat protein, an F-box protein (PP2, and a major latex, pathogenesis-related (MLP-like protein, were induced in local leaves, systemic leaves and roots after foliar application of EBR onto mature leaves. Our results demonstrated that EBR-induced systemic tolerance is accompanied with increased transcript of genes in the defense response in other organs. The potential role of phloem mRNAs as signaling components in mediating BR-regulated systemic resistance is discussed.

  11. Occurrence of brassinosteroids in non-flowering land plants, liverwort, moss, lycophyte and fern.

    Science.gov (United States)

    Yokota, Takao; Ohnishi, Toshiyuki; Shibata, Kyomi; Asahina, Masashi; Nomura, Takahito; Fujita, Tomomichi; Ishizaki, Kimitsune; Kohchi, Takayuki

    2017-04-01

    Endogenous brassinosteroids (BRs) in non-flowering land plants were analyzed. BRs were found in a liverwort (Marchantia polymorpha), a moss (Physcomitrella patens), lycophytes (Selaginella moellendorffii and S. uncinata) and 13 fern species. A biologically active BR, castasterone (CS), was identified in most of these non-flowering plants but another biologically active BR, brassinolide, was not. It may be distinctive that levels of CS in non-flowering plants were orders of magnitude lower than those in flowering plants. 22-Hydroxycampesterol and its metabolites were identified in most of the non-flowering plants suggesting that the biosynthesis of BRs via 22-hydroxylation of campesterol occurs as in flowering plants. Phylogenetic analyses indicated that M. polymorpha, P. patens and S. moellendorffii have cytochrome P450s in the CYP85 clans which harbors BR biosynthesis enzymes, although the P450 profiles are simpler as compared with Arabidopsis and rice. Furthermore, these basal land plants were found to have multiple P450s in the CYP72 clan which harbors enzymes to catabolize BRs. These findings indicate that green plants were able to synthesize and inactivate BRs from the land-transition stage.

  12. Brassinosteroid Regulates Seed Size and Shape in Arabidopsis1[W][OPEN

    Science.gov (United States)

    Jiang, Wen-Bo; Huang, Hui-Ya; Hu, Yu-Wei; Zhu, Sheng-Wei; Wang, Zhi-Yong; Lin, Wen-Hui

    2013-01-01

    Seed development is important for agriculture productivity. We demonstrate that brassinosteroid (BR) plays crucial roles in determining the size, mass, and shape of Arabidopsis (Arabidopsis thaliana) seeds. The seeds of the BR-deficient mutant de-etiolated2 (det2) are smaller and less elongated than those of wild-type plants due to a decreased seed cavity, reduced endosperm volume, and integument cell length. The det2 mutant also showed delay in embryo development, with reduction in both the size and number of embryo cells. Pollination of det2 flowers with wild-type pollen yielded seeds of normal size but still shortened shape, indicating that the BR produced by the zygotic embryo and endosperm is sufficient for increasing seed volume but not for seed elongation, which apparently requires BR produced from maternal tissues. BR activates expression of SHORT HYPOCOTYL UNDER BLUE1, MINISEED3, and HAIKU2, which are known positive regulators of seed size, but represses APETALA2 and AUXIN RESPONSE FACTOR2, which are negative regulators of seed size. These genes are bound in vivo by the BR-activated transcription factor BRASSINAZOLE-RESISTANT1 (BZR1), and they are known to influence specific processes of integument, endosperm, and embryo development. Our results demonstrate that BR regulates seed size and seed shape by transcriptionally modulating specific seed developmental pathways. PMID:23771896

  13. Brassinosteroids can regulate cellulose biosynthesis by controlling the expression of CESA genes in Arabidopsis.

    Science.gov (United States)

    Xie, Liqiong; Yang, Cangjing; Wang, Xuelu

    2011-08-01

    The phytohormones, brassinosteroids (BRs), play important roles in regulating cell elongation and cell size, and BR-related mutants in Arabidopsis display significant dwarf phenotypes. Cellulose is a biopolymer which has a major contribution to cell wall formation during cell expansion and elongation. However, whether BRs regulate cellulose synthesis, and if so, what the underlying mechanism of cell elongation induced by BRs is, is unknown. The content of cellulose and the expression levels of the cellulose synthase genes (CESAs) was measured in BR-related mutants and their wild-type counterpart. The chromatin immunoprecipitation (CHIP) experiments and genetic analysis were used to demonstrate that BRs regulate CESA genes. It was found here that the BR-deficient or BR-perceptional mutants contain less cellulose than the wild type. The expression of CESA genes, especially those related to primary cell wall synthesis, was reduced in det2-1 and bri1-301, and was only inducible by BRs in the BR-deficient mutant det2-1. CHIP experiments show that the BR-activated transcription factor BES1 can associate with upstream elements of most CESA genes particularly those related with the primary cell wall. Furthermore, over-expression of the BR receptor BRI1 in CESA1, 3, and 6 mutants can only partially rescue the dwarf phenotypes. Our findings provide potential insights into the mechanism that BRs regulate cellulose synthesis to accomplish the cell elongation process in plant development.

  14. Dissection of brassinosteroid-regulated proteins in rice embryos during germination by quantitative proteomics

    Science.gov (United States)

    Li, Qian-Feng; Xiong, Min; Xu, Peng; Huang, Li-Chun; Zhang, Chang-Quan; Liu, Qiao-Quan

    2016-01-01

    Brassinosteroids (BRs), essential plant-specific steroidal hormones, function in a wide spectrum of plant growth and development events, including seed germination. Rice is not only a monocotyledonous model plant but also one of the most important staple food crops of human beings. Rice seed germination is a decisive event for the next-generation of plant growth and successful seed germination is critical for rice yield. However, little is known about the molecular mechanisms on how BR modulates seed germination in rice. In the present study, we used isobaric tags for relative and absolute quantification (iTRAQ) based proteomic approach to study BR-regulated proteome during the early stage of seed germination. The results showed that more than 800 BR-responsive proteins were identified, including 88 reliable target proteins responsive to stimuli of both BR-deficiency and BR-insensitivity. Moreover, 90% of the 88 target proteins shared a similar expression change pattern. Gene ontology and string analysis indicated that ribosomal structural proteins, as well as proteins involved in protein biosynthesis and carbohydrate metabolisms were highly clustered. These findings not only enrich BR-regulated protein database in rice seeds, but also allow us to gain novel insights into the molecular mechanism of BR regulated seed germination. PMID:27703189

  15. Recent Advances in the Regulation of Brassinosteroid Signaling and Biosynthesis Pathways

    Institute of Scientific and Technical Information of China (English)

    Huaxun Ye; Lei Li; Yanhai Yin

    2011-01-01

    Brassinosteroids (BRs) play important roles in plant growth, development and responses to environmental cues. BRs signal through plasma membrane receptor BRI1 and co-receptor BAK1, and several positive (BSK1, BSU1, PP2A) and negative (BKI1, BIN2 and 14-3-3) regulators to control the activities of BES1 and BZR1 family transcription factors,which regulate the expression of hundreds to thousands of genes for various BR responses. Recent studies identified novel signaling components in the BR pathways and started to establish the detailed mechanisms on the regulation of BR signaling. In addition, the molecular mechanism and transcriptional network through which BES1 and BZR1 control gene expression and various BR responses are beginning to be revealed. BES1 recruits histone demethylases ELF6 and REF6 as well as a transcription elongation factor IWS1 to regulate target gene expression. Identification of BES1 and BZR1 target genes established a transcriptional network for BR response and crosstalk with other signaling pathways. Recent studies also revealed regulatory mechanisms of BRs in many developmental processes and regulation of BR biosynthesis. Here we provide an overview and discuss some of the most recent progress in the regulation of BR signaling and biosynthesis pathways.

  16. Brassinosteroids stimulate plant tropisms through modulation of polar auxin transport in Brassica and Arabidopsis.

    Science.gov (United States)

    Li, Li; Xu, Jian; Xu, Zhi-Hong; Xue, Hong-Wei

    2005-10-01

    Brassinosteroids (BRs) are important plant growth regulators in multiple developmental processes. Previous studies have indicated that BR treatment enhanced auxin-related responses, but the underlying mechanisms remain unknown. Using (14)C-labeled indole-3-acetic acid and Arabidopsis thaliana plants harboring an auxin-responsive reporter construct, we show that the BR brassinolide (BL) stimulates polar auxin transport capacities and modifies the distribution of endogenous auxin. In plants treated with BL or defective in BR biosynthesis or signaling, the transcription of PIN genes, which facilitate functional auxin transport in plants, was differentially regulated. In addition, BL enhanced plant tropistic responses by promoting the accumulation of the PIN2 protein from the root tip to the elongation zone and stimulating the expression and dispersed localization of ROP2 during tropistic responses. Constitutive overexpression of ROP2 results in enhanced polar accumulation of PIN2 protein in the root elongation region and increased gravitropism, which is significantly affected by latrunculin B, an inhibitor of F-actin assembly. The ROP2 dominant negative mutants (35S-ROP2-DA/DN) show delayed tropistic responses, and this delay cannot be reversed by BL addition, strongly supporting the idea that ROP2 modulates the functional localization of PIN2 through regulation of the assembly/reassembly of F-actins, thereby mediating the BR effects on polar auxin transport and tropistic responses.

  17. Involvement of Auxin and Brassinosteroid in Dwarfism of Autotetraploid Apple (Malus × domestica).

    Science.gov (United States)

    Ma, Yue; Xue, Hao; Zhang, Lei; Zhang, Feng; Ou, Chunqing; Wang, Feng; Zhang, Zhihong

    2016-01-01

    The plant height is an important trait in fruit tree. However, the molecular mechanism on dwarfism is still poorly understood. We found that colchicine-induced autotetraploid apple plants (Malus × domestica) exhibited a dwarf phenotype. The vertical length of cortical parenchyma cells was shorter in autotetraploids than in diploids, by observing paraffin sections. Hormone levels of indoleacetic acid (IAA) and brassinosteroid (BR) were significantly decreased in 3- and 5-year-old autotetraploid plants. Digital gene expression (DGE) analysis showed that the differentially expressed genes were mainly involved in IAA and BR pathways. microRNA390 was significantly upregulated according to microarray analysis. Exogenous application of IAA and BR promoted stem elongation of both apple plants grown in medium. The results show that dwarfing in autotetraploid apple plants is most likely regulated by IAA and BR. The dwarf phenotype of autotetraploid apple plants could be due to accumulation of miR390 after genome doubling, leading to upregulation of apple trans-acting short-interfering RNA 3 (MdTAS3) expression, which in turn downregulates the expression of MdARF3. Overall, this leads to partial interruption of the IAA and BR signal transduction pathway. Our study provides important insights into the molecular mechanisms underlying dwarfism in autopolyploid apple plants.

  18. Genome-Wide Analysis Revealed the Complex Regulatory Network of Brassinosteroid Effects in Photomorphogenesis

    Institute of Scientific and Technical Information of China (English)

    Li Song; Xiao-Yi Zhou; Li Li; Liang-Jiao Xue; Xi Yang; Hong-Wei Xue

    2009-01-01

    Light and brassinosteroids (BRs) have been proved to be crucial in regulating plant growth and development;however,the mechanism of how they synergistically function is still largely unknown.To explore the underlying mechanisms in photomorphogenesis,genome-wide analyses were carried out through examining the gene expressions of the dark-grown WT or BR biosynthesis-defective mutant det2 seedlings in the presence of light stimuli or exogenous Brassinolide (BL).Results showed that BR deficiency stimulates,while BL treatment suppresses,the expressions of lightresponsive genes and photomorphogenesis,confirming the negative effects of BR in photomorphogenesis.This is consistent with the specific effects of BR on the expression of genes involved in cell wall modification,cellular metabolism and energy utilization during dark-light transition.Further analysis revealed that hormone biosynthesis and signaling-related genes,especially those of auxin,were altered under BL treatment or light stimuli,indicating that BR may modulate photomorphogenesis through synergetic regulation with other hormones.Additionally,suppressed ubiquitin-cycle pathway during light-dark transition hinted the presence of a complicated network among light,hormone,and protein degradation.The study provides the direct evidence of BR effects in photomorphogenesis and identified the genes involved in BR and light signaling pathway,which will help to elucidate the molecular mechanism of plant photomorphogenesis.

  19. Effects of brassinazole, an inhibitor of brassinosteroid biosynthesis, on light- and dark-grown Chlorella vulgaris.

    Science.gov (United States)

    Bajguz, Andrzej; Asami, Tadao

    2004-03-01

    Treatment of cultured Chlorella vulgaris Beijerinck cells with 0.1-10 microM brassinazole (Brz2001), an inhibitor of brassinosteroid (BR) biosynthesis, inhibits their growth during the first 48 h of cultivation in the light. This inhibition is prevented by the co-application of BR. This result suggests that the presence of endogenous BRs during the initial steps of the C. vulgaris cell cycle is indispensable for their normal growth in the light. In darkness, a treatment with 10 nM brassinolide (BL) promotes growth through the first 24 h of culture, but during the following 24 h the cells undergo complete stagnation. Treatment of dark-grown cells with either Brz2001 alone, or a mixture of 10 nM BL and 0.1/10 microM Brz2001, also stimulates their growth. The effects of treatment with 10 nM BL mixed with 0.1-10 microM of a mevalonate-pathway inhibitor (mevinolin), or a non-mevalonate-pathway inhibitor (clomazone), were also investigated. Mevinolin at these concentrations did not inhibit growth of C. vulgaris; however, clomazone did. Addition of BL overcame the inhibition. These results suggest that the mevalonate pathway does not function in C. vulgaris, and that the non-mevalonate pathway for isopentenyl diphosphate biosynthesis is responsible for the synthesis of one of the primary precursors in BR biosynthesis.

  20. Structural Modifications of Deoxycholic Acid to Obtain Three Known Brassinosteroid Analogues and Full NMR Spectroscopic Characterization.

    Science.gov (United States)

    Herrera, Heidy; Carvajal, Rodrigo; Olea, Andrés F; Espinoza, Luis

    2016-08-27

    An improved synthesis route for obtaining known brassinosteroid analogues, i.e., methyl 2α,3α-dihydroxy-6-oxo-5α-cholan-24-oate (11), methyl 3α-hydroxy-6-oxo-7-oxa-5α-cholan-24-oate (15) and methyl 3α-hydroxy-6-oxa-7-oxo-5α-cholan-24-oate (16), from hyodeoxycholic acid (4) maintaining the native side chain is described. In the alternative procedure, the di-oxidized product 6, obtained in the oxidation of methyl hyodeoxycholate 5, was converted almost quantitatively into the target monoketone 7 by stereoselective reduction with NaBH₄, increasing the overall yield of this synthetic route to 96.8%. The complete ¹H- and (13)C-NMR assignments for all compounds synthesized in this work have been made by 1D and 2D heteronuclear correlation gs-HSQC and gs-HMBC techniques. Thus, it was possible to update the spectroscopic information of ¹H-NMR and to accomplish a complete assignment of all (13)C-NMR signals for analogues 5-16, which were previously reported only in partial form.

  1. Role of brassinosteroid in plant adaptation to abiotic stresses and its interplay with other hormones.

    Science.gov (United States)

    Ahammed, Golam J; Xia, Xiao-Jian; Li, Xin; Shi, Kai; Yu, Jing-Quan; Zhou, Yan-Hong

    2015-01-01

    Brassinosteroids (BRs) are ubiquitous plant steroid hormones, playing diverse roles in plant growth, development and stress responses. Defects in BRs biosynthesis or signaling result in physiologic and phenotypic abnormalities. To date, numerous studies have highlighted BRs-induced stress tolerance to various environmental extremes such as high temperature, chilling, drought, salinity and heavy metals in a range of plant species. However, the in-depth mechanisms of BRs-induced stress tolerance still remain largely unknown. It is now clear that BRs-induced stress responses are strictly concentration dependent and the optimal concentration for improving the plant adaptability may vary depending on the plant species, developmental stages and environmental conditions as well. Conflicting evidences concerning regulation of stress adaptation by BRs demand further elucidation of mechanism of BRs action in response to environmental stresses in plants. Recent advances in phytohormone research suggest that the effect of BRs on stress tolerance relies largely on its interplay with other hormones. In this review, we critically analyze the multifaceted roles of BRs in various abiotic stresses and its potential crosstalk with other hormones in stress adaptation. The discrepancy in the dose and mode of application of BRs analogues for stress management is also discussed.

  2. Reactive oxygen species are involved in brassinosteroid-induced stress tolerance in cucumber.

    Science.gov (United States)

    Xia, Xiao-Jian; Wang, Yan-Jie; Zhou, Yan-Hong; Tao, Yuan; Mao, Wei-Hua; Shi, Kai; Asami, Tadao; Chen, Zhixiang; Yu, Jing-Quan

    2009-06-01

    Brassinosteroids (BRs) induce plant tolerance to a wide spectrum of stresses. To study how BR induces stress tolerance, we manipulated the BR levels in cucumber (Cucumis sativus) through a chemical genetics approach and found that BR levels were positively correlated with the tolerance to photo-oxidative and cold stresses and resistance to Cucumber mosaic virus. We also showed that BR treatment enhanced NADPH oxidase activity and elevated H(2)O(2) levels in apoplast. H(2)O(2) levels were elevated as early as 3 h and returned to basal levels 3 d after BR treatment. BR-induced H(2)O(2) accumulation was accompanied by increased tolerance to oxidative stress. Inhibition of NADPH oxidase and chemical scavenging of H(2)O(2) reduced BR-induced oxidative and cold tolerance and defense gene expression. BR treatment induced expression of both regulatory genes, such as RBOH, MAPK1, and MAPK3, and genes involved in defense and antioxidant responses. These results strongly suggest that elevated H(2)O(2) levels resulting from enhanced NADPH oxidase activity are involved in the BR-induced stress tolerance.

  3. Brassinosteroid signaling directs formative cell divisions and protophloem differentiation in Arabidopsis root meristems.

    Science.gov (United States)

    Kang, Yeon Hee; Breda, Alice; Hardtke, Christian S

    2017-01-15

    Brassinosteroids (BRs) trigger an intracellular signaling cascade through its receptors BR INSENSITIVE 1 (BRI1), BRI1-LIKE 1 (BRL1) and BRL3. Recent studies suggest that BR-independent inputs related to vascular differentiation, for instance root protophloem development, modulate downstream BR signaling components. Here, we report that protophloem sieve element differentiation is indeed impaired in bri1 brl1 brl3 mutants, although this effect might not be mediated by canonical downstream BR signaling components. We also found that their small meristem size is entirely explained by reduced cell elongation, which is, however, accompanied by supernumerary formative cell divisions in the radial dimension. Thus, reduced cell expansion in conjunction with growth retardation, because of the need to accommodate supernumerary formative divisions, can account for the overall short root phenotype of BR signaling mutants. Tissue-specific re-addition of BRI1 activity partially rescued subsets of these defects through partly cell-autonomous, partly non-cell-autonomous effects. However, protophloem-specific BRI1 expression essentially rescued all major bri1 brl1 brl3 root meristem phenotypes. Our data suggest that BR perception in the protophloem is sufficient to systemically convey BR action in the root meristem context.

  4. OsGSR1 is involved in crosstalk between gibberellins and brassinosteroids in rice.

    Science.gov (United States)

    Wang, Li; Wang, Zhen; Xu, Yunyuan; Joo, Se-Hwan; Kim, Seong-Ki; Xue, Zhen; Xu, Zhihong; Wang, Zhiyong; Chong, Kang

    2009-02-01

    Gibberellins (GAs) and brassinosteroids (BRs), two growth-promoting phytohormones, regulate many common physiological processes. Their interactions at the molecular level remain unclear. Here, we demonstrate that OsGSR1, a member of the GAST (GA-stimulated transcript) gene family, is induced by GA and repressed by BR. RNA interference (RNAi) transgenic rice plants with reduced OsGSR1 expression show phenotypes similar to plants deficient in BR, including short primary roots, erect leaves and reduced fertility. The OsGSR1 RNAi transgenic rice shows a reduced level of endogenous BR, and the dwarf phenotype could be rescued by the application of brassinolide. The yeast two-hybrid assay revealed that OsGSR1 interacts with DIM/DWF1, an enzyme that catalyzes the conversion from 24-methylenecholesterol to campesterol in BR biosynthesis. These results suggest that OsGSR1 activates BR synthesis by directly regulating a BR biosynthetic enzyme at the post-translational level. Furthermore, OsGSR1 RNAi plants show a reduced sensitivity to GA treatment, an increased expression of the GA biosynthetic gene OsGA20ox2, which is feedback inhibited by GA signaling, and an elevated level of endogenous GA: together, these suggest that OsGSR1 is a positive regulator of GA signaling. These results demonstrate that OsGSR1 plays important roles in both BR and GA pathways, and also mediates an interaction between the two signaling pathways.

  5. Connecting growth and defense: the emerging roles of brassinosteroids and gibberellins in plant innate immunity.

    Science.gov (United States)

    De Bruyne, Lieselotte; Höfte, Monica; De Vleesschauwer, David

    2014-06-01

    Brassinosteroids (BRs) and gibberellins (GAs) are two groups of phytohormones that regulate many common developmental processes throughout the plant life cycle. Fueled by large-scale 'omics' technologies and the burgeoning field of plant computational biology, the past few years have witnessed paradigm-shifting advances in our understanding of how BRs and GA are perceived and their signals transduced. Accumulating evidence also implicates BR and GA in the coordination and integration of plant immune responses. Similarly to other growth regulators, BR and GA play ambiguous roles in molding pathological outcomes, the effects of which may depend not only on the pathogen's lifestyle and infection strategy, but also on specialized features of each interaction. Analysis of the underpinning molecular mechanisms points to a crucial role of GA-inhibiting DELLA proteins and the BR-regulated transcription factor BZR1. Acting at the interface of developmental and defense signaling, these proteins likely serve as central hubs for pathway crosstalk and signal integration, allowing appropriate modulation of plant growth and defense in response to various stimuli. In this review, we outline the latest discoveries dealing with BR and GA modulation of plant innate immunity and highlight interactions between BR and GA signaling, plant defense, and microbial virulence.

  6. Ethylene and hydrogen peroxide are involved in brassinosteroid-induced salt tolerance in tomato

    Science.gov (United States)

    Zhu, Tong; Deng, Xingguang; Zhou, Xue; Zhu, Lisha; Zou, Lijuan; Li, Pengxu; Zhang, Dawei; Lin, Honghui

    2016-01-01

    Crosstalk between phytohormone pathways is essential in plant growth, development and stress responses. Brassinosteroids (BRs) and ethylene are both pivotal plant growth regulators, and the interaction between these two phytohormones in the tomato response to salt stress is still unclear. Here, we explored the mechanism by which BRs affect ethylene biosynthesis and signaling in tomato seedlings under salt stress. The activity of 1-aminocyclopropane-1-carboxylate synthase (ACS), an ethylene synthesis enzyme, and the ethylene signaling pathway were activated in plants pretreated with BRs. Scavenging of ethylene production or silencing of ethylene signaling components inhibited BR-induced salt tolerance and blocked BR-induced activities of several antioxidant enzymes. Previous studies have reported that BRs can induce plant tolerance to a variety of environmental stimuli by triggering the generation of H2O2 as a signaling molecule. We also found that H2O2 might be involved in the crosstalk between BRs and ethylene in the tomato response to salt stress. Simultaneously, BR-induced ethylene production was partially blocked by pretreated with a reactive oxygen species scavenger or synthesis inhibitor. These results strongly demonstrated that ethylene and H2O2 play important roles in BR-dependent induction of plant salt stress tolerance. Furthermore, we also investigated the relationship between BR signaling and ethylene signaling pathways in plant processes responding to salt stress. PMID:27739520

  7. Dynamics of brassinosteroid response modulated by negative regulator LIC in rice.

    Directory of Open Access Journals (Sweden)

    Cui Zhang

    Full Text Available Brassinosteroids (BRs regulate rice plant architecture, including leaf bending, which affects grain yield. Although BR signaling has been investigated in Arabidopsis thaliana, the components negatively regulating this pathway are less well understood. Here, we demonstrate that Oryza sativa LEAF and TILLER ANGLE INCREASED CONTROLLER (LIC acts as an antagonistic transcription factor of BRASSINAZOLE-RESISTANT 1 (BZR1 to attenuate the BR signaling pathway. The gain-of-function mutant lic-1 and LIC-overexpressing lines showed erect leaves, similar to BZR1-depleted lines, which indicates the opposite roles of LIC and BZR1 in regulating leaf bending. Quantitative PCR revealed LIC transcription rapidly induced by BR treatment. Image analysis and immunoblotting showed that upon BR treatment LIC proteins translocate from the cytoplasm to the nucleus in a phosphorylation-dependent fashion. Phosphorylation assay in vitro revealed LIC phosphorylated by GSK3-like kinases. For negative feedback, LIC bound to the core element CTCGC in the BZR1 promoter on gel-shift and chromatin immunoprecipitation assay and repressed its transcription on transient transformation assay. LIC directly regulated target genes such as INCREASED LEAF INCLINATION 1 (ILI1 to oppose the action of BZR1. Repression of LIC in ILI1 transcription in protoplasts was partially rescued by BZR1. Phenotypic analysis of the crossed lines depleted in both LIC and BZR1 suggested that BZR1 functionally depends on LIC. Molecular and physiology assays revealed that LIC plays a dominant role at high BR levels, whereas BZR1 is dominant at low levels. Thus, LIC regulates rice leaf bending as an antagonistic transcription factor of BZR1. The phenotypes of lic-1 and LIC-overexpressing lines in erect leaves contribute to ideal plant architecture. Improving this phenotype may be a potential approach to molecular breeding for high yield in rice.

  8. Foliar application of brassinosteroids alleviates adverse effects of zinc toxicity in radish (Raphanus sativus L.) plants.

    Science.gov (United States)

    Ramakrishna, Bellamkonda; Rao, S Seeta Ram

    2015-03-01

    Growth chamber experiments were conducted to investigate the comparative effect of 24-epibrassinolide (EBL) and 28-homobrassinolide (HBL) at 0.5, 1.0, or 2.0 μM concentrations by foliar application on radish plants growing under Zn(2+) stress. In radish plants exposed to excess Zn(2+), growth was substantially reduced in terms of shoot and root length, fresh and dry weight. However, foliar application of brassinosteroids (BRs) was able to alleviate Zn(2+)-induced stress and significantly improve the above growth traits. Zinc stress decreased chlorophyll a, b, and carotenoids levels in radish plants. However, follow-up treatment with BRs increased the photosynthetic pigments in stressed and stress-free plants. The treatment of BRs led to reduced levels of H2O2, lipid peroxidation and, electrolyte leakage (ELP) and improved the leaf relative water content (RWC) in stressed plants. Increased levels of carbonyls indicating enhanced protein oxidation under Zn(2+) stress was effectively countered by supplementation of BRs. Under Zn(2+) stress, the activities of catalase (CAT), ascorbate peroxidase (APX), and superoxidase dismutase (SOD) were increased but peroxidase (POD) and glutathione reductase (GR) decreased. Foliar spraying of BRs enhanced all these enzymatic activities in radish plants under Zn(2+) stress. The BRs application greatly enhanced contents of ascorbate (ASA), glutathione (GSH), and proline under Zn(2+) stress. The decrease in the activity of nitrate reductase (NR) caused by Zn(2+) stress was restored to the level of control by application of BRs. These results point out that BRs application elevated levels of antioxidative enzymes as well as antioxidants could have conferred resistance to radish plants against Zn(2+) stress resulting in improved plant growth, relative water content and photosynthetic attributes. Of the two BRs, EBL was most effective in amelioration of Zn(2+) stress.

  9. Gene expression and functional analyses in brassinosteroid-mediated stress tolerance.

    Science.gov (United States)

    Divi, Uday K; Rahman, Tawhidur; Krishna, Priti

    2016-01-01

    The plant hormone brassinosteroid (BR) plays essential roles in plant growth and development, while also controlling plant stress responses. This dual ability of BR is intriguing from a mechanistic point of view and as a viable solution for stabilizing crop yields under the changing climatic conditions. Here we report a time course analysis of BR responses under both stress and no-stress conditions, the results of which establish that BR incorporates many stress-related features even under no-stress conditions, which are then accompanied by a dynamic stress response under unfavourable conditions. Found within the BR transcriptome were distinct molecular signatures of two stress hormones, abscisic acid and jasmonic acid, which were correlated with enhanced endogenous levels of the two hormones in BR-treated seedlings. The marked presence of genes related to protein metabolism and modification, defence responses and calcium signalling highlights the significance of their associated mechanisms and roles in BR processes. Functional analysis of loss-of-function mutants of a subset of genes selected from the BR transcriptome identified abiotic stress-related roles for ACID PHOSPHATASE5 (ACP5), WRKY33, JACALIN-RELATED LECTIN1-3 (JAC-LEC1-3) and a BR-RESPONSIVE-RECEPTOR-LIKE KINASE (BRRLK). Overall, the results of this study provide a clear link between the molecular changes impacted by BR and its ability to confer broad-range stress tolerance, emphasize the importance of post-translational modification and protein turnover as BR regulatory mechanisms and demonstrate the BR transcriptome as a repertoire of new stress-related regulatory and structural genes.

  10. Interaction of brassinosteroid functions and sucrose transporter SlSUT2 regulate the formation of arbuscular mycorrhiza.

    Science.gov (United States)

    Bitterlich, Michael; Krügel, Undine; Boldt-Burisch, Katja; Franken, Philipp; Kühn, Christina

    2014-01-01

    Transgenic tomato plants with reduced expression of the sucrose transporter SlSUT2 showed higher efficiency of mycorrhization suggesting a sucrose retrieval function of SlSUT2 from the peri-arbuscular space back into the cell cytoplasm plant cytoplasm thereby limiting mycorrhiza fungal development. Sucrose uptake in colonized root cells requires efficient plasma membrane-targeting of SlSUT2 which is often retained intracellularly in vacuolar vesicles. Protein-protein interaction studies suggested a link between SISUT2 function and components of brassinosteroid biosynthesis and signaling. Indeed, the tomato DWARF mutant d(x) defective in BR synthesis (1) showed significantly reduced mycorrhization parameters. (2) The question has been raised whether the impact of brassinosteroids on mycorrhization is a general phenomenon. Here, we include a rice mutant defective in DIM1/DWARF1 involved in BR biosynthesis to investigate the effects on mycorrhization. A model is presented where brassinolides are able to impact mycorrhization by activating SUT2 internalization and inhibiting its role in sucrose retrieval.

  11. Interaction of brassinosteroid functions and sucrose transporter SlSUT2 regulate the formation of arbuscular mycorrhiza

    Science.gov (United States)

    Bitterlich, Michael; Krügel, Undine; Boldt-Burisch, Katja; Franken, Philipp; Kühn, Christina

    2014-01-01

    Transgenic tomato plants with reduced expression of the sucrose transporter SlSUT2 showed higher efficiency of mycorrhization suggesting a sucrose retrieval function of SlSUT2 from the peri-arbuscular space back into the cell cytoplasm plant cytoplasm thereby limiting mycorrhiza fungal development. Sucrose uptake in colonized root cells requires efficient plasma membrane-targeting of SlSUT2 which is often retained intracellularly in vacuolar vesicles. Protein-protein interaction studies suggested a link between SISUT2 function and components of brassinosteroid biosynthesis and signaling. Indeed, the tomato DWARF mutant dx defective in BR synthesis1 showed significantly reduced mycorrhization parameters.2 The question has been raised whether the impact of brassinosteroids on mycorrhization is a general phenomenon. Here, we include a rice mutant defective in DIM1/DWARF1 involved in BR biosynthesis to investigate the effects on mycorrhization. A model is presented where brassinolides are able to impact mycorrhization by activating SUT2 internalization and inhibiting its role in sucrose retrieval. PMID:25482803

  12. Analysis of In Vitro DNA Interactions of Brassinosteroid-Controlled Transcription Factors Using Electrophoretic Mobility Shift Assay.

    Science.gov (United States)

    Unterholzner, Simon J; Rozhon, Wilfried; Poppenberger, Brigitte

    2017-01-01

    Most signaling cascades ultimately lead to changes in gene expression by modulating the activity of transcription factors (TFs). The electrophoretic mobility shift assay (EMSA) is a simple but powerful in vitro method for investigation of specific protein-DNA interactions. It makes use of the fact that protein-DNA complexes have a lower electrophoretic mobility in gels than free DNA has. The application of labeled probes in combination with unlabeled competitors allows investigation of DNA-binding specificity and identification of binding motifs with single base-pair resolution. Here we describe the application of EMSAs for the study of interactions of the brassinosteroid-regulated TFs, BRASSINAZOLE-RESISTANT1, (BZR1), BRI1-ETHYL METHANESULFONATE-SUPPRESSOR1 (BES1)/BZR2, and CESTA with putative binding sites. The classical approach using radiolabeled probes, as well as the more recent application of fluorescent probes, is described and the advantages and disadvantages of both methods are discussed.

  13. Membrane steroid-binding protein 1 (MSBP1) negatively regulates brassinosteroid signaling by enhancing the endocytosis of BAK1

    Institute of Scientific and Technical Information of China (English)

    Li Song; Qiu-Ming Shi; Xiao-Hua Yang; Zhi-Hong Xu; Hong-Wei Xue

    2009-01-01

    Brassinosteroids (BRs) are perceived by transmembrane receptors and play vital roles in plant growth and devel-opment, as well as cell in responses to environmental stimuli. The transmembrane receptor BRI1 can directly bind to brassinolide (BL), and BAK1 interacts with BRI1 to enhance the BRll-mediated BR signaling. Our previous studies indicated that a membrane steroid-binding protein 1 (MSBP1) could bind to BL in vitro and is negatively involved in BR signaling. To further elucidate the underlying mechanism, we here show that MSBP1 specifically interacts with the extracellular domain of BAKI in vivo in a BL-independent manner. Suppressed cell expansion and BR responses by increased expression of MSBPI can be recovered by overexpressing BAKI or its intracellular kinase domain, sug-gesting that MSBPI may suppress BR signaling through interacting with BAK1. Subcellular localization studies re-vealed that both MSBPI and BAKI are localized to plasma membrane and endocytic vesicles and MSBPI accelerates BAKI endocytosis, which results in suppressed BR signaling by shifting the equilibrium of BAKI toward endosomes. Indeed, enhanced MSBPI expression reduces the interaction between BRI1 and BAK1 in vivo, demonstrating that MSBPI acts as a negative factor at an early step of the BR signaling pathway.

  14. Genetic variation in plant CYP51s confers resistance against voriconazole, a novel inhibitor of brassinosteroid-dependent sterol biosynthesis.

    Directory of Open Access Journals (Sweden)

    Wilfried Rozhon

    Full Text Available Brassinosteroids (BRs are plant steroid hormones with structural similarity to mammalian sex steroids and ecdysteroids from insects. The BRs are synthesized from sterols and are essential regulators of cell division, cell elongation and cell differentiation. In this work we show that voriconazole, an antifungal therapeutic drug used in human and veterinary medicine, severely impairs plant growth by inhibiting sterol-14α-demethylation and thereby interfering with BR production. The plant growth regulatory properties of voriconazole and related triazoles were identified in a screen for compounds with the ability to alter BR homeostasis. Voriconazole suppressed growth of the model plant Arabidopsis thaliana and of a wide range of both monocotyledonous and dicotyledonous plants. We uncover that voriconazole toxicity in plants is a result of a deficiency in BRs that stems from an inhibition of the cytochrome P450 CYP51, which catalyzes a step of BR-dependent sterol biosynthesis. Interestingly, we found that the woodland strawberry Fragaria vesca, a member of the Rosaceae, is naturally voriconazole resistant and that this resistance is conferred by the specific CYP51 variant of F. vesca. The potential of voriconazole as a novel tool for plant research is discussed.

  15. Suppression of Wolffia arrhiza growth by brassinazole, an inhibitor of brassinosteroid biosynthesis and its restoration by endogenous 24-epibrassinolide.

    Science.gov (United States)

    Bajguz, Andrzej; Asami, Tadao

    2005-08-01

    The effect of the brassinosteroid (BR) 24-epibrassinolide (epiBL; 10(-13)-10(-6)M) on growth and levels of chlorophylls, carotenoids, sugars and protein in Wolffia arrhiza after 7 days of cultivation is reported. Application of epiBL to W. arrhiza cultures stimulates the growth and increases the content of photosynthetic pigments, sugar and protein. The greatest effect of epiBL is observed at a concentration of 10(-9)M. We tested the action of Brz2001, a specific BR biosynthesis inhibitor, in the range of 10(-6)-10(-4)M. Addition of Brz2001 to W. arrhiza cultures inhibits their growth after 7 days of cultivation. The inhibition of growth could be reversed by the addition of epiBL. Moreover, there was not complete recovery to the level of control, especially at 5 x 10(-5)-10(-4)M Brz2001. The effects of treatment with 10(-9)M epiBL mixed with a mevalonate pathway inhibitor (mevinolin), or a 2-methylerythritol 4-phosphate pathway inhibitor (clomazone), were also investigated. Mevinolin did not inhibit growth of W. arrhiza after 7 days of cultivation. However, clomazone did. Addition of epiBL overcame this inhibition. These results suggest that the mevalonate pathway may not function well in W. arrhiza and that biosynthesis of BRs through the non-mevalonate pathway in W. arrhiza could be possible.

  16. A brassinosteroid transcriptional network revealed by genome-wide identification of BESI target genes in Arabidopsis thaliana.

    Science.gov (United States)

    Yu, Xiaofei; Li, Lei; Zola, Jaroslaw; Aluru, Maneesha; Ye, Huaxun; Foudree, Andrew; Guo, Hongqing; Anderson, Sarah; Aluru, Srinivas; Liu, Peng; Rodermel, Steve; Yin, Yanhai

    2011-02-01

    Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of the BES1 and BZR1 family transcription factors. The transcriptional network through which BES1 and BZR regulate large number of target genes is mostly unknown. By combining chromatin immunoprecipitation coupled with Arabidopsis tiling arrays (ChIP-chip) and gene expression studies, we have identified 1609 putative BES1 target genes, 404 of which are regulated by BRs and/or in gain-of-function bes1-D mutant. BES1 targets contribute to BR responses and interactions with other hormonal or light signaling pathways. Computational modeling of gene expression data using Algorithm for the Reconstruction of Accurate Cellular Networks (ARACNe) reveals that BES1-targeted transcriptional factors form a gene regulatory network (GRN). Mutants of many genes in the network displayed defects in BR responses. Moreover, we found that BES1 functions to inhibit chloroplast development by repressing the expression of GLK1 and GLK2 transcription factors, confirming a hypothesis generated from the GRN. Our results thus provide a global view of BR regulated gene expression and a GRN that guides future studies in understanding BR-regulated plant growth.

  17. Ethylene is involved in brassinosteroids induced alternative respiratory pathway in cucumber (Cucumis sativus L. seedlings response to abiotic stress

    Directory of Open Access Journals (Sweden)

    Lijie eWei

    2015-11-01

    Full Text Available Effects of brassinosteroids (BRs on cucumber (Cucumis sativus L. abiotic stresses resistance to salt, polyethylene glycol (PEG, cold and the potential mechanisms were investigated in this work. Previous reports have indicated that BRs can induce ethylene production and enhance alternative oxidase (AOX pathway. The mechanisms whether ethylene is involved as a signal molecule which connected BR with AOX in regulating stress tolerance are still unknown. Here, we found that pretreatment with 1 µM brassinolide (BL, the most active BRs relieved stress-caused oxidative damage in cucumber seedlings and clearly enhanced the capacity of AOX and the ethylene biosynthesis. Furthermore, transcription level of ethylene signaling biosynthesis genes including ripening-related ACC synthase1 (CSACS1, ripening-related ACC synthase2 (CSACS2, ripening-related ACC synthase3 (CSACS3, 1-aminocyclopropane-1-carboxylate oxidase1 (CSACO1, 1-aminocyclopropane-1-carboxylate oxidase2 (CSACO2 and CSAOX were increased after BL treatment. Importantly, the application of the salicylhydroxamic acid (SHAM, AOX inhibitor and ethylene biosynthesis inhibitor aminooxyacetic acid (AOA decreased plant resistance to environmental stress by blocking BRs-induced alternative respiration. Taken together, our results demonstrated that ethylene was involved in BRs-induced AOX activity which played important roles in abiotic stresses tolerance in cucumber seedlings.

  18. Organ-specific effects of brassinosteroids on stomatal production coordinate with the action of TOO MANY MOUTHS

    Institute of Scientific and Technical Information of China (English)

    Ming Wang; Kezhen Yang; Jie Le

    2015-01-01

    In Arabidopsis, stomatal development initiates after protodermal cel s acquire stomatal lineage cel fate. Stomata or their precursors communicate with their neighbor epidermal cel s to ensure the“one cel spacing”rule. The signals from EPF/EPFL peptide ligands received by TOO MANY MOUTHS (TMM) and ERECTA‐family receptors are supposed to be transduced by YODA MAPK cascade. A basic helix‐loop‐helix transcription factor SPEECHLESS (SPCH) is another key regulator of stomatal cel fate determination and asymmetric entry divisions, and SPCH activity is regulated by YODA MAPK cascade. Brassinos-teroid (BR) signaling, one of the most wel characterized signal transduction pathways in plants, contributes to the control of stomatal production. But opposite organ‐specific effects of BR on stomatal production were reported. Here we confirm that stomatal production in hypocotyls is control ed by BR levels. YODA and CYCD4 are not essential for BR stomata‐promoting function. Furthermore, we found that BR could confer tmm hypocotyls clustered stomatal phenotype, indicating that the BR organ‐specific effects on stomatal production might coordi-nate with the TMM organ‐specific actions.

  19. After-ripening induced transcriptional changes of hormonal genes in wheat seeds: the cases of brassinosteroids, ethylene, cytokinin and salicylic acid.

    Directory of Open Access Journals (Sweden)

    Vijaya R Chitnis

    Full Text Available Maintenance and release of seed dormancy is regulated by plant hormones; their levels and seed sensitivity being the critical factors. This study reports transcriptional regulation of brassinosteroids (BR, ethylene (ET, cytokinin (CK and salicylic acid (SA related wheat genes by after-ripening, a period of dry storage that decays dormancy. Changes in the expression of hormonal genes due to seed after-ripening did not occur in the anhydrobiotic state but rather in the hydrated state. After-ripening induced dormancy decay appears to be associated with imbibition mediated increase in the synthesis and signalling of BR, via transcriptional activation of de-etiolated2, dwarf4 and brassinosteroid signaling kinase, and repression of brassinosteroid insensitive 2. Our analysis is also suggestive of the significance of increased ET production, as reflected by enhanced transcription of 1-aminocyclopropane-1-carboxylic acid oxidase in after-ripened seeds, and tight regulation of seed response to ET in regulating dormancy decay. Differential transcriptions of lonely guy, zeatin O-glucosyltransferases and cytokinin oxidases, and pseudo-response regulator between dormant and after-ripened seeds implicate CK in the regulation of seed dormancy in wheat. Our analysis also reflects the association of dormancy decay in wheat with seed SA level and NPR independent SA signaling that appear to be regulated transcriptionally by phenylalanine ammonia lyase, and whirly and suppressor of npr1 inducible1 genes, respectively. Co-expression clustering of the hormonal genes implies the significance of synergistic and antagonistic interaction between the different plant hormones in regulating wheat seed dormancy. These results contribute to further our understanding of the molecular features controlling seed dormancy in wheat.

  20. Brassinosteroide e adubação nitrogenada no crescimento e estado nutricional de mudas de abacaxizeiro provenientes do seccionamento de caule

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    Sílvio de Jesus Freitas

    2012-06-01

    Full Text Available O objetivo deste trabalho foi verificar o efeito da adubação nitrogenada e de um análogo de brassinosteroide no crescimento e na nutrição de mudas provenientes do seccionamento do caule do abacaxizeiro 'Smooth Cayenne'. O experimento foi conduzido no delineamento em blocos casualizados, em esquema fatorial 3x4, sendo foram avaliados três doses de N (5; 10 e 15 g L-1, utilizando ureia como fonte, e quatro doses de um análogo de brassinosteroide (0; 0,5; 0,75 e 1,0 mg L-1, com quatro repetições. Cada parcela experimental foi composta por 20 secções de caule. Aos 270 dias após o plantio das secções, as mudas foram colhidas e avaliadas em relação ao comprimento, diâmetro, número de folhas e à área foliar. Em seguida, as mudas foram colocadas para secar em estufa a 70ºC, para a obtenção da massa seca e análise nutricional do tecido foliar, em que se avaliaram os teores de N, K, Ca, Mg, S, Fe, Cu, Zn e Mn. O análogo de brassinosteroide promoveu incremento em todas as características de crescimento vegetativo da parte aérea das mudas de abacaxizeiro avaliadas, além de proporcionar maior teor de nitrogênio na parte aérea das mudas. A adubação nitrogenada apenas resultou em pequeno aumento do comprimento e diâmetro das mudas e não afetou o número de folhas, a área foliar, a massa seca e o estado nutricional das mudas.

  1. ABA Affects Brassinosteroid-Induced Antioxidant Defense via ZmMAP65-1a in Maize Plants.

    Science.gov (United States)

    Zhu, Yuan; Liu, Weijuan; Sheng, Yu; Zhang, Juan; Chiu, Tsanyu; Yan, Jingwei; Jiang, Mingyi; Tan, Mingpu; Zhang, Aying

    2015-07-01

    Brassinosteroids (BRs) and ABA co-ordinately regulate water deficit tolerance in maize leaves. ZmMAP65-1a, a maize microtubule-associated protein (MAP) which plays an essential role in BR-induced antioxidant defense, has been characterized previously. However, the interactions among BR, ABA and ZmMAP65-1a in water deficit tolerance remain unexplored. In this study, we demonstrated that ABA was required for BR-induced antioxidant defense via ZmMAP65-1a by using biochemical blocking and ABA biosynthetic mutants. The expression of ZmMAP65-1a in maize leaves and mesophyll protoplasts could be increased under polyethylene glycol- (PEG) stimulated water deficit and ABA treatments. Furthermore, the importance of ABA in the early pathway of BR-induced water deficit tolerance was demonstrated by limiting ABA availability. Blocking ABA biosynthesis biochemically or by a null mutation inhibited the downstream gene expression of ZmMAP65-1a and the activity of ZmMAPK5 in the pathway. It also affected the activities of BR-induced antioxidant defense-related enzymes, namely ascorbate peroxidase (APX), catalase (CAT), glutathione reductase (GR), superoxide dismutase (SOD) and NADPH oxidase. In addition, combining results from transiently overexpressed or silenced ZmMAP65-1a in mesophyll protoplasts, we discovered that ZmMAP65-1a mediated the ABA-induced gene expression and activities of APX and SOD. Surprisingly, silencing of ZmMAP65-1a in mesophyll protoplasts did not alter the gene expression of ZmCCaMK and vice versa in response to ABA. Taken together, our data indicate that water deficit-induced ABA is a key mediator in BR-induced antioxidant defense via ZmMAP65-1a in maize.

  2. Brassinosteroids make plant life easier under abiotic stresses mainly by modulating major components of antioxidant defense system

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    Bojjam V. Vardhini

    2015-01-01

    Full Text Available Various abiotic stress factors significantly contribute to major worldwide-losses in crop productivity by mainly impacting plant’s stress tolerance/adaptive capacity. The latter is largely governed by the efficiency of antioxidant defense system for the metabolism of elevated reactive oxygen species (ROS, caused by different abiotic stresses. Plant antioxidant defense system includes both enzymatic (such as superoxide dismutase, SOD, E.C. 1.15.1.1; catalase, CAT, E.C. 1.11.1.6; glutathione reductase, GR, E.C. 1.6.4.2; peroxidase, POD, E.C. 1.11.1.7; ascorbate peroxidase, APX, E.C. 1.11.1.11; guaiacol peroxidase, GPX, E.C. 1.11.1.7 and non-enzymatic (such as ascorbic acid, AsA; glutathione, GSH; tocopherols; phenolics, proline etc. components. Research reports on the status of various abiotic stresses and their impact on plant growth, development and productivity are extensive. However, least information is available on sustainable strategies for the mitigation of abiotic stress-mediated major consequences in plants. Brassinosteroids (BRs are a novel group of phytohormones with significant growth promoting nature. BRs are considered as growth regulators with pleiotropic effects, as they influence diverse physiological processes like growth, germination of seeds, rhizogenesis, senescence etc. and also confer abiotic stress resistance in plants. In the light of recent reports this paper: (a overviews major abiotic stresses and plant antioxidant defense system, (b introduces BRs and highlights their significance in general plant growth and development, and (c appraises recent literature available on BRs mediated modulation of various components of antioxidant defense system in plants under major abiotic stresses including metals/metalloids, drought, salinity, and temperature regimes. The outcome can be significant in devising future research in the current direction.

  3. The sucrose transporter SlSUT2 from tomato interacts with brassinosteroid functioning and affects arbuscular mycorrhiza formation.

    Science.gov (United States)

    Bitterlich, Michael; Krügel, Undine; Boldt-Burisch, Katja; Franken, Philipp; Kühn, Christina

    2014-06-01

    Mycorrhizal plants benefit from the fungal partners by getting better access to soil nutrients. In exchange, the plant supplies carbohydrates to the fungus. The additional carbohydrate demand in mycorrhizal plants was shown to be balanced partially by higher CO2 assimilation and increased C metabolism in shoots and roots. In order to test the role of sucrose transport for fungal development in arbuscular mycorrhizal (AM) tomato, transgenic plants with down-regulated expression of three sucrose transporter genes were analysed. Plants that carried an antisense construct of SlSUT2 (SlSUT2as) repeatedly exhibited increased mycorrhizal colonization and the positive effect of plants to mycorrhiza was abolished. Grafting experiments between transgenic and wild-type rootstocks and scions indicated that mainly the root-specific function of SlSUT2 has an impact on colonization of tomato roots with the AM fungus. Localization of SISUT2 to the periarbuscular membrane indicates a role in back transport of sucrose from the periarbuscular matrix into the plant cell thereby affecting hyphal development. Screening of an expression library for SlSUT2-interacting proteins revealed interactions with candidates involved in brassinosteroid (BR) signaling or biosynthesis. Interaction of these candidates with SlSUT2 was confirmed by bimolecular fluorescence complementation. Tomato mutants defective in BR biosynthesis were analysed with respect to mycorrhizal symbiosis and showed indeed decreased mycorrhization. This finding suggests that BRs affect mycorrhizal infection and colonization. If the inhibitory effect of SlSUT2 on mycorrhizal growth involves components of BR synthesis and of the BR signaling pathway is discussed.

  4. BZS1, a B-box Protein, Promotes Photomorphogenesis Downstream of Both Brassinosteroid and Light Signaling Pathways

    Institute of Scientific and Technical Information of China (English)

    Xi-Ying Fan; Kang Chong; Zhi-Yong Wang; Yu Sun; Dong-Mei Cao; Ming-Yi Bai; Xiao-Min Luo; Hong-Juan Yang; Chuang-Qi Wei; Sheng-Wei Zhu; Ying Sun

    2012-01-01

    Photomorphogenesis is controlled by multiple signaling pathways,including the light and brassinosteroid (BR) pathways.BR signaling activates the BZR1 transcription factor,which is required for suppressing photomorphogenesis in the dark.We identified a suppressor of the BR hypersensitive mutant bzr1-1D and named it bzr1-1D suppressor1-Dominant (bzs1-D).The bzs1-D mutation was caused by overexpression of a B-box zinc finger protein BZS1,which is transcriptionally repressed by BZR1.Overexpression of BZS1 causes de-etiolation in the dark,short hypocotyls in the light,reduced sensitivity to BR treatment,and repression of many BR-activated genes.Knockdown of BZS1 by co-suppression partly suppressed the short hypocotyl phenotypes of BR-deficient or insensitive mutants.These results support that BZS1 is a negative regulator of BR response.BZS1 overexpressors are hypersensitive to different wavelengths of light and loss of function of BZS1 reduces plant sensitivity to light and partly suppresses the constitutive photomorphogenesis 1 (cop1) mutant in the dark,suggesting a positive role in light response.BZS1 protein accumulates at an increased level after light treatment of dark-grown BZS1-OX plants and in the cop1 mutants,and BZS1 interacts with COP1 in vitro,suggesting that light regulates BZS1 through COP1-mediated ubiquitination and proteasomal degradation.These results demonstrate that BZS1 mediates the crosstalk between BR and light pathways.

  5. Hydrogen peroxide functions as a secondary messenger for brassinosteroids-induced CO2 assimilation and carbohydrate metabolism in Cucumis sativus.

    Science.gov (United States)

    Jiang, Yu-ping; Cheng, Fei; Zhou, Yan-hong; Xia, Xiao-jian; Mao, Wei-hua; Shi, Kai; Chen, Zhi-xiang; Yu, Jing-quan

    2012-10-01

    Brassinosteroids (BRs) are potent regulators of photosynthesis and crop yield in agricultural crops; however, the mechanism by which BRs increase photosynthesis is not fully understood. Here, we show that foliar application of 24-epibrassinolide (EBR) resulted in increases in CO(2) assimilation, hydrogen peroxide (H(2)O(2)) accumulation, and leaf area in cucumber. H(2)O(2) treatment induced increases in CO(2) assimilation whilst inhibition of the H(2)O(2) accumulation by its generation inhibitor or scavenger completely abolished EBR-induced CO(2) assimilation. Increases of light harvesting due to larger leaf areas in EBR- and H(2)O(2)-treated plants were accompanied by increases in the photochemical efficiency of photosystem II (Φ(PSII)) and photochemical quenching coefficient (q(P)). EBR and H(2)O(2) both activated carboxylation efficiency of ribulose-1,5-bisphosphate oxygenase/carboxylase (Rubisco) from analysis of CO(2) response curve and in vitro measurement of Rubisco activities. Moreover, EBR and H(2)O(2) increased contents of total soluble sugar, sucrose, hexose, and starch, followed by enhanced activities of sugar metabolism such as sucrose phosphate synthase, sucrose synthase, and invertase. Interestingly, expression of transcripts of enzymes involved in starch and sugar utilization were inhibited by EBR and H(2)O(2). However, the effects of EBR on carbohydrate metabolisms were reversed by the H(2)O(2) generation inhibitor diphenyleneodonium (DPI) or scavenger dimethylthiourea (DMTU) pretreatment. All of these results indicate that H(2)O(2) functions as a secondary messenger for EBR-induced CO(2) assimilation and carbohydrate metabolism in cucumber plants. Our study confirms that H(2)O(2) mediates the regulation of photosynthesis by BRs and suggests that EBR and H(2)O(2) regulate Calvin cycle and sugar metabolism via redox signaling and thus increase the photosynthetic potential and yield of crops.

  6. Hydrogen peroxide functions as a secondary messenger for brassinosteroids-induced CO2 assimilation and carbohydrate metabolism in Cucumis sativus

    Institute of Scientific and Technical Information of China (English)

    Yu-ping JIANG; Fei CHENG; Yan-hong ZHOU; Xiao-jian XIA; Wei-hua MAO; Kai SHI; Zhi-xiang CHEN; Jing-quan YU

    2012-01-01

    Brassinosteroids (BRs) are potent regulators of photosynthesis and crop yield in agricultural crops;however,the mechanism by which BRs increase photosynthesis is not fully understood.Here,we show that foliar application of 24-epibrassinolide (EBR) resulted in increases in CO2 assimilation,hydrogen peroxide (H2O2) accumulation,and leaf area in cucumber.H2O2 treatment induced increases in CO2 assimilation whilst inhibition of the H2O2 accumulation by its generation inhibitor or scavenger completely abolished EBR-induced CO2 assimilation.Increases of light harvesting due to larger leaf areas in EBR- and H2O2-treated plants were accompanied by increases in the photochemical efficiency of photosystem Ⅱ (ΦPSⅡ) and photochemical quenching coefficient (qp).EBR and H2O2 both activated carboxylation efficiency of ribulose-1,5-bisphosphate oxygenase/carboxylase (Rubisco) from analysis of CO2 response curve and in vitro measurement of Rubisco activities.Moreover,EBR and H2O2 increased contents of total soluble sugar,sucrose,hexose,and starch,followed by enhanced activities of sugar metabolism such as sucrose phosphate synthase,sucrose synthase,and invertase.Interestingly,expression of transcripts of enzymes involved in starch and sugar utilization were inhibited by EBR and H2O2.However,the effects of EBR on carbohydrate metabolisms were reversed by the H2O2 generation inhibitor diphenyleneodonium (DPI) or scavenger dimethylthiourea (DMTU) pretreatment.All of these results indicate that H2O2 functions as a secondary messenger for EBR-induced CO2 assimilation and carbohydrate metabolism in cucumber plants.Our study confirms that H2O2 mediates the regulation of photosynthesis by BRs and suggests that EBR and H2O2 regulate Calvin cycle and sugar metabolism via redox signaling and thus increase the photosynthetic potential and yield of crops.

  7. Interactive effect of brassinosteroids and cytokinins on growth, chlorophyll, monosaccharide and protein content in the green alga Chlorella vulgaris (Trebouxiophyceae).

    Science.gov (United States)

    Bajguz, Andrzej; Piotrowska-Niczyporuk, Alicja

    2014-07-01

    Interaction between brassinosteroids (BRs) (brassinolide, BL; 24-epibrassinolide, 24-epiBL; 28-homobrassinolide, 28-homoBL; castasterone, CS; 24-epicastasterone, 24-epiCS; 28-homocastasterone, 28-homoCS) and adenine- (trans-zeatin, tZ; kinetin, Kin) as well as phenylurea-type (1,3-diphenylurea, DPU) cytokinins (CKs) in the regulation of cell number, phytohormone level and the content of chlorophyll, monosaccharide and protein in unicellular green alga Chlorella vulgaris (Trebouxiophyceae) were examined. Chlorella vulgaris exhibited sensitivity to CKs in the following order of their stimulating properties: 10 nM tZ > 100 nM Kin >1 μM DPU. Exogenously applied BRs possessed the highest biological activity in algal cells at concentration of 10 nM. Among the BRs, BL was characterized by the highest activity, while 28-homoCS - by the lowest. The considerable increase in the level of all endogenous BRs by 27-46% was observed in C. vulgaris culture treated with exogenous 10 nM tZ. It can be speculated that CKs may stimulate BR activity in C. vulgaris by inducing the accumulation of endogenous BRs. CKs interacted synergistically with BRs increasing the number of cells and endogenous accumulation of proteins, chlorophylls and monosaccharides in C. vulgaris. The highest stimulation of algal growth and the contents of analyzed biochemical parameters were observed for BL applied in combination with tZ, whereas the lowest in the culture treated with both 28-homoCS and DPU. However, regardless of the applied mixture of BRs with CKs, the considerable increase in cell number and the metabolite accumulation was found above the level obtained in cultures treated with any single phytohormone in unicellular green alga C. vulgaris.

  8. Endosidin1 defines a compartment involved in endocytosis of the brassinosteroid receptor BRI1 and the auxin transporters PIN2 and AUX1.

    Science.gov (United States)

    Robert, Stéphanie; Chary, S Narasimha; Drakakaki, Georgia; Li, Shundai; Yang, Zhenbiao; Raikhel, Natasha V; Hicks, Glenn R

    2008-06-17

    Although it is known that proteins are delivered to and recycled from the plasma membrane (PM) via endosomes, the nature of the compartments and pathways responsible for cargo and vesicle sorting and cellular signaling is poorly understood. To define and dissect specific recycling pathways, chemical effectors of proteins involved in vesicle trafficking, especially through endosomes, would be invaluable. Thus, we identified chemicals affecting essential steps in PM/endosome trafficking, using the intensely localized PM transport at the tips of germinating pollen tubes. The basic mechanisms of this localized growth are likely similar to those of non-tip growing cells in seedlings. The compound endosidin 1 (ES1) interfered selectively with endocytosis in seedlings, providing a unique tool to dissect recycling pathways. ES1 treatment induced the rapid agglomeration of the auxin translocators PIN2 and AUX1 and the brassinosteroid receptor BRI1 into distinct endomembrane compartments termed "endosidin bodies"; however, the markers PIN1, PIN7, and other PM proteins were unaffected. Endosidin bodies were defined by the syntaxin SYP61 and the V-ATPase subunit VHA-a1, two trans-Golgi network (TGN)/endosomal proteins. Interestingly, brassinosteroid (BR)-induced gene expression was inhibited by ES1 and treated seedlings displayed a brassinolide (BL)-insensitive phenotype similar to a bri1 loss-of-function mutant. No effect was detected in auxin signaling. Thus, PIN2, AUX1, and BRI1 use interactive pathways involving an early SYP61/VHA-a1 endosomal compartment.

  9. DNA sequences encoding erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Lin, F.K.

    1987-10-27

    A purified and isolated DNA sequence is described consisting essentially of a DNA sequence encoding a polypeptide having an amino acid sequence sufficiently duplicative of that of erythropoietin to allow possession of the biological property of causing bone marrow cells to increase production of reticulocytes and red blood cells, and to increase hemoglobin synthesis or iron uptake.

  10. Negative Beta Encoder

    CERN Document Server

    Kohda, Tohru; Aihara, Kazuyuki

    2008-01-01

    A new class of analog-digital (A/D), digital-analog (D/A) converters as an alternative to conventional ones, called $\\beta$-encoder, has been shown to have exponential accuracy in the bit rates while possessing self-correction property for fluctuations of amplifier factor $\\beta$ and quantizer threshold $\

  11. Time-Encoded Imagers.

    Energy Technology Data Exchange (ETDEWEB)

    Marleau, Peter; Brubaker, Erik

    2014-11-01

    This report provides a short overview of the DNN R&D funded project, Time-Encoded Imagers. The project began in FY11 and concluded in FY14. The Project Description below provides the overall motivation and objectives for the project as well as a summary of programmatic direction. It is followed by a short description of each task and the resulting deliverables.

  12. Brassinosteroids Improve Quality of Summer Tea (Camellia sinensis L.) by Balancing Biosynthesis of Polyphenols and Amino Acids

    Science.gov (United States)

    Li, Xin; Ahammed, Golam J.; Li, Zhi-Xin; Zhang, Lan; Wei, Ji-Peng; Shen, Chen; Yan, Peng; Zhang, Li-Ping; Han, Wen-Yan

    2016-01-01

    Summer grown green tea is less popular due to bitterness and high astringency, which are attributed to high levels of tea polyphenols (TP) and low levels of amino acids (AA) in tea leaves (Camellia sinensis L.). Brassinosteroids (BRs), a group of steroidal plant hormones can regulate primary and secondary metabolism in a range of plant species under both normal and stress conditions. However, specific effects of BRs on the photosynthesis of tea plants and the quality of summer green tea are largely unknown. Here we show that 24-epibrassinolide (EBR), a bioactive BR, promoted photosynthesis in tea plants in a concentration-dependent manner. Stimulation in photosynthesis by EBR resulted in an increased summer tea yield. Although all tested concentrations (0.01, 0.05, 0.1, 0.5, and 1.0 ppm) of EBR increased concentrations of TP and AA, a moderate concentration (0.5 ppm) caused the highest decrease in TP to AA ratio, an important feature of quality tea. Time-course analysis using 0.5 ppm EBR as foliar spray revealed that TP or AA concentration increased as early as 3 h after EBR application, reaching the highest peak at 24 h and that remained more or less stable. Importantly, such changes in TP and AA concentration by EBR resulted in a remarkably decreased but stable TP to AA ratio at 24 h and onward. Furthermore, concentrations of catechins and theanine increased, while that of caffeine remained unaltered following treatment with EBR. EBR improved activity of phenylalanine ammonia-lyase (PAL) and glutamine: 2-oxoglutarate aminotransferase (GOGAT) enzymes involved in catechins and theanine biosynthesis, respectively. Transcript analysis revealed that transcript levels of CsPAL and CsGS peaked as early as 6 h, while that of CsGOGAT peaked at 12 h following application of EBR, implying that EBR increased the concentration of TP and AA by inducing their biosynthesis. These results suggest a positive role of BR in enhancing green tea quality, which might have potential

  13. Chromium stress mitigation by polyamine-brassinosteroid application involves phytohormonal and physiological strategies in Raphanus sativus L.

    Directory of Open Access Journals (Sweden)

    Sikander Pal Choudhary

    Full Text Available Brassinosteroids (BRs and polyamines (PAs are well-established growth regulators playing key roles in stress management among plants. In the present study, we evaluated the effects of epibrassinolide (EBL, an active BR and spermidine (Spd, an active PA on the tolerance of radish to oxidative stress induced by Cr (VI metal. Our investigation aimed to study the impacts of EBL (10(-9 M and/or Spd (1 mM on the biochemical and physiological responses of radish (Raphanus sativus L. under Cr-stress. Applications of EBL and/or Spd were found to improve growth of Cr-stressed seedlings in terms of root length, shoot length and fresh weight. Our data also indicated that applications of EBL and Spd have significant impacts, particularly when applied together, on the endogenous titers of PAs, free and bound forms of IAA and ABA in seedlings treated with Cr-stress. Additionally, co-applications of EBL and Spd modulated more remarkably the titers of antioxidants (glutathione, ascorbic acid, proline, glycine betaine and total phenol and activities of antioxidant enzymes (guaicol peroxidase, catalase, superoxide dismutase and glutathione reductase in Cr-stressed plants than their individual applications. Attenuation of Cr-stress by EBL and/or Spd (more efficient with EBL and Spd combination was also supported by enhanced values of stress indices, such as phytochelatins, photosynthetic pigments and total soluble sugars, and reduction in malondialdehyde and H(2O(2 levels in Cr-treated seedlings. Diminution of ROS production and enhanced ROS scavenging capacities were also noted for EBL and/or Spd under Cr-stress. However, no significant reduction in Cr uptake was observed for co-application of EBL and Spd when compared to their individual treatments in Cr-stressed seedlings. Taken together, our results demonstrate that co-applications of EBL and Spd are more effective than their independent treatments in lowering the Cr-induced oxidative stress in radish, leading

  14. Chromium stress mitigation by polyamine-brassinosteroid application involves phytohormonal and physiological strategies in Raphanus sativus L.

    Science.gov (United States)

    Choudhary, Sikander Pal; Kanwar, Mukesh; Bhardwaj, Renu; Yu, Jing-Quan; Tran, Lam-Son Phan

    2012-01-01

    Brassinosteroids (BRs) and polyamines (PAs) are well-established growth regulators playing key roles in stress management among plants. In the present study, we evaluated the effects of epibrassinolide (EBL, an active BR) and spermidine (Spd, an active PA) on the tolerance of radish to oxidative stress induced by Cr (VI) metal. Our investigation aimed to study the impacts of EBL (10(-9) M) and/or Spd (1 mM) on the biochemical and physiological responses of radish (Raphanus sativus L.) under Cr-stress. Applications of EBL and/or Spd were found to improve growth of Cr-stressed seedlings in terms of root length, shoot length and fresh weight. Our data also indicated that applications of EBL and Spd have significant impacts, particularly when applied together, on the endogenous titers of PAs, free and bound forms of IAA and ABA in seedlings treated with Cr-stress. Additionally, co-applications of EBL and Spd modulated more remarkably the titers of antioxidants (glutathione, ascorbic acid, proline, glycine betaine and total phenol) and activities of antioxidant enzymes (guaicol peroxidase, catalase, superoxide dismutase and glutathione reductase) in Cr-stressed plants than their individual applications. Attenuation of Cr-stress by EBL and/or Spd (more efficient with EBL and Spd combination) was also supported by enhanced values of stress indices, such as phytochelatins, photosynthetic pigments and total soluble sugars, and reduction in malondialdehyde and H(2)O(2) levels in Cr-treated seedlings. Diminution of ROS production and enhanced ROS scavenging capacities were also noted for EBL and/or Spd under Cr-stress. However, no significant reduction in Cr uptake was observed for co-application of EBL and Spd when compared to their individual treatments in Cr-stressed seedlings. Taken together, our results demonstrate that co-applications of EBL and Spd are more effective than their independent treatments in lowering the Cr-induced oxidative stress in radish, leading to

  15. Brassinosteroids Improve Quality of Summer Tea by Balancing Biosynthesis of Polyphenols and Amino Acids in Camellia sinensis L.

    Directory of Open Access Journals (Sweden)

    Xin Li

    2016-08-01

    Full Text Available Summer grown green tea is less popular due to bitterness and high astringency that are attributed to high levels of tea polyphenol (TP and low levels of amino acids (AA in tea leaves (Camellia sinensis L.. Brassinosteroids (BRs, a group of steroidal plant hormones can regulate primary and secondary metabolism in a range of plant species under both normal and stress conditions. However, specific effects of BRs on the photosynthesis of tea plants and the quality of summer green tea are largely unknown. Here we show that 24-epibrassinolide (EBR, a bioactive BR, promoted photosynthesis in tea plants in a concentration-dependent manner. Stimulation in photosynthesis by EBR resulted in an increased summer tea yield. Although all tested concentrations (0.01, 0.05, 0.1, 0.5 and 1.0 ppm increased concentrations of TP and AA, a moderate concentration of EBR (0.5 ppm caused the highest decrease in TP to AA ratio, an important feature of quality tea. Time-course analysis using 0.5 ppm EBR as foliar spray revealed that TP or AA concentration increased as early as 3 h after EBR application, reaching the highest peak at 24 h and that remained more or less stable. Importantly, such changes in TP and AA concentration by EBR resulted in a remarkably decreased but stable TP to AA ratio at 24 h and onward. Furthermore, concentrations of catechins and theanine increased, while that of caffeine remained unaltered following treatment with EBR. EBR improved activity of phenylalanine ammonia-lyase (PAL and glutamine: 2-oxoglutarate (GOGAT enzymes involved in catechins and theanine biosynthesis, respectively. Transcript analysis revealed that transcript levels of CsPAL and CsGS peaked as early as 6 h, while that of CsGOGAT peaked at 12 h following application of EBR, implying that EBR increased the concentration of TP and AA by inducing their biosynthesis. These results suggest a positive role of BR in enhancing green tea quality, which might have potential implication

  16. Ameliorative Effects of Brassinosteroid on Excess Manganese-Induced Oxidative Stress in Zea mays L.Leaves

    Institute of Scientific and Technical Information of China (English)

    WANG Hai-hua; FENG Tao; PENG Xi-xu; YAN Ming-li; ZHOU Ping-lan; TANG Xin-ke

    2009-01-01

    Manganese (Mn) is becoming an important factor limiting crop growth and yields especially on acid soils.The present study was designed to explore the hypothesis that brassinosteroid application can enhance the tolerance of maize(Zea mays L.)to Mn stress and if so,whether or not the mechanism underlying involves regulation of antioxidative metabolism in leaves.The effects of 24-epibrassinosteroid(EBR)on the growth,photosynthesis,water status,lipid peroxidation,accumulation of reactive oxygen species,and activities or contents of antioxidant defense system in maize plants under Mn stress were investigated by a pot experiment.At supplemented Mn concentrations of 150-750 mg kg-1 soil,the growth of plants was inhibited in a concentration-dependent manner.The semi-lethal concentration was 550 mg Mn kg-1 soil.Foliage application with 0.1 mg L-1 EBR significantly reduced the decrease in dry mass,chlorophyll content,photosynthetic rate,leaf water content,and water potential of plants grown in the soil spiked with 550 mg kg-1 Mn.The oxidative stress caused by excess Mn,as reflected by the increase in malondialdehyde (MDA) content and lipoxygenase (LOX,EC 1.13.11.12) activity,accumulation of superoxide radical and H2O2,was greatly decreased by EBR treatment.Further investigations revealed that EBR application enhanced the activities ofsuperoxide dismutase (SOD,EC 1.15.1.1),peroxidase (POD,EC 1.11.1.7),catalase (EC 1.11.1.6),ascorbate peroxidase (APX,EC 1.11.1.11),dehydroascorbate reductase (DHAR,EC1.8.5.1),and glutathione reductase (GR,EC 1.6.4.2),and the contents of reduced ascorbate and glutathione,compared with the plants without EBR treatment.It iS concluded that the ameliorative effects of EBR on Mn toxicity are due to the upregulation of antioxidative capacity in maize under Mn stress.

  17. Down-regulation of BdBRI1, a putative brassinosteroid receptor gene produces a dwarf phenotype with enhanced drought tolerance in Brachypodium distachyon.

    Science.gov (United States)

    Feng, Ying; Yin, Yanhai; Fei, Shuizhang

    2015-05-01

    Brassinosteroids (BRs) play important roles in plant growth, development and responses to a range of environmental cues. Although the mechanism of how BRs regulate growth and development is well-understood in Arabidopsis, the effect of BRs on stress tolerance, particularly drought tolerance remains unknown. We isolated a BRI1 (BRASSINOSTEROID INSENSITIVE 1) homologous gene, BdBRI1 from Brachypodium distachyon, a model for temperate grasses and cereals, created and characterized RNA interference (RNAi) knockdown mutants for BdBRI1 in Brachypodium. The loss-of-function BdBRI1-RNAi mutants exhibited reduced plant height, shortened internodes, narrow and short leaf, and reduced expression of BR signaling genes, BdBES1, BdBZR1, BdBLE2, and enhanced expression of BR biosynthesis genes BdD2, BdCPD and BdDWF4. More importantly, BdBRI1 RNAi mutants exhibited enhanced drought tolerance, accompanied by highly elevated expression of drought-responsive genes, BdP5CS, BdCOR47/BdRD17, together with BdERD1 and BdRD26, two putative targets of the transcription factors BES1 and BZR1 that are key components of the BR signaling pathway. Our results suggest that BR signaling and biosynthesis are largely conserved among Arabidopsis, rice and Brachypodium, and that BR signaling plays an important role in drought tolerance by directly regulating expression of key drought-responsive genes. The effect of BR biosynthesis or crosstalks between BR and other hormones or components of stress signaling pathways on drought tolerance is discussed.

  18. Spectrally encoded confocal microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Tearney, G.J.; Webb, R.H.; Bouma, B.E. [Wellman Laboratories of Photomedicine, Massachusetts General Hospital, 50 Blossom Street, BAR 703, Boston, Massachusetts 02114 (United States)

    1998-08-01

    An endoscope-compatible, submicrometer-resolution scanning confocal microscopy imaging system is presented. This approach, spectrally encoded confocal microscopy (SECM), uses a quasi-monochromatic light source and a transmission diffraction grating to detect the reflectivity simultaneously at multiple points along a transverse line within the sample. Since this method does not require fast spatial scanning within the probe, the equipment can be miniaturized and incorporated into a catheter or endoscope. Confocal images of an electron microscope grid were acquired with SECM to demonstrate the feasibility of this technique. {copyright} {ital 1998} {ital Optical Society of America}

  19. Antagonistic regulation of growth and immunity by the Arabidopsis basic helix-loop-helix transcription factor homolog of brassinosteroid enhanced expression2 interacting with increased leaf inclination1 binding bHLH1

    DEFF Research Database (Denmark)

    Malinovsky, Frederikke Gro; Batoux, Martine; Schwessinger, Benjamin;

    2014-01-01

    Plants need to finely balance resources allocated to growth and immunity to achieve optimal fitness. A tradeoff between pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and brassinosteroid (BR)-mediated growth was recently reported, but more information about the underlying...... to different PAMPs. HBI1 overexpression leads to reduced PAMP-triggered responses. This inhibition correlates with reduced steady-state expression of immune marker genes, leading to increased susceptibility to the bacterium Pseudomonas syringae. Overexpression of the HBI1-related bHLHs brassinosteroid enhanced...... expression2 (BEE2) and cryptochrome-interacting bHLH (CIB1) partially inhibits immunity, indicating that BEE2 and CIB1 may act redundantly with HBI1. In contrast to its expression pattern upon PAMP treatment, HBI1 expression is enhanced by BR treatment. Also, HBI1-overexpressing plants are hyperresponsive...

  20. Selecting Operations for Assembler Encoding

    Directory of Open Access Journals (Sweden)

    Tomasz Praczyk

    2010-04-01

    Full Text Available Assembler Encoding is a neuro-evolutionary method in which a neural network is represented in the form of a simple program called Assembler Encoding Program. The task of the program is to create the so-called Network Definition Matrix which maintains all the information necessary to construct the network. To generate Assembler Encoding Programs and the subsequent neural networks evolutionary techniques are used.
    The performance of Assembler Encoding strongly depends on operations used in Assembler Encoding Programs. To select the most effective operations, experiments in the optimization and the predator-prey problem were carried out. In the experiments, Assembler Encoding Programs equipped with different types of operations were tested. The results of the tests are presented at the end of the paper.

  1. Brassinosteroid-induced CO{sub 2} assimilation is associated with increased stability of redox-sensitive photosynthetic enzymes in the chloroplasts in cucumber plants

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Yu Ping; Cheng, Fei; Zhou, Yan Hong; Xia, Xiao Jian; Mao, Wei Hua; Shi, Kai [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Chen, Zhi Xiang [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907-2054 (United States); Yu, Jing Quan, E-mail: jqyu@zju.edu.cn [Department of Horticulture, Zijingang Campus, Zhejiang University, Yuhangtang Road 866, Hangzhou 310058 (China); Key Laboratory of Horticultural Plants Growth, Development and Quality Improvement, Ministry of Agriculture of China, Yuhangtang Road 866, Hangzhou 310058 (China)

    2012-09-28

    Highlights: Black-Right-Pointing-Pointer Activity of certain Calvin cycle enzymes and CO{sub 2} assimilation are induced by BRs. Black-Right-Pointing-Pointer BRs upregulate the activity of the ascorbate-glutathione cycle in the chloroplasts. Black-Right-Pointing-Pointer BRs increase the chloroplast thiol reduction state. Black-Right-Pointing-Pointer A BR-induced reducing environment increases the stability of photosynthetic enzymes. -- Abstract: Brassinosteroids (BRs) play important roles in plant growth, development, photosynthesis and stress tolerance; however, the mechanism underlying BR-enhanced photosynthesis is currently unclear. Here, we provide evidence that an increase in the BR level increased the quantum yield of PSII, activities of Rubisco activase (RCA) and fructose-1,6-bisphosphatase (FBPase), and CO{sub 2} assimilation. BRs upregulated the transcript levels of genes and activity of enzymes involved in the ascorbate-glutathione cycle in the chloroplasts, leading to an increased ratio of reduced (GSH) to oxidized (GSSG) glutathione in the chloroplasts. An increased GSH/GSSG ratio protected RCA from proteolytic digestion and increased the stability of redox-sensitive enzymes in the chloroplasts. These results strongly suggest that BRs are capable of regulating the glutathione redox state in the chloroplasts through the activation of the ascorbate-glutathione cycle. The resulting increase in the chloroplast thiol reduction state promotes CO{sub 2} assimilation, at least in part, by enhancing the stability and activity of redox-sensitive photosynthetic enzymes through post-translational modifications.

  2. PNA-encoded chemical libraries.

    Science.gov (United States)

    Zambaldo, Claudio; Barluenga, Sofia; Winssinger, Nicolas

    2015-06-01

    Peptide nucleic acid (PNA)-encoded chemical libraries along with DNA-encoded libraries have provided a powerful new paradigm for library synthesis and ligand discovery. PNA-encoding stands out for its compatibility with standard solid phase synthesis and the technology has been used to prepare libraries of peptides, heterocycles and glycoconjugates. Different screening formats have now been reported including selection-based and microarray-based methods that have yielded specific ligands against diverse target classes including membrane receptors, lectins and challenging targets such as Hsp70.

  3. Cell encoding recombinant human erythropoietin

    Energy Technology Data Exchange (ETDEWEB)

    Beck, A.K.; Withy, R.M.; Zabrecky, J.R.; Masiello, N.C.

    1990-09-04

    This patent describes a C127 cell transformed with a recombinant DNA vector. It comprises: a DNA sequence encoding human erythropoietin, the transformed cell being capable of producing N-linked and O-linked glycosylated human erythropoietin.

  4. Compressed Encoding for Rank Modulation

    CERN Document Server

    Gad, Eyal En; Jiang,; Bruck, Jehoshua

    2011-01-01

    Rank modulation has been recently proposed as a scheme for storing information in flash memories. While rank modulation has advantages in improving write speed and endurance, the current encoding approach is based on the "push to the top" operation that is not efficient in the general case. We propose a new encoding procedure where a cell level is raised to be higher than the minimal necessary subset - instead of all - of the other cell levels. This new procedure leads to a significantly more compressed (lower charge levels) encoding. We derive an upper bound for a family of codes that utilize the proposed encoding procedure, and consider code constructions that achieve that bound for several special cases.

  5. Self-Organising Stochastic Encoders

    CERN Document Server

    Luttrell, Stephen

    2010-01-01

    The processing of mega-dimensional data, such as images, scales linearly with image size only if fixed size processing windows are used. It would be very useful to be able to automate the process of sizing and interconnecting the processing windows. A stochastic encoder that is an extension of the standard Linde-Buzo-Gray vector quantiser, called a stochastic vector quantiser (SVQ), includes this required behaviour amongst its emergent properties, because it automatically splits the input space into statistically independent subspaces, which it then separately encodes. Various optimal SVQs have been obtained, both analytically and numerically. Analytic solutions which demonstrate how the input space is split into independent subspaces may be obtained when an SVQ is used to encode data that lives on a 2-torus (e.g. the superposition of a pair of uncorrelated sinusoids). Many numerical solutions have also been obtained, using both SVQs and chains of linked SVQs: (1) images of multiple independent targets (encod...

  6. Research Progress on Brassinosteroids for Improving Stress Resistance Vegetable Crops%油菜素内酯提高蔬菜作物抗逆性的研究进展

    Institute of Scientific and Technical Information of China (English)

    李程; 梁宝魁; 王晓峰

    2015-01-01

    Brassinosteroids,a kind of novel plant endogenous hormone,are universally acknowledged as plant growth regulator with high activity,broad spectrum application,and non-toxic sterols in agricultural production.In recent years,it has been found that brassinosteroids can enhance plant resistance to various biotic and abiotic stresses, and promote plant growth and development,thus to further increase crops production. This paper summarizes the research progress made on brassinosteroids mediating vegetable resistance to multiple environmental stresses, including water,temperature,salt,pathogen,and heavy metal stress, etc.The paper also prospected some research directions in the future.%油菜素内酯化合物(Brassinosteroids,BRs)是国际上公认的一类高效、广谱、无毒的新型植物甾醇类生长激素。近年来研究发现,BRs的使用可显著提高植物对生物和非生物逆境的抗性,从而促进植物生长发育,大幅度提高作物产量。本文综述了BRs的类型、应用方式以及在提高蔬菜抵抗干旱、低氧、温度、盐离子、病害、重金属等环境胁迫方面的研究成果,并对未来的研究方向进行了展望。

  7. 受体激酶介导的油菜素内酯信号转导途径%Receptor kinases mediated brassinosteroid signal transduction in plants

    Institute of Scientific and Technical Information of China (English)

    卫卓赟; 黎家

    2011-01-01

    油菜素内酯(brassinosteroids,BRs)是一类重要的类固醇激素,参与调控植物生长发育的许多过程.结合应用遗传学、生物化学以及蛋白质组学等研究手段现已基本阐明了BR信号转导的主要过程.BRI1作为受体在细胞表面感知BR,BRI1抑制子BKI1从质膜上解离下来,使BRI1与其共受体BAK1结合.BRI1和BAK1通过顺序磷酸化将BR信号完全激活.活化的BRI1将BSK磷酸化激活,BSK活化BSU1,BSU1将BIN2去磷酸化使其失活,解除BIN2对BES 1/BZR1的抑制功能.PP2A可以将BES1/BZR1去磷酸化激活,又可以将受体BRI1去磷酸化促使其降解.BR信号的传递最终使去磷酸化状态的BES1/BZR1在细胞内累积,激活BR信号通路下游的转录调控.%Brassinosteroids (BRs) are a class of steroidal hormones, playing essential roles in a wide range of processes during plant growth and development. The combined genetics, biochemistry and proteomics approaches have been employed to elucidate the major events in BR signaling pathway, mainly via a series of reversible phosphorylation and dephosphorylation processes. Perception of BR by the BR receptor BRI1 at cell surface leads to the dissociation of BRI1 kinase inhibitor BKI1 from the plasma membrane and association of BRI1 with its co-receptor BAK1. Sequential transphosphorylation of the paired BRJ1/BAK1 receptor kinases completely activates the BR signaling cascade. BRI1 phosphorylation of the BSK kinases leads to the activation of the BSU1 phosphatases, which can function to dephosphorylate and inactivate the BIN2 kinase. PP2A phosphatases play dual roles in mediating BR signaling pathway including dephosphorylating BES1/BZR1 transcription factors to promote their functions and dephosphorylating BRI1 to make it less stable. These events result in the accumulation of unphosphorylated BES1/BZR1 transcription factors in the nucleus and subsequent activation of the downstream transcriptional network.

  8. Multidimensionally encoded magnetic resonance imaging.

    Science.gov (United States)

    Lin, Fa-Hsuan

    2013-07-01

    Magnetic resonance imaging (MRI) typically achieves spatial encoding by measuring the projection of a q-dimensional object over q-dimensional spatial bases created by linear spatial encoding magnetic fields (SEMs). Recently, imaging strategies using nonlinear SEMs have demonstrated potential advantages for reconstructing images with higher spatiotemporal resolution and reducing peripheral nerve stimulation. In practice, nonlinear SEMs and linear SEMs can be used jointly to further improve the image reconstruction performance. Here, we propose the multidimensionally encoded (MDE) MRI to map a q-dimensional object onto a p-dimensional encoding space where p > q. MDE MRI is a theoretical framework linking imaging strategies using linear and nonlinear SEMs. Using a system of eight surface SEM coils with an eight-channel radiofrequency coil array, we demonstrate the five-dimensional MDE MRI for a two-dimensional object as a further generalization of PatLoc imaging and O-space imaging. We also present a method of optimizing spatial bases in MDE MRI. Results show that MDE MRI with a higher dimensional encoding space can reconstruct images more efficiently and with a smaller reconstruction error when the k-space sampling distribution and the number of samples are controlled.

  9. C-23 hydroxylation by Arabidopsis CYP90C1 and CYP90D1 reveals a novel shortcut in brassinosteroid biosynthesis.

    Science.gov (United States)

    Ohnishi, Toshiyuki; Szatmari, Anna-Maria; Watanabe, Bunta; Fujita, Satomi; Bancos, Simona; Koncz, Csaba; Lafos, Marcel; Shibata, Kyomi; Yokota, Takao; Sakata, Kanzo; Szekeres, Miklos; Mizutani, Masaharu

    2006-11-01

    Brassinosteroids (BRs) are biosynthesized from campesterol via several cytochrome P450 (P450)-catalyzed oxidative reactions. We report the functional characterization of two BR-biosynthetic P450s from Arabidopsis thaliana: CYP90C1/ROTUNDIFOLIA3 and CYP90D1. The cyp90c1 cyp90d1 double mutant exhibits the characteristic BR-deficient dwarf phenotype, although the individual mutants do not display this phenotype. These data suggest redundant roles for these P450s. In vitro biochemical assays using insect cell-expressed proteins revealed that both CYP90C1 and CYP90D1 catalyze C-23 hydroxylation of various 22-hydroxylated BRs with markedly different catalytic efficiencies. Both enzymes preferentially convert 3-epi-6-deoxocathasterone, (22S,24R)-22-hydroxy-5alpha-ergostan-3-one, and (22S,24R)-22-hydroxyergost-4-en-3-one to 23-hydroxylated products, whereas they are less active on 6-deoxocathasterone. Likewise, cyp90c1 cyp90d1 plants were deficient in 23-hydroxylated BRs, and in feeding experiments using exogenously supplied intermediates, only 23-hydroxylated BRs rescued the growth deficiency of the cyp90c1 cyp90d1 mutant. Thus, CYP90C1 and CYP90D1 are redundant BR C-23 hydroxylases. Moreover, their preferential substrates are present in the endogenous Arabidopsis BR pool. Based on these results, we propose C-23 hydroxylation shortcuts that bypass campestanol, 6-deoxocathasterone, and 6-deoxoteasterone and lead directly from (22S,24R)-22-hydroxy-5alpha-ergostan-3-one and 3-epi-6-deoxocathasterone to 3-dehydro-6-deoxoteasterone and 6-deoxotyphasterol.

  10. C-23 Hydroxylation by Arabidopsis CYP90C1 and CYP90D1 Reveals a Novel Shortcut in Brassinosteroid Biosynthesis[W

    Science.gov (United States)

    Ohnishi, Toshiyuki; Szatmari, Anna-Maria; Watanabe, Bunta; Fujita, Satomi; Bancos, Simona; Koncz, Csaba; Lafos, Marcel; Shibata, Kyomi; Yokota, Takao; Sakata, Kanzo; Szekeres, Miklos; Mizutani, Masaharu

    2006-01-01

    Brassinosteroids (BRs) are biosynthesized from campesterol via several cytochrome P450 (P450)–catalyzed oxidative reactions. We report the functional characterization of two BR-biosynthetic P450s from Arabidopsis thaliana: CYP90C1/ROTUNDIFOLIA3 and CYP90D1. The cyp90c1 cyp90d1 double mutant exhibits the characteristic BR-deficient dwarf phenotype, although the individual mutants do not display this phenotype. These data suggest redundant roles for these P450s. In vitro biochemical assays using insect cell-expressed proteins revealed that both CYP90C1 and CYP90D1 catalyze C-23 hydroxylation of various 22-hydroxylated BRs with markedly different catalytic efficiencies. Both enzymes preferentially convert 3-epi-6-deoxocathasterone, (22S,24R)-22-hydroxy-5α-ergostan-3-one, and (22S,24R)-22-hydroxyergost-4-en-3-one to 23-hydroxylated products, whereas they are less active on 6-deoxocathasterone. Likewise, cyp90c1 cyp90d1 plants were deficient in 23-hydroxylated BRs, and in feeding experiments using exogenously supplied intermediates, only 23-hydroxylated BRs rescued the growth deficiency of the cyp90c1 cyp90d1 mutant. Thus, CYP90C1 and CYP90D1 are redundant BR C-23 hydroxylases. Moreover, their preferential substrates are present in the endogenous Arabidopsis BR pool. Based on these results, we propose C-23 hydroxylation shortcuts that bypass campestanol, 6-deoxocathasterone, and 6-deoxoteasterone and lead directly from (22S,24R)-22-hydroxy-5α-ergostan-3-one and 3-epi-6-deoxocathasterone to 3-dehydro-6-deoxoteasterone and 6-deoxotyphasterol. PMID:17138693

  11. Synergistic effect of auxins and brassinosteroids on the growth and regulation of metabolite content in the green alga Chlorella vulgaris (Trebouxiophyceae).

    Science.gov (United States)

    Bajguz, Andrzej; Piotrowska-Niczyporuk, Alicja

    2013-10-01

    The relationships between brassinosteroids (BRs) (brassinolide, BL; 24-epiBL; 28-homoBL; castasterone, CS; 24-epiCS; 28-homoCS) and auxins (indole-3-acetic acid, IAA; indole-3-butyric acid, IBA; indole-3-propionic acid, IPA) in the regulation of cell number, phytohormone level and metabolism in green alga Chlorella vulgaris were investigated. Exogenously applied auxins had the highest biological activity in algal cells at 50 μM. Among the auxins, IAA was characterized by the highest activity, while IBA - by the lowest. BRs at 0.01 μM were characterized by the highest biological activity in relation to auxin-treated and untreated cultures of C. vulgaris. The application of 50 μM IAA stimulated the level of all detected endogenous BRs in C. vulgaris cells. The stimulatory effect of BRs in green algae was arranged in the following order: BL > 24-epiBL > 28-homoBL > CS > 24-epiCS > 28-homoCS. Auxins cooperated synergistically with BRs stimulating algal cell proliferation and endogenous accumulation of proteins, chlorophylls and monosaccharides in C. vulgaris. The highest stimulation of algal growth and the contents of analyzed biochemical parameters were observed for the mixture of BL with IAA, whereas the lowest in the culture treated with both 28-homoCS and IBA. However, regardless of the applied mixture of BRs with auxins, the considerable increase in cell number and the metabolite accumulation was found above the level obtained in cultures treated with any single phytohormone. Obtained results confirm that both groups of plant hormones cooperate synergistically in the control of growth and metabolism of unicellular green alga C. vulgaris.

  12. Virally encoded 7TM receptors

    DEFF Research Database (Denmark)

    Rosenkilde, M M; Waldhoer, M; Lüttichau, H R

    2001-01-01

    A number of herpes- and poxviruses encode 7TM G-protein coupled receptors most of which clearly are derived from their host chemokine system as well as induce high expression of certain 7TM receptors in the infected cells. The receptors appear to be exploited by the virus for either immune evasion...... in various parts of the viral life cyclus. Most of the receptors encoded by human pathogenic virus are still orphan receptors, i.e. the endogenous ligand is unknown. In the few cases where it has been possible to characterize these receptors pharmacologically, they have been found to bind a broad spectrum...... expression of this single gene in certain lymphocyte cell lineages leads to the development of lesions which are remarkably similar to Kaposi's sarcoma, a human herpesvirus 8 associated disease. Thus, this and other virally encoded 7TM receptors appear to be attractive future drug targets....

  13. Synaptic encoding of temporal contiguity

    Directory of Open Access Journals (Sweden)

    Srdjan eOstojic

    2013-04-01

    Full Text Available Often we need to perform tasks in an environment that changes stochastically. In these situations it is important to learn the statistics of sequences of events in order to predict the future and the outcome of our actions. The statistical description of many of these sequences can be reduced to the set of probabilities that a particular event follows another event (temporal contiguity. Under these conditions, it is important to encode and store in our memory these transition probabilities. Here we show that for a large class of synaptic plasticity models, the distribution of synaptic strengths encodes transitions probabilities. Specifically, when the synaptic dynamics depend on pairs of contiguous events and the synapses can remember multiple instances of the transitions, then the average synaptic weights are a monotonic function of the transition probabilities. The synaptic weights converge to the distribution encoding the probabilities also when the correlations between consecutive synaptic modifications are considered. We studied how this distribution depends on the number of synaptic states for a specific model of a multi-state synapse with hard bounds. In the case of bistable synapses, the average synaptic weights are a smooth function of the transition probabilities and the accuracy of the encoding depends on the learning rate. As the number of synaptic states increases, the average synaptic weights become a step function of the transition probabilities. We finally show that the information stored in the synaptic weights can be read out by a simple rate-based neural network. Our study shows that synapses encode transition probabilities under general assumptions and this indicates that temporal contiguity is likely to be encoded and harnessed in almost every neural circuit in the brain.

  14. Encoding information into precipitation structures

    Science.gov (United States)

    Martens, Kirsten; Bena, Ioana; Droz, Michel; Rácz, Zoltan

    2008-12-01

    Material design at submicron scales would be profoundly affected if the formation of precipitation patterns could be easily controlled. It would allow the direct building of bulk structures, in contrast to traditional techniques which consist of removing material in order to create patterns. Here, we discuss an extension of our recent proposal of using electrical currents to control precipitation bands which emerge in the wake of reaction fronts in A+ + B- → C reaction-diffusion processes. Our main result, based on simulating the reaction-diffusion-precipitation equations, is that the dynamics of the charged agents can be guided by an appropriately designed time-dependent electric current so that, in addition to the control of the band spacing, the width of the precipitation bands can also be tuned. This makes straightforward the encoding of information into precipitation patterns and, as an amusing example, we demonstrate the feasibility by showing how to encode a musical rhythm.

  15. Geometric Hyperplanes: Desargues Encodes Doily

    CERN Document Server

    Saniga, Metod

    2011-01-01

    It is shown that the structure of the generalized quadrangle of order two is fully encoded in the properties of the Desargues configuration. A point of the quadrangle is represented by a geometric hyperplane of the Desargues configuration and its line by a set of three hyperplanes such that one of them is the complement of the symmetric difference of the remaining two and they all share a pair of non-collinear points.

  16. Vector Encoding in Biochemical Networks

    Science.gov (United States)

    Potter, Garrett; Sun, Bo

    Encoding of environmental cues via biochemical signaling pathways is of vital importance in the transmission of information for cells in a network. The current literature assumes a single cell state is used to encode information, however, recent research suggests the optimal strategy utilizes a vector of cell states sampled at various time points. To elucidate the optimal sampling strategy for vector encoding, we take an information theoretic approach and determine the mutual information of the calcium signaling dynamics obtained from fibroblast cells perturbed with different concentrations of ATP. Specifically, we analyze the sampling strategies under the cases of fixed and non-fixed vector dimension as well as the efficiency of these strategies. Our results show that sampling with greater frequency is optimal in the case of non-fixed vector dimension but that, in general, a lower sampling frequency is best from both a fixed vector dimension and efficiency standpoint. Further, we find the use of a simple modified Ornstein-Uhlenbeck process as a model qualitatively captures many of our experimental results suggesting that sampling in biochemical networks is based on a few basic components.

  17. Hall effect encoding of brushless dc motors

    Science.gov (United States)

    Berard, C. A.; Furia, T. J.; Goldberg, E. A.; Greene, R. C.

    1970-01-01

    Encoding mechanism integral to the motor and using the permanent magnets embedded in the rotor eliminates the need for external devices to encode information relating the position and velocity of the rotating member.

  18. Molecular mechanisms for protein-encoded inheritance

    Energy Technology Data Exchange (ETDEWEB)

    Wiltzius, Jed J.W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David; (Cornell); (HHMI)

    2009-12-01

    In prion inheritance and transmission, strains are phenotypic variants encoded by protein 'conformations'. However, it is unclear how a protein conformation can be stable enough to endure transmission between cells or organisms. Here we describe new polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of {beta}-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct {beta}-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains. These molecular mechanisms for transfer of protein-encoded information into prion strains share features with the familiar mechanism for transfer of nucleic acid-encoded information into microbial strains, including sequence specificity and recognition by noncovalent bonds.

  19. Molecular mechanisms for protein-encoded inheritance.

    Science.gov (United States)

    Wiltzius, Jed J W; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R; Apostol, Marcin I; Goldschmidt, Lukasz; Soriaga, Angela B; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

    2009-09-01

    In prion inheritance and transmission, strains are phenotypic variants encoded by protein 'conformations'. However, it is unclear how a protein conformation can be stable enough to endure transmission between cells or organisms. Here we describe new polymorphic crystal structures of segments of prion and other amyloid proteins, which offer two structural mechanisms for the encoding of prion strains. In packing polymorphism, prion strains are encoded by alternative packing arrangements (polymorphs) of beta-sheets formed by the same segment of a protein; in segmental polymorphism, prion strains are encoded by distinct beta-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring conformations capable of encoding strains. These molecular mechanisms for transfer of protein-encoded information into prion strains share features with the familiar mechanism for transfer of nucleic acid-encoded information into microbial strains, including sequence specificity and recognition by noncovalent bonds.

  20. Novelty's effect on memory encoding.

    Science.gov (United States)

    Rangel-Gomez, Mauricio; Janenaite, Sigita; Meeter, Martijn

    2015-07-01

    It is often thought that novelty benefits memory formation. However, support for this idea mostly comes from paradigms that are open to alternative explanations. In the present study we manipulated novelty in a word-learning task through task-irrelevant background images. These background images were either standard (presented repeatedly), or novel (presented only once). Two types of background images were used: Landscape pictures and fractals. EEG was also recorded during encoding. Contrary to the idea that novelty aids memory formation, memory performance was not affected by the novelty of the background. In the evoked response potentials, we found evidence of distracting effects of novelty: both the N1 and P3b components were smaller to words studied with novel backgrounds, and the amplitude of the N2b component correlated negatively with subsequent retrieval. We conclude that although evidence from other studies does suggest benefits on a longer time scale, novelty has no instantaneous benefits for learning.

  1. NMDA receptors and memory encoding.

    Science.gov (United States)

    Morris, Richard G M

    2013-11-01

    It is humbling to think that 30 years have passed since the paper by Collingridge, Kehl and McLennan showing that one of Jeff Watkins most interesting compounds, R-2-amino-5-phosphonopentanoate (d-AP5), blocked the induction of long-term potentiation in vitro at synapses from area CA3 of the hippocampus to CA1 without apparent effect on baseline synaptic transmission (Collingridge et al., 1983). This dissociation was one of the key triggers for an explosion of interest in glutamate receptors, and much has been discovered since that collectively contributes to our contemporary understanding of glutamatergic synapses - their biophysics and subunit composition, of the agonists and antagonists acting on them, and their diverse functions in different networks of the brain and spinal cord. It can be fairly said that Collingridge et al.'s (1983) observation was the stimulus that has led, on the one hand, to structural biological work at the atomic scale describing the key features of NMDA receptors that enables their coincidence function to happen; and, on the other, to work with whole animals investigating the contributions that calcium signalling via this receptor can have on rhythmical activities controlled by spinal circuits, memory encoding in the hippocampus (the topic of this article), visual cortical plasticity, sensitization in pain, and other functions. In this article, I lay out how my then interest in long-term potentiation (LTP) as a model of memory enabled me to recognise the importance of Collingridge et al.'s discovery - and how I and my colleagues endeavoured to take things forward in the area of learning and memory. This is in some respects a personal story, and I tell it as such. The idea that NMDA receptor activation is essential for memory encoding, though not for storage, took time to develop and to be accepted. Along the way, there have been confusions, challenges, and surprises surrounding the idea that activation of NMDA receptors can

  2. Computational Intelligence and Its Encoding Mechanism

    Institute of Scientific and Technical Information of China (English)

    LIU Man-dan

    2004-01-01

    The origin and characteristics of computational intelligence, and several typical computational intelligence algorithms such as genetic algorithm and DNA computing are described, and the influence of evolution strategies and convergence properties on the encoding mechanism is discussed. A novel genetic algorithm based on degressive carry number encoding is then proposed. This algorithm uses degressive carry number encoding in the evolutionary process instead of commonly used fixed carry number. Finally a novel encoding mechanism and a new algorithm are proposed, which combine modern computational intelligence with the traditional Chinese methodology.

  3. Computational Intelligence and Its Encoding Mechanism

    Institute of Scientific and Technical Information of China (English)

    LIUMan-dan

    2004-01-01

    The origin and characteristics of computational intelligence, and several typical computational intelligence algorithms such as genetic algorithm and DNA computing are described, and the influence of evolution strategies and convergence properties on the encoding mechanism is discussed. A novel genetic algorithm based on degressive carry number encoding is then proposed. This algorithm uses degressive carry number encoding in the evolutionary process instead of commonly used fixed carry number. Finally a novel encoding mechanism and a new algorithm are proposed, which combine modem computational intelligence with the traditional Chinese methodology.

  4. Encoder designed to work in harsh environments

    Energy Technology Data Exchange (ETDEWEB)

    Toop, L.

    2007-05-15

    Dynapar has developed the Acuro AX71 absolute encoder for use on offshore or land-based oil rig operations. It provides feedback on the operation of automated systems such as draw works, racking systems, rotary tables and top drives. By ensuring that automated systems function properly, this encoder responds to a need by the oil and gas industry to keep workers safe and improve efficiency, particularly for operations in rugged situations. The encoder provides feedback from motor systems to controllers, giving information about position and speed of downhole drill bits. This newly developed encoder is better than commonly used incremental encoders which are not precise in strong electrical noise environments. Rather, the absolute encoder uses a different method of reporting to the controller. A digital signal is transmitted constantly as the device operates. It is less susceptible to noise issues. It is highly accurate, tolerant of noise and is not affected by power outages. However, the absolute encoder is generally more delicate in drilling applications with high ambient temperatures and shock levels. Dynapar addressed this issue by developing compact stainless steel housing that is useful for corrosion resistance in marine applications. The AX71 absolute encoder can withstand up to 100 G of mechanical shock and ambient temperatures of up to 60 degrees C. The encoder is ATEX certified without barriers, and offers the high resolution feedback of 4,000 counts of multiturn rotation and 16,000 counts of position. 1 fig.

  5. Cellular encoding for interactive evolutionary robotics

    NARCIS (Netherlands)

    Gruau, F.C.; Quatramaran, K.

    1996-01-01

    This work reports experiments in interactive evolutionary robotics. The goal is to evolve an Artificial Neural Network (ANN) to control the locomotion of an 8-legged robot. The ANNs are encoded using a cellular developmental process called cellular encoding. In a previous work similar experiments ha

  6. A METHOD OF SHAPE ENCODING AND RETRIEVAL

    Institute of Scientific and Technical Information of China (English)

    Huang Xianglin; Song Lei; Shen Lansun

    2002-01-01

    A method of shape encoding and retrieval is proposed in this letter, which uses centripetal code to encode shape and extracts shape's convex for retrieval. For the rotation invariance and translation invariance of the centripetal code and the normalization of convex,the proposed retrieval method is similarity transform resistant, Experimental results confirm this capability.

  7. The Arabic Diatessaron Project: Digitalizing, Encoding, Lemmatization

    Directory of Open Access Journals (Sweden)

    Giuliano Lancioni

    2016-04-01

    Full Text Available The Arabic Diatessaron Project (henceforth ADP is an international research project in Digital Humanities that aims to collect, digitalise and encode all known manuscripts of the Arabic Diatessaron (henceforth AD, a text that has been relatively neglected in scholarly research. ADP’s final goal is to provide a number of tools that can enable scholars to effectively query, compare and investigate all known variants of the text that will be encoded as far as possible in compliance with the Text Encoding Initiative (TEI guidelines. The paper addresses a number of issues involved in the process of digitalising manuscripts included in the two existing editions (Ciasca 1888 and Marmardji 1935, adding variants in unedited manuscripts, encoding and lemmatising the text. Issues involved in the design of the ADP include presentation of variants, choice of the standard text, applicability of TEI guidelines, automatic translation between different encodings, cross-edition concordances and principles of lemmatisation.

  8. A model for visual memory encoding.

    Directory of Open Access Journals (Sweden)

    Rodolphe Nenert

    Full Text Available Memory encoding engages multiple concurrent and sequential processes. While the individual processes involved in successful encoding have been examined in many studies, a sequence of events and the importance of modules associated with memory encoding has not been established. For this reason, we sought to perform a comprehensive examination of the network for memory encoding using data driven methods and to determine the directionality of the information flow in order to build a viable model of visual memory encoding. Forty healthy controls ages 19-59 performed a visual scene encoding task. FMRI data were preprocessed using SPM8 and then processed using independent component analysis (ICA with the reliability of the identified components confirmed using ICASSO as implemented in GIFT. The directionality of the information flow was examined using Granger causality analyses (GCA. All participants performed the fMRI task well above the chance level (>90% correct on both active and control conditions and the post-fMRI testing recall revealed correct memory encoding at 86.33 ± 5.83%. ICA identified involvement of components of five different networks in the process of memory encoding, and the GCA allowed for the directionality of the information flow to be assessed, from visual cortex via ventral stream to the attention network and then to the default mode network (DMN. Two additional networks involved in this process were the cerebellar and the auditory-insular network. This study provides evidence that successful visual memory encoding is dependent on multiple modules that are part of other networks that are only indirectly related to the main process. This model may help to identify the node(s of the network that are affected by a specific disease processes and explain the presence of memory encoding difficulties in patients in whom focal or global network dysfunction exists.

  9. A model for visual memory encoding.

    Science.gov (United States)

    Nenert, Rodolphe; Allendorfer, Jane B; Szaflarski, Jerzy P

    2014-01-01

    Memory encoding engages multiple concurrent and sequential processes. While the individual processes involved in successful encoding have been examined in many studies, a sequence of events and the importance of modules associated with memory encoding has not been established. For this reason, we sought to perform a comprehensive examination of the network for memory encoding using data driven methods and to determine the directionality of the information flow in order to build a viable model of visual memory encoding. Forty healthy controls ages 19-59 performed a visual scene encoding task. FMRI data were preprocessed using SPM8 and then processed using independent component analysis (ICA) with the reliability of the identified components confirmed using ICASSO as implemented in GIFT. The directionality of the information flow was examined using Granger causality analyses (GCA). All participants performed the fMRI task well above the chance level (>90% correct on both active and control conditions) and the post-fMRI testing recall revealed correct memory encoding at 86.33 ± 5.83%. ICA identified involvement of components of five different networks in the process of memory encoding, and the GCA allowed for the directionality of the information flow to be assessed, from visual cortex via ventral stream to the attention network and then to the default mode network (DMN). Two additional networks involved in this process were the cerebellar and the auditory-insular network. This study provides evidence that successful visual memory encoding is dependent on multiple modules that are part of other networks that are only indirectly related to the main process. This model may help to identify the node(s) of the network that are affected by a specific disease processes and explain the presence of memory encoding difficulties in patients in whom focal or global network dysfunction exists.

  10. Tangerineira ‘Cleópatra’ submetida a micorrização e a um análogo de brassinosteróide = ‘Cleópatra’ mandarin submitted to mycorrhization and to a brassinosteroid analogue

    Directory of Open Access Journals (Sweden)

    Jalille Amim Altoé

    2008-01-01

    Full Text Available O objetivo deste estudo foi avaliar o efeito de diferentes concentrações de um análogo de brassinosteróide e a inoculação com o fungo micorrízico Ac aulospora scrobiculata (FMA sobre o crescimento e estado nutricional da tangerineira ‘Cleópatra’, da semeadura àrepicagem. O experimento foi realizado em condições de casa de vegetação na Universidade Estadual do Norte Fluminense. Utilizou-se o delineamento experimental em blocos casualizados, em esquema fatorial 5x2 com quatro repetições, sendo cinco concentrações de um análogo de brassinosteróide, Biobras-16 (0,0; 0,1; 0,5; 0,75 e 1,00 mg L-1 e com ou sem inoculação com FMA. A inoculação com o FMA promoveu maior crescimento em altura, número de folhas, diâmetro do caule, área foliar e na massa seca das folhas e do caule. O Biobras-16 promoveu efeito benéfico no diâmetro do caule. Os conteúdos de P, K, Fe e Mnforam mais elevados nas plantas inoculadas. Os resultados mostraram que a associação dos dois fatores estudados modificam o crescimento do porta-enxerto.The objective of this study was to evaluate the effects of different concentrations of a brassinosteroid analogue and inoculation of the vesiculararbuscular mycorrhizal fungi (AMF Acaulospora scrobiculata on the ‘Cleópatra’ mandarin from the sowing until transplant point. The experiment was conducted under greenhouse conditions at Universidade Estadual do Norte Fluminense. The experimental designutilized was a randomized block with a 5x2 factorial scheme with 4 replications, using 5 concentrations of a brassinosteroid analogue, Biobras-16 (0.0; 0.1; 0.5 and 1.00 mg L-1 and with or without AMF inoculation. The AMF inoculation caused increment in height,number of leaves, diameter of the stem, leaf area and dry mass of the leaf and stem. The Biobras-16 promoted an increment of the diameter of the stem. The P, K, Fe and Mn contents were higher in the AMF inoculated plants. Results show that the association

  11. Genes involved in brassinosteroids's metabolism and signal transduction pathways Genes envolvidos nas vias de biossíntese e de transdução de sinal de brassinoesteróides

    Directory of Open Access Journals (Sweden)

    Adaucto Bellarmino Pereira-Netto

    2007-07-01

    Full Text Available Brassinosteroids (BRs are plant steroids essential for the normal growth and development, which carry an oxygen moiety at C-3 and additional ones at one or more of the C-2, C-6, C-22 and C-23 carbon atoms. In the past few years, application of molecular genetics allowed significant progress on the understanding of the BRs biosynthetic pathway regulation and on the identification of several components of their signal transduction pathway, as well. Search in eletronic databases show dozens of records for brassinosteroid-related genes for the last twelve months, demonstrating the big efforts being carried out in this field. This review highlights the recent advances on the characterization of genes and mutations that are helping to unravel the molecular mechanisms involved in the BRs synthesis/metabolism, perception and response, with especial emphasis on their role in plant cell elongation. Aspects of the involvement of BRs on the regulation of cell cycle-controlling proteins are discussed as well.Brassinoesteróides são esteróides vegetais, essenciais para o crescimento e o desenvolvimento, que apresentam um oxigênio no carbono C-3 e oxigênios adicionais em um ou mais dos átomos de carbono C-2, C-6, C-22 e C-23. Nos últimos anos, a aplicação de técnicas de genética molecular possibilitou progresso significativo no entendimento da regulação da via biossintética e na identificação de vários componentes da via de transdução de sinal de brassinoesteróides. Buscas em bases de dados eletrônicas mostram dúzias de registros para genes relacionados a brassinoesteróides nos últimos doze meses, demonstrando os grandes esforços desenvolvidos neste campo. Esta revisão destaca os recentes avanços na caracterização de genes e mutações que estão auxiliando na elucidação dos mecanismos moleculares envolvidos na síntese/metabolismo, e percepção e resposta de brassinoesteróides, com ênfase especial no seu papel no alongamento

  12. Silencing Brassinosteroid Receptor BRI1 Impairs Herbivory-elicited Accumulation of Jasmonic Acid-isoleucine and Diterpene Glycosides, but not Jasmonic Acid and Trypsin Proteinase Inhibitors in Nicotiana attenuata

    Institute of Scientific and Technical Information of China (English)

    Da-Hai Yang; lan T.Baldwin; Jianqiang Wu

    2013-01-01

    The brassinosteroid (BR) receptor,BR insensitive 1 (BRI1),plays a critical role in plant development,but whether BRI1-mediated BR signaling is involved in plant defense responses to herbivores was largely unknown.Here,we examined the function of BRI1 in the resistance of Nicotiana attenuata (Solanaceae) to its specialist insect herbivore Manduca sexta.Jasmonic acid (JA) and JA-isoleucine conjugate (JA-Ile) are important hormones that mediate resistance to herbivores and we found that after wounding or simulated herbivory NaBRI1 had little effect on JA levels,but was important for the induction of JA-Ile.Further experiments revealed that decreased JAR (the enzyme for JA-Ile production) activity and availability of lie in NaBRI1-silenced plants were likely responsible for the low JA-Ile levels.Consistently,M.sexta larvae gained more weight on NaBRI1-silenced plants than on the control plants.Quantification of insect feeding-induced secondary metabolites revealed that silencing NaBRI1 resulted in decreased levels of carbon-rich defensive secondary metabolites (hydroxygeranyllinalool diterpene glycosides,chlorogenic acid,and rutin),but had little effect on the nitrogen-rich ones (nicotine and trypsin proteinase inhibitors).Thus,NaBRI1-mediated BR signaling is likely involved in plant defense responses to M.sexta,including maintaining JA-Ile levels and the accumulation of several carbon-rich defensive secondary metabolites.

  13. Chemical Space of DNA-Encoded Libraries.

    Science.gov (United States)

    Franzini, Raphael M; Randolph, Cassie

    2016-07-28

    In recent years, DNA-encoded chemical libraries (DECLs) have attracted considerable attention as a potential discovery tool in drug development. Screening encoded libraries may offer advantages over conventional hit discovery approaches and has the potential to complement such methods in pharmaceutical research. As a result of the increased application of encoded libraries in drug discovery, a growing number of hit compounds are emerging in scientific literature. In this review we evaluate reported encoded library-derived structures and identify general trends of these compounds in relation to library design parameters. We in particular emphasize the combinatorial nature of these libraries. Generally, the reported molecules demonstrate the ability of this technology to afford hits suitable for further lead development, and on the basis of them, we derive guidelines for DECL design.

  14. Cellobiohydrolase variants and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Wogulis, Mark

    2017-04-04

    The present invention relates to variants of a parent cellobiohydrolase II. The present invention also relates to polynucleotides encoding the variants; nucleic acid constructs, vectors, and host cells comprising the polynucleotides; and methods of using the variants.

  15. Using XML to encode TMA DES metadata

    Directory of Open Access Journals (Sweden)

    Oliver Lyttleton

    2011-01-01

    Full Text Available Background: The Tissue Microarray Data Exchange Specification (TMA DES is an XML specification for encoding TMA experiment data. While TMA DES data is encoded in XML, the files that describe its syntax, structure, and semantics are not. The DTD format is used to describe the syntax and structure of TMA DES, and the ISO 11179 format is used to define the semantics of TMA DES. However, XML Schema can be used in place of DTDs, and another XML encoded format, RDF, can be used in place of ISO 11179. Encoding all TMA DES data and metadata in XML would simplify the development and usage of programs which validate and parse TMA DES data. XML Schema has advantages over DTDs such as support for data types, and a more powerful means of specifying constraints on data values. An advantage of RDF encoded in XML over ISO 11179 is that XML defines rules for encoding data, whereas ISO 11179 does not. Materials and Methods: We created an XML Schema version of the TMA DES DTD. We wrote a program that converted ISO 11179 definitions to RDF encoded in XML, and used it to convert the TMA DES ISO 11179 definitions to RDF. Results: We validated a sample TMA DES XML file that was supplied with the publication that originally specified TMA DES using our XML Schema. We successfully validated the RDF produced by our ISO 11179 converter with the W3C RDF validation service. Conclusions: All TMA DES data could be encoded using XML, which simplifies its processing. XML Schema allows datatypes and valid value ranges to be specified for CDEs, which enables a wider range of error checking to be performed using XML Schemas than could be performed using DTDs.

  16. Clustering of polarization-encoded images.

    Science.gov (United States)

    Zallat, Jihad; Collet, Christophe; Takakura, Yoshitate

    2004-01-10

    Polarization-encoded imaging consists of the distributed measurements of polarization parameters for each pixel of an image. We address clustering of multidimensional polarization-encoded images. The spatial coherence of polarization information is considered. Two methods of analysis are proposed: polarization contrast enhancement and a more-sophisticated image-processing algorithm based on a Markovian model. The proposed algorithms are applied and validated with two different Mueller images acquired by a fully polarimetric imaging system.

  17. Neurally Encoding Time for Olfactory Navigation.

    Directory of Open Access Journals (Sweden)

    In Jun Park

    2016-01-01

    Full Text Available Accurately encoding time is one of the fundamental challenges faced by the nervous system in mediating behavior. We recently reported that some animals have a specialized population of rhythmically active neurons in their olfactory organs with the potential to peripherally encode temporal information about odor encounters. If these neurons do indeed encode the timing of odor arrivals, it should be possible to demonstrate that this capacity has some functional significance. Here we show how this sensory input can profoundly influence an animal's ability to locate the source of odor cues in realistic turbulent environments-a common task faced by species that rely on olfactory cues for navigation. Using detailed data from a turbulent plume created in the laboratory, we reconstruct the spatiotemporal behavior of a real odor field. We use recurrence theory to show that information about position relative to the source of the odor plume is embedded in the timing between odor pulses. Then, using a parameterized computational model, we show how an animal can use populations of rhythmically active neurons to capture and encode this temporal information in real time, and use it to efficiently navigate to an odor source. Our results demonstrate that the capacity to accurately encode temporal information about sensory cues may be crucial for efficient olfactory navigation. More generally, our results suggest a mechanism for extracting and encoding temporal information from the sensory environment that could have broad utility for neural information processing.

  18. Visually Improved Image Compression by Combining EZW Encoding with Texture Modeling using Huffman Encoder

    Directory of Open Access Journals (Sweden)

    Vinay U. Kale

    2010-05-01

    Full Text Available This paper proposes a technique for image compression which uses the Wavelet-based Image/Texture Coding Hybrid (WITCH scheme [1] in combination with Huffman encoder. It implements a hybrid coding approach, while nevertheless preserving the features of progressive and lossless coding. The hybrid scheme was designed to encode the structural image information by Embedded Zerotree Wavelet (EZW encoding algorithm [2] and the stochastic texture in a model-based manner and this encoded data is then compressed using Huffman encoder. The scheme proposed here achieves superior subjective quality while increasing the compression ratio by more than a factor of three or even four. With this technique, it is possible to achieve compression ratios as high as 10 to 12 but with some minor distortions in the encoded image.

  19. Multichannel compressive sensing MRI using noiselet encoding.

    Science.gov (United States)

    Pawar, Kamlesh; Egan, Gary; Zhang, Jingxin

    2015-01-01

    The incoherence between measurement and sparsifying transform matrices and the restricted isometry property (RIP) of measurement matrix are two of the key factors in determining the performance of compressive sensing (CS). In CS-MRI, the randomly under-sampled Fourier matrix is used as the measurement matrix and the wavelet transform is usually used as sparsifying transform matrix. However, the incoherence between the randomly under-sampled Fourier matrix and the wavelet matrix is not optimal, which can deteriorate the performance of CS-MRI. Using the mathematical result that noiselets are maximally incoherent with wavelets, this paper introduces the noiselet unitary bases as the measurement matrix to improve the incoherence and RIP in CS-MRI. Based on an empirical RIP analysis that compares the multichannel noiselet and multichannel Fourier measurement matrices in CS-MRI, we propose a multichannel compressive sensing (MCS) framework to take the advantage of multichannel data acquisition used in MRI scanners. Simulations are presented in the MCS framework to compare the performance of noiselet encoding reconstructions and Fourier encoding reconstructions at different acceleration factors. The comparisons indicate that multichannel noiselet measurement matrix has better RIP than that of its Fourier counterpart, and that noiselet encoded MCS-MRI outperforms Fourier encoded MCS-MRI in preserving image resolution and can achieve higher acceleration factors. To demonstrate the feasibility of the proposed noiselet encoding scheme, a pulse sequences with tailored spatially selective RF excitation pulses was designed and implemented on a 3T scanner to acquire the data in the noiselet domain from a phantom and a human brain. The results indicate that noislet encoding preserves image resolution better than Fouirer encoding.

  20. Multichannel compressive sensing MRI using noiselet encoding.

    Directory of Open Access Journals (Sweden)

    Kamlesh Pawar

    Full Text Available The incoherence between measurement and sparsifying transform matrices and the restricted isometry property (RIP of measurement matrix are two of the key factors in determining the performance of compressive sensing (CS. In CS-MRI, the randomly under-sampled Fourier matrix is used as the measurement matrix and the wavelet transform is usually used as sparsifying transform matrix. However, the incoherence between the randomly under-sampled Fourier matrix and the wavelet matrix is not optimal, which can deteriorate the performance of CS-MRI. Using the mathematical result that noiselets are maximally incoherent with wavelets, this paper introduces the noiselet unitary bases as the measurement matrix to improve the incoherence and RIP in CS-MRI. Based on an empirical RIP analysis that compares the multichannel noiselet and multichannel Fourier measurement matrices in CS-MRI, we propose a multichannel compressive sensing (MCS framework to take the advantage of multichannel data acquisition used in MRI scanners. Simulations are presented in the MCS framework to compare the performance of noiselet encoding reconstructions and Fourier encoding reconstructions at different acceleration factors. The comparisons indicate that multichannel noiselet measurement matrix has better RIP than that of its Fourier counterpart, and that noiselet encoded MCS-MRI outperforms Fourier encoded MCS-MRI in preserving image resolution and can achieve higher acceleration factors. To demonstrate the feasibility of the proposed noiselet encoding scheme, a pulse sequences with tailored spatially selective RF excitation pulses was designed and implemented on a 3T scanner to acquire the data in the noiselet domain from a phantom and a human brain. The results indicate that noislet encoding preserves image resolution better than Fouirer encoding.

  1. An encyclopedia of mouse DNA elements (Mouse ENCODE).

    Science.gov (United States)

    Stamatoyannopoulos, John A; Snyder, Michael; Hardison, Ross; Ren, Bing; Gingeras, Thomas; Gilbert, David M; Groudine, Mark; Bender, Michael; Kaul, Rajinder; Canfield, Theresa; Giste, Erica; Johnson, Audra; Zhang, Mia; Balasundaram, Gayathri; Byron, Rachel; Roach, Vaughan; Sabo, Peter J; Sandstrom, Richard; Stehling, A Sandra; Thurman, Robert E; Weissman, Sherman M; Cayting, Philip; Hariharan, Manoj; Lian, Jin; Cheng, Yong; Landt, Stephen G; Ma, Zhihai; Wold, Barbara J; Dekker, Job; Crawford, Gregory E; Keller, Cheryl A; Wu, Weisheng; Morrissey, Christopher; Kumar, Swathi A; Mishra, Tejaswini; Jain, Deepti; Byrska-Bishop, Marta; Blankenberg, Daniel; Lajoie, Bryan R; Jain, Gaurav; Sanyal, Amartya; Chen, Kaun-Bei; Denas, Olgert; Taylor, James; Blobel, Gerd A; Weiss, Mitchell J; Pimkin, Max; Deng, Wulan; Marinov, Georgi K; Williams, Brian A; Fisher-Aylor, Katherine I; Desalvo, Gilberto; Kiralusha, Anthony; Trout, Diane; Amrhein, Henry; Mortazavi, Ali; Edsall, Lee; McCleary, David; Kuan, Samantha; Shen, Yin; Yue, Feng; Ye, Zhen; Davis, Carrie A; Zaleski, Chris; Jha, Sonali; Xue, Chenghai; Dobin, Alex; Lin, Wei; Fastuca, Meagan; Wang, Huaien; Guigo, Roderic; Djebali, Sarah; Lagarde, Julien; Ryba, Tyrone; Sasaki, Takayo; Malladi, Venkat S; Cline, Melissa S; Kirkup, Vanessa M; Learned, Katrina; Rosenbloom, Kate R; Kent, W James; Feingold, Elise A; Good, Peter J; Pazin, Michael; Lowdon, Rebecca F; Adams, Leslie B

    2012-08-13

    To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.

  2. Challenges in Decomposing Encodings of Verification Problems

    Directory of Open Access Journals (Sweden)

    Peter Schrammel

    2016-07-01

    Full Text Available Modern program verifiers use logic-based encodings of the verification problem that are discharged by a back end reasoning engine. However, instances of such encodings for large programs can quickly overwhelm these back end solvers. Hence, we need techniques to make the solving process scale to large systems, such as partitioning (divide-and-conquer and abstraction. In recent work, we showed how decomposing the formula encoding of a termination analysis can significantly increase efficiency. The analysis generates a sequence of logical formulas with existentially quantified predicates that are solved by a synthesis-based program analysis engine. However, decomposition introduces abstractions in addition to those required for finding the unknown predicates in the formula, and can hence deteriorate precision. We discuss the challenges associated with such decompositions and their interdependencies with the solving process.

  3. RNA chaperones encoded by RNA viruses

    Institute of Scientific and Technical Information of China (English)

    Jie Yang; Hongjie Xia; Qi Qian; Xi Zhou

    2015-01-01

    RNAs are functionally diverse macromolecules whose proper functions rely strictly upon their correct tertiary structures. However, because of their high structural flexibility, correct folding of RNAs is challenging and slow. Therefore, cells and viruses encode a variety of RNA remodeling proteins, including helicases and RNA chaperones. In RNA viruses, these proteins are believed to play pivotal roles in all the processes involving viral RNAs during the life cycle. RNA helicases have been studied extensively for decades, whereas RNA chaperones, particularly virus-encoded RNA chaperones, are often overlooked. This review describes the activities of RNA chaperones encoded by RNA viruses, particularly the ones identified and characterized in recent years, and the functions of these proteins in different steps of viral life cycles, and presents an overview of this unique group of proteins.

  4. Cluster parallel rendering based on encoded mesh

    Institute of Scientific and Technical Information of China (English)

    QIN Ai-hong; XIONG Hua; PENG Hao-yu; LIU Zhen; SHI Jiao-ying

    2006-01-01

    Use of compressed mesh in parallel rendering architecture is still an unexplored area, the main challenge of which is to partition and sort the encoded mesh in compression-domain. This paper presents a mesh compression scheme PRMC (Parallel Rendering based Mesh Compression) supplying encoded meshes that can be partitioned and sorted in parallel rendering system even in encoded-domain. First, we segment the mesh into submeshes and clip the submeshes' boundary into Runs, and then piecewise compress the submeshes and Runs respectively. With the help of several auxiliary index tables, compressed submeshes and Runs can serve as rendering primitives in parallel rendering system. Based on PRMC, we design and implement a parallel rendering architecture. Compared with uncompressed representation, experimental results showed that PRMC meshes applied in cluster parallel rendering system can dramatically reduce the communication requirement.

  5. Fidelity enhancement by logical qubit encoding.

    Science.gov (United States)

    Henry, Michael K; Ramanathan, Chandrasekhar; Hodges, Jonathan S; Ryan, Colm A; Ditty, Michael J; Laflamme, Raymond; Cory, David G

    2007-11-30

    We demonstrate coherent control of two logical qubits encoded in a decoherence free subspace (DFS) of four dipolar-coupled protons in an NMR quantum information processor. A pseudopure fiducial state is created in the DFS, and a unitary logical qubit entangling operator evolves the system to a logical Bell state. The four-spin molecule is partially aligned by a liquid crystal solvent, which introduces strong dipolar couplings among the spins. Although the system Hamiltonian is never fully specified, we demonstrate high fidelity control over the logical degrees of freedom. In fact, the DFS encoding leads to higher fidelity control than is available in the full four-spin Hilbert space.

  6. Exogenous Brassinosteroid Induced the Salt Resistance of Cucumber (Cucumis sativus L.) Seedlings%外源BR诱导黄瓜(Cucumis sativus L.)幼苗的抗盐性

    Institute of Scientific and Technical Information of China (English)

    尚庆茂; 宋士清; 张志刚; 郭世荣

    2006-01-01

    [目的] 明确外源油菜素甾醇(Brassinosteroid,BR)对黄瓜(Cucumis sativus L.)幼苗抗盐性的诱导作用.[方法] 采用根际注射结合叶面喷施外源BR(0、0.005、0.01、0.05、0.1、0.2 mg·L-1)的方法,比较分析了盐胁迫下幼苗植株盐害指数、抗氧化酶活性、渗透调节物质含量等生理指标.[结果] 外源BR能够明显改善盐胁迫下黄瓜幼苗植株的生长发育状况,降低盐害指数,最高幅度达40.2个百分点(P<0.01),极显著地提高叶片细胞游离脯氨酸(Pro)和可溶性糖的含量、超氧化物歧化酶(SOD)、过氧化物酶(POD)、过氧化氢酶(CAT)等抗氧化酶活性(P<0.01),进而保护细胞膜的稳定性.[结论] 外源BR可以有效诱导黄瓜幼苗的抗盐性,并且最佳浓度范围是0.01~0.05 mg·L-1.

  7. Functional analyses of Populus euphratica brassinosteroid biosynthesis enzyme genes DWF4 (PeDWF4) and CPD (PeCPD) in the regulation of growth and development of Arabidopsis thaliana

    Indian Academy of Sciences (India)

    JIANPING SI; YAN SUN; LU WANG; YING QIN; CHONGYING WANG; XINYU WANG

    2016-12-01

    DWF4 and CPD are key brassinosteroids (BRs) biosynthesis enzyme genes. To explore the function of Populuseuphratica DWF4 (PeDWF4) and CPD (PeCPD), Arabidopsis thaliana transgenic lines (TLs) expressing PeDWF4,PeCPD or PeDWF4 plus PeCPD, namely PeDWF4-TL, PeCPD-TL and PeCP/DW-TL, were characterized. Comparedwith wild type (WT), the changes of both PeDWF4-TL and PeCPD-TL in plant heights, silique and hypocotylslengths and seed yields were similar, but in bolting time and stem diameters, they were opposite. PeCP/DW-TL wasmore in plant heights and the lengths of primary root, silique, and fruit stalk, but less in silique numbers and seedyields than either PeDWF4-TL or PeCPD-TL. PeDWF4 and PeCPD specially expressed in PeDWF4-TL or PeCPDTL,and the transcription level of PeDWF4 was higher than that of PeCPD. In PeCP/DW-TL, their expressions wereall relatively reduced. Additionally, the expression of PeDWF4 and PeCPD differentially made the expression levelsof AtDWF4, AtCPD, AtBR6OX2, AtFLC, AtTCP1 and AtGA5 change in the TLs. The total BRs contents werePeDWF4-TL > PeCP/DW-TL > WT > PeCPD-TL. These results imply that PeDWF4 is functionally not exactly thesame as PeCPD and there may be a synergistic and antagonistic effects in physiology between both of them in theregulation of plant growth and development.

  8. Encoding and Decoding Procedures for Arrangements

    Directory of Open Access Journals (Sweden)

    Alexander A. Babaev

    2012-05-01

    Full Text Available This article discusses an algorithm based on the encoding procedure for representing a set of arrangement elements as a single number. Also the author provides the procedure for the inverse transformation of the code into arrangement elements. In addition the Article includes recommendations on the use of the above procedures in combinatorial algorithms of optimization.

  9. Encoded Archival Description as a Halfway Technology

    Science.gov (United States)

    Dow, Elizabeth H.

    2009-01-01

    In the mid 1990s, Encoded Archival Description (EAD) appeared as a revolutionary technology for publishing archival finding aids on the Web. The author explores whether or not, given the advent of Web 2.0, the archival community should abandon EAD and look for something to replace it. (Contains 18 notes.)

  10. JPEG 2000 Encoding with Perceptual Distortion Control

    Science.gov (United States)

    Watson, Andrew B.; Liu, Zhen; Karam, Lina J.

    2008-01-01

    An alternative approach has been devised for encoding image data in compliance with JPEG 2000, the most recent still-image data-compression standard of the Joint Photographic Experts Group. Heretofore, JPEG 2000 encoding has been implemented by several related schemes classified as rate-based distortion-minimization encoding. In each of these schemes, the end user specifies a desired bit rate and the encoding algorithm strives to attain that rate while minimizing a mean squared error (MSE). While rate-based distortion minimization is appropriate for transmitting data over a limited-bandwidth channel, it is not the best approach for applications in which the perceptual quality of reconstructed images is a major consideration. A better approach for such applications is the present alternative one, denoted perceptual distortion control, in which the encoding algorithm strives to compress data to the lowest bit rate that yields at least a specified level of perceptual image quality. Some additional background information on JPEG 2000 is prerequisite to a meaningful summary of JPEG encoding with perceptual distortion control. The JPEG 2000 encoding process includes two subprocesses known as tier-1 and tier-2 coding. In order to minimize the MSE for the desired bit rate, a rate-distortion- optimization subprocess is introduced between the tier-1 and tier-2 subprocesses. In tier-1 coding, each coding block is independently bit-plane coded from the most-significant-bit (MSB) plane to the least-significant-bit (LSB) plane, using three coding passes (except for the MSB plane, which is coded using only one "clean up" coding pass). For M bit planes, this subprocess involves a total number of (3M - 2) coding passes. An embedded bit stream is then generated for each coding block. Information on the reduction in distortion and the increase in the bit rate associated with each coding pass is collected. This information is then used in a rate-control procedure to determine the

  11. How Attention Modulates Encoding of Dynamic Stimuli

    Science.gov (United States)

    Oren, Noga; Shapira-Lichter, Irit; Lerner, Yulia; Tarrasch, Ricardo; Hendler, Talma; Giladi, Nir; Ash, Elissa L.

    2016-01-01

    When encoding a real-life, continuous stimulus, the same neural circuits support processing and integration of prior as well as new incoming information. This ongoing interplay is modulated by attention, and is evident in regions such as the prefrontal cortex section of the task positive network (TPN), and in the posterior cingulate cortex (PCC), a hub of the default mode network (DMN). Yet the exact nature of such modulation is still unclear. To investigate this issue, we utilized an fMRI task that employed movies as the encoded stimuli and manipulated attentional load via an easy or hard secondary task that was performed simultaneously with encoding. Results showed increased intersubject correlation (inter-SC) levels when encoding movies in a condition of high, as compared to low attentional load. This was evident in bilateral ventrolateral and dorsomedial prefrontal cortices and the dorsal PCC (dPCC). These regions became more attuned to the combination of the movie and the secondary task as the attentional demand of the latter increased. Activation analyses revealed that at higher load the prefrontal TPN regions were more activated, whereas the dPCC was more deactivated. Attentional load also influenced connectivity within and between the networks. At high load the dPCC was anti-correlated to the prefrontal regions, which were more functionally coherent amongst themselves. Finally and critically, greater inter-SC in the dPCC at high load during encoding predicted lower memory strength when that information was retrieved. This association between inter-SC levels and memory strength suggest that as attentional demands increased, the dPCC was more attuned to the secondary task at the expense of the encoded stimulus, thus weakening memory for the encoded stimulus. Together, our findings show that attentional load modulated the function of core TPN and DMN regions. Furthermore, the observed relationship between memory strength and the modulation of the dPCC points

  12. Amygdala neurons differentially encode motivation and reinforcement.

    Science.gov (United States)

    Tye, Kay M; Janak, Patricia H

    2007-04-11

    Lesion studies demonstrate that the basolateral amygdala complex (BLA) is important for assigning motivational significance to sensory stimuli, but little is known about how this information is encoded. We used in vivo electrophysiology procedures to investigate how the amygdala encodes motivating and reinforcing properties of cues that induce reinstatement of reward-seeking behavior. Two groups of rats were trained to respond to a sucrose reward. The "paired" group was trained with a reward-predictive cue, whereas the "unpaired" group was trained with a randomly presented cue. Both groups underwent identical extinction and reinstatement procedures during which the reward was withheld. The proportion of neurons that were phasically cue responsive during reinstatement was significantly higher in the paired group (46 of 100) than in the unpaired group (8 of 112). Cues that induce reward-seeking behavior can do so by acting as incentives or reinforcers. Distinct populations of neurons responded to the cue in trials in which the cue acted as an incentive, triggering a motivated reward-seeking state, or as a reinforcer, supporting continued instrumental responding. The incentive motivation-encoding population of neurons (34 of 46 cue-responsive neurons; 74%) extinguished in temporal agreement with a decrease in the rate of instrumental responding. The conditioned reinforcement-encoding population of neurons (12 of 46 cue-responsive neurons; 26%) maintained their response for the duration of cue-reinforced instrumental responding. These data demonstrate that separate populations of cue-responsive neurons in the BLA encode the motivating or reinforcing properties of a cue previously associated with a reward.

  13. An Encoder/Decoder Scheme of OCDMA Based on Waveguide

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A new encoder/decoder scheme of OCDMA based on waveguide isproposed in this paper. The principle as well as the structure of waveguide encoder/decoder is given. It can be seen that all-optical OCDMA encoder/decoder can be realized by the proposed scheme of the waveguide encoder/decoder. It can also make the OCDMA encoder/decoder integrated easily and the access controlled easily. The system based on this scheme can work under the entirely asynchronous condition.

  14. Shape-Reprogrammable Polymers: Encoding, Erasing, and Re-Encoding (Postprint)

    Science.gov (United States)

    2014-11-01

    4. TITLE AND SUBTITLE SHAPE-REPROGRAMMABLE POLYMERS: ENCODING, ERASING, AND RE-ENCODING (POSTPRINT) 5a. CONTRACT NUMBER In- House 5b. GRANT...heating, which leads to the formation of dome structures that resemble the profi le of a 3D Gaussian shape (Supporting Information, Figure S2a–c...S14). By changing the fi lm stretch ratios, various dome shapes can be created (Figure 2 e). In all cases, the buckling direction is towards the

  15. Robust macroscopic entanglement without complex encodings

    CERN Document Server

    Chaves, Rafael; Acín, Antonio

    2011-01-01

    One of the main challenges for the experimental manipulation and storage of macroscopic entanglement is its fragility under noise. We present a simple recipe for the systematic enhancement of the resistance of multipartite entanglement against any local noise with a privileged direction in the Bloch sphere. For the case of exact local dephasing along any given basis, and for all noise strengths, our prescription grants full robustness: even states whose entanglement decays exponentially with the number of parts are mapped to states whose entanglement is constant. In contrast to previous techniques resorting to complex logical-qubit encodings, such enhancement is attained simply by performing local unitary rotations before the noise acts. The scheme is therefore highly experimentally-friendly, as it brings no overhead of extra physical qubits to encode logical ones. In addition, we show that, apart from entanglement, the resilience of the states as resources for useful practical tasks such as metrology and non...

  16. Genetically Encoded Voltage Indicators in Circulation Research.

    Science.gov (United States)

    Kaestner, Lars; Tian, Qinghai; Kaiser, Elisabeth; Xian, Wenying; Müller, Andreas; Oberhofer, Martin; Ruppenthal, Sandra; Sinnecker, Daniel; Tsutsui, Hidekazu; Miyawaki, Atsushi; Moretti, Alessandra; Lipp, Peter

    2015-09-08

    Membrane potentials display the cellular status of non-excitable cells and mediate communication between excitable cells via action potentials. The use of genetically encoded biosensors employing fluorescent proteins allows a non-invasive biocompatible way to read out the membrane potential in cardiac myocytes and other cells of the circulation system. Although the approaches to design such biosensors date back to the time when the first fluorescent-protein based Förster Resonance Energy Transfer (FRET) sensors were constructed, it took 15 years before reliable sensors became readily available. Here, we review different developments of genetically encoded membrane potential sensors. Furthermore, it is shown how such sensors can be used in pharmacological screening applications as well as in circulation related basic biomedical research. Potentials and limitations will be discussed and perspectives of possible future developments will be provided.

  17. Nucleic acid compositions and the encoding proteins

    Science.gov (United States)

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  18. DNA-Encoded Dynamic Combinatorial Chemical Libraries.

    Science.gov (United States)

    Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin

    2015-06-26

    Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions.

  19. Encoded Dynamical Recoupling with Shaped Pulses

    Science.gov (United States)

    Li, Yunfan; Lidar, Daniel A.; Pryadko, Leonid P.

    2008-03-01

    Encoded Dynamical Recoupling is a passive error correction techique which can be used to enhance the performance of a quantum error correction code (QECC) against low-frequency component of the thermal bath. The elements of the stabilizer group are used in the decoupling cycle which makes the encoded logic operations fault-tolerant. We studied the effectiveness of this techique both analytically and numerically for several three- and five-qubit codes, with decoupling sequences utilizing either Gaussian or self-refocusing pulse shapes. When logic pulses are intercalated between the decoupling cycles, the technique may be very effective in cancelling constant perturbation terms, but its performance is much weaker against a time-dependent perturbation simulated as a classical correlated noise. The decoupling accuracy can be substantially improved if logic is applied slowly and concurrently with the decoupling, so that a certain adiabaticity condition is satisfied.

  20. Asymmetric synthesis using chiral-encoded metal

    Science.gov (United States)

    Yutthalekha, Thittaya; Wattanakit, Chularat; Lapeyre, Veronique; Nokbin, Somkiat; Warakulwit, Chompunuch; Limtrakul, Jumras; Kuhn, Alexander

    2016-08-01

    The synthesis of chiral compounds is of crucial importance in many areas of society and science, including medicine, biology, chemistry, biotechnology and agriculture. Thus, there is a fundamental interest in developing new approaches for the selective production of enantiomers. Here we report the use of mesoporous metal structures with encoded geometric chiral information for inducing asymmetry in the electrochemical synthesis of mandelic acid as a model molecule. The chiral-encoded mesoporous metal, obtained by the electrochemical reduction of platinum salts in the presence of a liquid crystal phase and the chiral template molecule, perfectly retains the chiral information after removal of the template. Starting from a prochiral compound we demonstrate enantiomeric excess of the (R)-enantiomer when using (R)-imprinted electrodes and vice versa for the (S)-imprinted ones. Moreover, changing the amount of chiral cavities in the material allows tuning the enantioselectivity.

  1. Parameter Estimation of Turbo Code Encoder

    Directory of Open Access Journals (Sweden)

    Mehdi Teimouri

    2014-01-01

    Full Text Available The problem of reconstruction of a channel code consists of finding out its design parameters solely based on its output. This paper investigates the problem of reconstruction of parallel turbo codes. Reconstruction of a turbo code has been addressed in the literature assuming that some of the parameters of the turbo encoder, such as the number of input and output bits of the constituent encoders and puncturing pattern, are known. However in practical noncooperative situations, these parameters are unknown and should be estimated before applying reconstruction process. Considering such practical situations, this paper proposes a novel method to estimate the above-mentioned code parameters. The proposed algorithm increases the efficiency of the reconstruction process significantly by judiciously reducing the size of search space based on an analysis of the observed channel code output. Moreover, simulation results show that the proposed algorithm is highly robust against channel errors when it is fed with noisy observations.

  2. Bacillus caldolyticus prs gene encoding phosphoribosyldiphosphate synthase

    DEFF Research Database (Denmark)

    Krath, Britta N.; Hove-Jensen, Bjarne

    1996-01-01

    The prs gene, encoding phosphoribosyl-diphosphate (PRPP) synthase, as well as the flanking DNA sequences were cloned and sequenced from the Gram-positive thermophile, Bacillus caldolyticus. Comparison with the homologous sequences from the mesophile, Bacillus subtilis, revealed a gene (gca......D) encoding N-acetylglucosamine-l-phosphate uridyltransferase upstream of prs, and a gene homologous to ctc downstream of prs. cDNA synthesis with a B. caldolyticus gcaD-prs-ctc-specified mRNA as template, followed by amplification utilising the polymerase chain reaction indicated that the three genes are co......-transcribed. Comparison of amino acid sequences revealed a high similarity among PRPP synthases across a wide phylogenetic range. An E. coli strain harbouring the B. caldolyticus prs gene in a multicopy plasmid produced PRPP synthase activity 33-fold over the activity of a haploid B. caldolyticus strain. B. caldolyticus...

  3. Compositional encoding for bounded model checking

    Institute of Scientific and Technical Information of China (English)

    Jun SUN; Yang LIU; Jin Song DONG; Jing SUN

    2008-01-01

    Verification techniques like SAT-based bounded model checking have been successfully applied to a variety of system models. Applying bounded model checking to compositional process algebras is, however, a highly non-trivial task. One challenge is that the number of system states for process algebra models is not statically known, whereas exploring the full state space is computa-tionally expensive. This paper presents a compositional encoding of hierarchical processes as SAT problems and then applies state-of-the-art SAT solvers for bounded model checking. The encoding avoids exploring the full state space for complex systems so as to deal with state space explosion. We developed an automated analyzer which combines complementing model checking tech-niques (I.e., bounded model checking and explicit on-the-fly model checking) to validate system models against event-based temporal properties. The experiment results show the analyzer handles large systems.

  4. Multichannel Compressive Sensing MRI Using Noiselet Encoding

    CERN Document Server

    Pawar, Kamlesh; Zhang, Jingxin

    2014-01-01

    The incoherence between measurement and sparsifying transform matrices and the restricted isometry property (RIP) of measurement matrix are two of the key factors in determining the performance of compressive sensing (CS). In CS-MRI, the randomly under-sampled Fourier matrix is used as the measurement matrix and the wavelet transform is usually used as sparsifying transform matrix. However, the incoherence between the randomly under-sampled Fourier matrix and the wavelet matrix is not optimal, which can deteriorate the performance of CS-MRI. Using the mathematical result that noiselets are maximally incoherent with wavelets, this paper introduces the noiselet unitary bases as the measurement matrix to improve the incoherence and RIP in CS-MRI, and presents a method to design the pulse sequence for the noiselet encoding. This novel encoding scheme is combined with the multichannel compressive sensing (MCS) framework to take the advantage of multichannel data acquisition used in MRI scanners. An empirical RIP a...

  5. Phase modulation pseudocolor encoding ghost imaging

    Institute of Scientific and Technical Information of China (English)

    段德洋; 张路; 杜少将; 夏云杰

    2015-01-01

    We present a ghost imaging scheme that can obtain a good pseudocolor image of black-and-white objects. The essential idea is to use the multi-wavelength thermal light source and the phase modulation pseudocolor encoding technique, which overcomes the disadvantages of other methods involved the spatial filtering. Therefore, the pseudocolor ghost image achieved by this imaging scheme is better than that obtained by other methods in brightness, color, and signal-to-noise ratio.

  6. Encoded libraries of chemically modified peptides.

    Science.gov (United States)

    Heinis, Christian; Winter, Greg

    2015-06-01

    The use of powerful technologies for generating and screening DNA-encoded protein libraries has helped drive the development of proteins as pharmaceutical ligands. However the development of peptides as pharmaceutical ligands has been more limited. Although encoded peptide libraries are typically several orders of magnitude larger than classical chemical libraries, can be more readily screened, and can give rise to higher affinity ligands, their use as pharmaceutical ligands is limited by their intrinsic properties. Two of the intrinsic limitations include the rotational flexibility of the peptide backbone and the limited number (20) of natural amino acids. However these limitations can be overcome by use of chemical modification. For example, the libraries can be modified to introduce topological constraints such as cyclization linkers, or to introduce new chemical entities such as small molecule ligands, fluorophores and photo-switchable compounds. This article reviews the chemistry involved, the properties of the peptide ligands, and the new opportunities offered by chemical modification of DNA-encoded peptide libraries.

  7. An Intensional Concurrent Faithful Encoding of Turing Machines

    Directory of Open Access Journals (Sweden)

    Thomas Given-Wilson

    2014-10-01

    Full Text Available The benchmark for computation is typically given as Turing computability; the ability for a computation to be performed by a Turing Machine. Many languages exploit (indirect encodings of Turing Machines to demonstrate their ability to support arbitrary computation. However, these encodings are usually by simulating the entire Turing Machine within the language, or by encoding a language that does an encoding or simulation itself. This second category is typical for process calculi that show an encoding of lambda-calculus (often with restrictions that in turn simulates a Turing Machine. Such approaches lead to indirect encodings of Turing Machines that are complex, unclear, and only weakly equivalent after computation. This paper presents an approach to encoding Turing Machines into intensional process calculi that is faithful, reduction preserving, and structurally equivalent. The encoding is demonstrated in a simple asymmetric concurrent pattern calculus before generalised to simplify infinite terms, and to show encodings into Concurrent Pattern Calculus and Psi Calculi.

  8. Effect of Brassinosteroid on the Physiological Characters and the Ca2+Distribution in Maize%油菜素内酯提高玉米幼苗抗病性与Ca2+分布的关系

    Institute of Scientific and Technical Information of China (English)

    由诗东; 张海丽; 高静; 张昊; 黄新; 李生辉; 王凤茹; 董金皋

    2014-01-01

    In this study,we adopted maize variety Jundan 20 to explore the effect of Brassinosteroid (BR) treat-ment on Ca2+distribution in maize seedling cells and resistance change of maize leaf against Fusarium proliferatum, aiming to verify the influence of BR on Ca 2+messenger system and its correlation with the enhancement of disease resistancein maize ,thus providing the theoretical basis for illuminating the mechanism of BR in enhancing disease resistance of maize .The results showed that the number of disease infected sheath decreased after BR treatment a-long with shrunken lesion area ,significant decrease of Ca 2+distribution in cell wall and obvious increase of Ca 2+distribution in intercellular space .In this way,the infected area will be more capable to resist softening compared with healthy tissues ,and further fungus infection will be inhibited .%为明确油菜素内酯(Brassinosteroid,BR)对Ca2+信使系统的影响及提高玉米抗病性的关系,为阐明BR提高玉米抗病性的机理提供理论依据。以玉米品种浚单20为材料,研究了BR处理后对玉米幼苗细胞中Ca2+分布的影响和玉米叶片对层出镰孢菌的抗性的变化情况。结果发现:BR处理后感病的叶鞘数目减少,病斑面积减小,细胞壁中Ca2+分布明显减少,细胞间隙中Ca2+分布明显增加,使得受侵染的部位比健康组织有更强的抗软化能力,抑制真菌的进一步侵染。

  9. Encoding the core electrons with graph concepts.

    Science.gov (United States)

    Pogliani, Lionello

    2004-01-01

    The core electron problem of atoms in chemical graph studies has always been considered as a minor problem. Usually, chemical graphs had to encode just a small set of second row atoms, i.e., C, N, O, and F, thus, graph and, in some cases, pseudograph concepts were enough to "graph" encode the molecules at hand. Molecular connectivity theory, together with its side-branch the electrotopological state, introduced two "ad hoc" algorithms for the core electrons of higher-row atoms based, mainly, on quantum concepts alike. Recently, complete graphs, and, especially, odd complete graphs have been introduced to encode the core electrons of higher-row atoms. By the aid of these types of graphs a double-valued algorithm has been proposed for the valence delta, deltav, of any type of atoms of the periodic table with a principal quantum number n > or =2. The new algorithm is centered on an invariant suggested by the hand-shaking theorem, and the values it gives rise to parallel in some way the values derived by the aid of the two old "quantum" algorithms. A thorough comparative analysis of the newly proposed algorithms has been undertaken for atoms of the group 1A-7A of the periodic table. This comparative study includes the electronegativity, the size of the atoms, the first ionization energy, and the electron affinity. The given algorithm has also been tested with sequential complete graphs, while the even complete graphs give rise to conceptual difficulties. QSAR/QSPR studies do not show a clear-cut preference for any of the two values the algorithm gives rise to, even if recent results seem to prefer one of the two values.

  10. Mouse redox histology using genetically encoded probes.

    Science.gov (United States)

    Fujikawa, Yuuta; Roma, Leticia P; Sobotta, Mirko C; Rose, Adam J; Diaz, Mauricio Berriel; Locatelli, Giuseppe; Breckwoldt, Michael O; Misgeld, Thomas; Kerschensteiner, Martin; Herzig, Stephan; Müller-Decker, Karin; Dick, Tobias P

    2016-03-15

    Mapping the in vivo distribution of endogenous oxidants in animal tissues is of substantial biomedical interest. Numerous health-related factors, including diet, physical activity, infection, aging, toxins, or pharmacological intervention, may cause redox changes. Tools are needed to pinpoint redox state changes to particular organs, tissues, cell types, and subcellular organelles. We describe a procedure that preserves the in vivo redox state of genetically encoded redox biosensors within histological tissue sections, thus providing "redox maps" for any tissue and comparison of interest. We demonstrate the utility of the technique by visualizing endogenous redox differences and changes in the context of tumor growth, inflammation, embryonic development, and nutrient starvation.

  11. Polynucleotides encoding TRF1 binding proteins

    Science.gov (United States)

    Campisi, Judith; Kim, Sahn-Ho

    2002-01-01

    The present invention provides a novel telomere associated protein (Trf1-interacting nuclear protein 2 "Tin2") that hinders the binding of Trf1 to its specific telomere repeat sequence and mediates the formation of a Tin2-Trf1-telomeric DNA complex that limits telomerase access to the telomere. Also included are the corresponding nucleic acids that encode the Tin2 of the present invention, as well as mutants of Tin2. Methods of making, purifying and using Tin2 of the present invention are described. In addition, drug screening assays to identify drugs that mimic and/or complement the effect of Tin2 are presented.

  12. Fractal image encoding based on adaptive search

    Institute of Scientific and Technical Information of China (English)

    Kya Berthe; Yang Yang; Huifang Bi

    2003-01-01

    Finding the optimal algorithm between an efficient encoding process and the rate distortion is the main research in fractal image compression theory. A new method has been proposed based on the optimization of the Least-Square Error and the orthogonal projection. A large number of domain blocks can be eliminated in order to speed-up fractal image compression. Moreover, since the rate-distortion performance of most fractal image coders is not satisfactory, an efficient bit allocation algorithm to improve the rate distortion is also proposed. The implementation and comparison have been done with the feature extraction method to prove the efficiency of the proposed method.

  13. Digitally encoded all-optical sensor multiplexing

    Science.gov (United States)

    Pervez, Anjum

    1992-01-01

    A digital, all-optical temperature sensor design concept based on optical sampling and digital encoding is presented. The proposed sensor generates 2M binary digital codewords of length M bits. The codewords are generated serially and, therefore, only a single output fiber line is required. A multiplexing scheme, which minimizes the power requirement per sensor array and facilitates a cost-effective digit regeneration for remote monitoring over long distance, is presented. The sensor arrays are used as building blocks to configure large scale sensor networks based on LAN topologies.

  14. The ENCODE (ENCyclopedia Of DNA Elements) Project.

    Science.gov (United States)

    2004-10-22

    The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional elements in the human genome sequence. The pilot phase of the Project is focused on a specified 30 megabases (approximately 1%) of the human genome sequence and is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function. The results of this pilot phase will guide future efforts to analyze the entire human genome.

  15. Rapidly-Indexing Incremental-Angle Encoder

    Science.gov (United States)

    Christon, Philip R.; Meyer, Wallace W.

    1989-01-01

    Optoelectronic system measures relative angular position of shaft or other device to be turned, also measures absolute angular position after device turned through small angle. Relative angular position measured with fine resolution by optoelectronically counting finely- and uniformly-spaced light and dark areas on encoder disk as disk turns past position-sensing device. Also includes track containing coarsely- and nonuniformly-spaced light and dark areas, angular widths varying in proportion to absolute angular position. This second track provides gating and indexing signal.

  16. Toward Chemical Implementation of Encoded Combinatorial Libraries

    DEFF Research Database (Denmark)

    Nielsen, John; Janda, Kim D.

    1994-01-01

    The recent application of "combinatorial libraries" to supplement existing drug screening processes might simplify and accelerate the search for new lead compounds or drugs. Recently, a scheme for encoded combinatorial chemistry was put forward to surmount a number of the limitations possessed...... by existing methodologies. Here we detail the synthesis of several matrices and the necessary chemistry to implement the conceptual scheme. In addition, we disclose how this novel technology permits a controlled ′dendritic" display of the chemical libraries. © 1994 Academic Press. All rights reserved....

  17. Encoding of Memory in Sheared Amorphous Solids

    Science.gov (United States)

    Fiocco, Davide; Foffi, Giuseppe; Sastry, Srikanth

    2014-01-01

    We show that memory can be encoded in a model amorphous solid subjected to athermal oscillatory shear deformations, and in an analogous spin model with disordered interactions, sharing the feature of a deformable energy landscape. When these systems are subjected to oscillatory shear deformation, they retain memory of the deformation amplitude imposed in the training phase, when the amplitude is below a "localization" threshold. Remarkably, multiple persistent memories can be stored using such an athermal, noise-free, protocol. The possibility of such memory is shown to be linked to the presence of plastic deformations and associated limit cycles traversed by the system, which exhibit avalanche statistics also seen in related contexts.

  18. Novel encoding methods for DNA-templated chemical libraries.

    Science.gov (United States)

    Li, Gang; Zheng, Wenlu; Liu, Ying; Li, Xiaoyu

    2015-06-01

    Among various types of DNA-encoded chemical libraries, DNA-templated library takes advantage of the sequence-specificity of DNA hybridization, enabling not only highly effective DNA-templated chemical reactions, but also high fidelity in library encoding. This brief review summarizes recent advances that have been made on the encoding strategies for DNA-templated libraries, and it also highlights their respective advantages and limitations for the preparation of DNA-encoded libraries.

  19. Self-encoding resin beads of combinatorial library screening

    Science.gov (United States)

    Lei, Du; Zhao, Yuandi; Cheng, Tongsheng; Zeng, Shaoqun; Luo, Qingming

    2003-07-01

    The latest self-encoding resin bead is a novel technology for solid phase synthesis combinatorial library screening. A new encode-positional deconvolution strategy which was based on that technology been illustrated compared with positional scanning and iterative strategies. The self-encoding resin beads technology provides an efficient method for improving the high-throughput screening of combinatorial library.

  20. Socialization Processes in Encoding and Decoding: Learning Effective Nonverbal Behavior.

    Science.gov (United States)

    Feldman, Robert S.; Coats, Erik

    This study examined the relationship of nonverbal encoding and decoding skills to the level of exposure to television. Subjects were children in second through sixth grade. Three nonverbal skills (decoding, spontaneous encoding, and posed encoding) were assessed for each of five emotions: anger, disgust, fear or surprise, happiness, and sadness.…

  1. DVB-S2 FEC Encoder: Implementation of DVB-S2 FEC encoder in FPGA

    OpenAIRE

    Myhr, Reidar

    2007-01-01

    This Master Thesis describe how DVB-S2 Forward Error Correction (FEC) encoding can be implemented in hardware like a FPGA. It include the design, simulation, verification and synthesis of a complete encoder for the DVB-S2 FEC system. First the Thesis gives a introduction to the history behind DVB-S2 and the FEC system. It describe shortly the theory behind the error correcting codes used in the FEC, BCH and LDPC codes. To get an effective implementation in hardware it was necessary to studies...

  2. Reading Neural Encodings using Phase Space Methods

    CERN Document Server

    Abarbanel, Henry D I; Abarbanel, Henry D I; Tumer, Evren C.

    2003-01-01

    Environmental signals sensed by nervous systems are often represented in spike trains carried from sensory neurons to higher neural functions where decisions and functional actions occur. Information about the environmental stimulus is contained (encoded) in the train of spikes. We show how to "read" the encoding using state space methods of nonlinear dynamics. We create a mapping from spike signals which are output from the neural processing system back to an estimate of the analog input signal. This mapping is realized locally in a reconstructed state space embodying both the dynamics of the source of the sensory signal and the dynamics of the neural circuit doing the processing. We explore this idea using a Hodgkin-Huxley conductance based neuron model and input from a low dimensional dynamical system, the Lorenz system. We show that one may accurately learn the dynamical input/output connection and estimate with high precision the details of the input signals from spike timing output alone. This form of "...

  3. Negative base encoding in optical linear algebra processors

    Science.gov (United States)

    Perlee, C.; Casasent, D.

    1986-01-01

    In the digital multiplication by analog convolution algorithm, the bits of two encoded numbers are convolved to form the product of the two numbers in mixed binary representation; this output can be easily converted to binary. Attention is presently given to negative base encoding, treating base -2 initially, and then showing that the negative base system can be readily extended to any radix. In general, negative base encoding in optical linear algebra processors represents a more efficient technique than either sign magnitude or 2's complement encoding, when the additions of digitally encoded products are performed in parallel.

  4. A method for encoding clinical datasets with SNOMED CT

    Directory of Open Access Journals (Sweden)

    Quan Hue

    2010-09-01

    Full Text Available Abstract Background Over the past decade there has been a growing body of literature on how the Systematised Nomenclature of Medicine Clinical Terms (SNOMED CT can be implemented and used in different clinical settings. Yet, for those charged with incorporating SNOMED CT into their organisation's clinical applications and vocabulary systems, there are few detailed encoding instructions and examples available to show how this can be done and the issues involved. This paper describes a heuristic method that can be used to encode clinical terms in SNOMED CT and an illustration of how it was applied to encode an existing palliative care dataset. Methods The encoding process involves: identifying input data items; cleaning the data items; encoding the cleaned data items; and exporting the encoded terms as output term sets. Four outputs are produced: the SNOMED CT reference set; interface terminology set; SNOMED CT extension set and unencodeable term set. Results The original palliative care database contained 211 data elements, 145 coded values and 37,248 free text values. We were able to encode ~84% of the terms, another ~8% require further encoding and verification while terms that had a frequency of fewer than five were not encoded (~7%. Conclusions From the pilot, it would seem our SNOMED CT encoding method has the potential to become a general purpose terminology encoding approach that can be used in different clinical systems.

  5. Radiofrequency encoded angular-resolved light scattering

    DEFF Research Database (Denmark)

    Buckley, Brandon W.; Akbari, Najva; Diebold, Eric D.

    2015-01-01

    The sensitive, specific, and label-free classification of microscopic cells and organisms is one of the outstanding problems in biology. Today, instruments such as the flow cytometer use a combination of light scatter measurements at two distinct angles to infer the size and internal complexity...... of cells at rates of more than 10,000 per second. However, by examining the entire angular light scattering spectrum it is possible to classify cells with higher resolution and specificity. Current approaches to performing these angular spectrum measurements all have significant throughput limitations...... Encoded Angular-resolved Light Scattering (REALS), this technique multiplexes angular light scattering in the radiofrequency domain, such that a single photodetector captures the entire scattering spectrum from a particle over approximately 100 discrete incident angles on a single shot basis. As a proof...

  6. Measurement of transient deformation by color encoding.

    Science.gov (United States)

    Mares, C; Barrientos, B; Blanco, A

    2011-12-05

    We present a method based on color encoding for measurement of transient 3D deformation in diffuse objects. The object is illuminated by structured light that consists of a fringe pattern with cyan fringes embedded in a white background. Color images are registered and information on each color channel is then separated. Surface features appear on the blue channel while fringes on the red channel. The in-plane components of displacement are calculated via digital correlation of the texture images. Likewise, the resulting fringes serve for the measuring of the out-of-plane component. As crossing of information between signals is avoided, the accuracy of the method is high. This is confirmed by a series of displacement measurements of an aluminum plate.

  7. Current questions on space and time encoding.

    Science.gov (United States)

    Hasselmo, Michael E; Stern, Chantal E

    2015-06-01

    The Nobel Prize in Physiology or Medicine 2014 celebrated the groundbreaking findings on place cells and grid cells by John O'Keefe and May-Britt Moser and Edvard Moser. These findings provided an essential foothold for understanding the cognitive encoding of space and time in episodic memory function. This foothold provides a closer view of a broad new world of important research questions raised by the phenomena of place cells and grid cells. These questions concern the mechanisms of generation of place and grid cell firing, including sensory influences, circuit dynamics and intrinsic properties. Similar questions concern the generation of time cells. In addition, questions concern the functional role of place cells, grid cells and time cells in mediating goal-directed behavior and episodic memory function.

  8. Schistosome satellite DNA encodes active hammerhead ribozymes.

    Science.gov (United States)

    Ferbeyre, G; Smith, J M; Cedergren, R

    1998-07-01

    Using a computer program designed to search for RNA structural motifs in sequence databases, we have found a hammerhead ribozyme domain encoded in the Smalpha repetitive DNA of Schistosoma mansoni. Transcripts of these repeats are expressed as long multimeric precursor RNAs that cleave in vitro and in vivo into unit-length fragments. This RNA domain is able to engage in both cis and trans cleavage typical of the hammerhead ribozyme. Further computer analysis of S. mansoni DNA identified a potential trans cleavage site in the gene coding for a synaptobrevin-like protein, and RNA transcribed from this gene was efficiently cleaved by the Smalpha ribozyme in vitro. Similar families of repeats containing the hammerhead domain were found in the closely related Schistosoma haematobium and Schistosomatium douthitti species but were not present in Schistosoma japonicum or Heterobilharzia americana, suggesting that the hammerhead domain was not acquired from a common schistosome ancestor.

  9. Ultrasonically encoded photoacoustic flowgraphy in biological tissue

    Science.gov (United States)

    Wang, Lidai; Xia, Jun; Yao, Junjie; Maslov, Konstantin I.; Wang, Lihong V.

    2014-01-01

    Blood flow speed is an important functional parameter. Doppler ultrasound flowmetry lacks sufficient sensitivity to slow blood flow (several to tens of millimeters per second) in deep tissue. To address this challenge, we developed ultrasonically encoded photoacoustic flowgraphy combining ultrasonic thermal tagging with photoacoustic imaging. Focused ultrasound generates a confined heat source in acoustically absorptive fluid. Thermal waves propagate with the flow and are directly visualized in pseudo color using photoacoustic computed tomography. The Doppler shift is employed to calculate the flow speed. This method requires only acoustic and optical absorption, and thus is applicable to continuous fluid. A blood flow speed as low as 0.24 mm·s−1 was successfully measured. Deep blood flow imaging was experimentally demonstrated under 5-mm-thick chicken breast tissue. PMID:24289689

  10. Encoding continuous spatial phenomena in GML

    Science.gov (United States)

    de Vries, M. E.; Ledoux, H.

    2009-04-01

    In the discussion about how to model and encode geographic information two meta-models of space exist: the 'object' view and the 'field' view. This difference in conceptual view is also reflected in different data models and encoding formats. Among GIS practitioners, ‘fields' (or ‘coverages') are being used almost exclusively in 2D, while in the geoscience community 3D and higher-dimensional fields are widely used. (Note that the dimensions in oceanographic/atmospheric coverages are not necessarily spatial dimensions, as any parameters (e.g. temperature of the air, or density of water) can be considered a dimension.) While standardisation work in ISO and OGC has led to agreement on how to best encode discrete spatial objects, for the modelling and encoding of continuous ‘fields' there are still a number of open issues. In the presentation we will shortly discuss the current standards related to fields, and look at their shortcomings and potential. In ISO 19123 for example a distinction is made between discrete and continuous coverages, but the difference is not very clear and hard to capture for implementers. As far as encoding is concerned: GML 3.x (ISO 19136) has a discrete coverage data type, but no continuous coverage type. We will then present an alternative solution to model fields, and show how it can be implemented using some parts of GML, but not the ISO/GML coverage type. This alternative data model for fields permits us to represent fields in 2D and 3D, although conceptually it can be easily extended to higher dimensions. Unlike current standards where there is a distinction between discrete and continuous fields/coverages, we argue that a field should always have one - and only one! - value for a given attribute at every location in the spatial domain (be this domain the surface of the Earth, a 3D volume, or even a 4D spatio-temporal hypercube). The principal idea behind the proposed model is that two things are needed to have a coverage: 1. a set

  11. Modular verification of chemical reaction network encodings via serializability analysis.

    Science.gov (United States)

    Lakin, Matthew R; Stefanovic, Darko; Phillips, Andrew

    2016-06-13

    Chemical reaction networks are a powerful means of specifying the intended behaviour of synthetic biochemical systems. A high-level formal specification, expressed as a chemical reaction network, may be compiled into a lower-level encoding, which can be directly implemented in wet chemistry and may itself be expressed as a chemical reaction network. Here we present conditions under which a lower-level encoding correctly emulates the sequential dynamics of a high-level chemical reaction network. We require that encodings are transactional, such that their execution is divided by a "commit reaction" that irreversibly separates the reactant-consuming phase of the encoding from the product-generating phase. We also impose restrictions on the sharing of species between reaction encodings, based on a notion of "extra tolerance", which defines species that may be shared between encodings without enabling unwanted reactions. Our notion of correctness is serializability of interleaved reaction encodings, and if all reaction encodings satisfy our correctness properties then we can infer that the global dynamics of the system are correct. This allows us to infer correctness of any system constructed using verified encodings. As an example, we show how this approach may be used to verify two- and four-domain DNA strand displacement encodings of chemical reaction networks, and we generalize our result to the limit where the populations of helper species are unlimited.

  12. High resolution absolute incremental combined-use encoder; Kobunkaino abusoryuto inkurimentaru ken`yo encoder

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1999-01-10

    Produced at Fuji Electric Co.,Ltd., on a commercial basis was a high resolution absolute incremental combined-use encoder, which is a serial transmission type with a resolution of 16bit per rotation, as a rotary sensor for a small high performance servo system FALDIC-{alpha} series. Accomplished in this encoder were a high resolution, which greatly improves uneven rotation at low speed and precision in positioning, and miniaturization which is on the top level in the industry, by means of a high performance CPU and a large scale LSI. In addition, less wiring by unique high-speed serial communication was contrived, as were protective functions of all types and intelligent systematization by data holding function. Moreover, a newly structured rotary disk was employed, greatly improving vibration resistance and impact resistance. By using the high resolution absolute incremental combined-use encoder as standard equipment in the servo motor, flexibility is secured in a system for a machine to which the device is applied. (NEDO)

  13. A ROBUST ADAPTIVE VIDEO ENCODER BASED ON HUMAN VISUAL MODEL

    Institute of Scientific and Technical Information of China (English)

    Yin Hao; Zhang Jiangshan; Zhu Yaoting; Zhu Guangxi

    2003-01-01

    A Robust Adaptive Video Encoder (RAVE) based on human visual model is proposed. The encoder combines the best features of Fine Granularity Scalable (FGS) coding, framedropping coding, video redundancy coding, and human visual model. According to packet loss and available bandwidth of the network, the encoder adjust the output bit rate by jointly adapting quantization step-size instructed by human visual model, rate shaping, and periodically inserting key frame. The proposed encoder is implemented based on MPEG-4 encoder and is compared with the case of a conventional FGS algorithm. It is shown that RAVE is a very efficient robust video encoder that provides improved visual quality for the receiver and consumes equal or less network resource. Results are confirmed by subjective tests and simulation tests.

  14. A ROBUST ADAPTIVE VIDEO ENCODER BASED ON HUMAN VISUAL MODEL

    Institute of Scientific and Technical Information of China (English)

    YinHao; ZhangJiangshan

    2003-01-01

    A Robust Adaptive Video Encoder (RAVE) based on human visual model is proposed.The encoder combines the best features of Fine Granularity Scalabla (FGS) coding,frame-dropping coding,video redundancy coding,and human visual model.According to packet loss and available bandwidth of the network,the encoder adjust the output bit rate by jointly adapting quantization step-size instructed by human visual model,rate shaping,and periodically inserting key frame.The proposed encoder is implemented based on MPEG-4 encoder and is compared with the case of a conventional FGS algorithm.It is shown that RAVE is a very efficient robust videl encoder that provides improved visual quality for the receiver and consumes equal or less network resource.Results are confirmed by subjective tests and simulation tests.

  15. The optimal encodings for biased association in linear associative memories.

    Science.gov (United States)

    Leung, Yee; Dong, Tian Xin; Xu, Zong Ben

    1998-07-01

    In this paper, optimal encoding schemes for linear associative memories are derived for biased association under both the white-noise and colored-noise situations. Analysis and simulation results all show that the biased encodings thus derived are optimal and superior to existing models in their performance. Together with the Wee-Kohonen unbiased encoding, the study settles the optimality issue of linear associative memories and enhances their practicalities.

  16. Oligonucleotide and Long Polymeric DNA Encoding

    Energy Technology Data Exchange (ETDEWEB)

    Miller, E; Mariella Jr., R P; Christian, A T; Gardner, S N; Williams, J M

    2003-11-24

    This report summarizes the work done at Lawrence Livermore National Laboratory for the Oligonucleotide and Long Polymeric DNA Encoding project, part of the Microelectronic Bioprocesses Program at DARPA. The goal of the project was to develop a process by which long (circa 10,000 base-pair) synthetic DNA molecules could be synthesized in a timely and economic manner. During construction of the long molecule, errors in DNA sequence occur during hybridization and/or the subsequent enzymatic process. The work done on this project has resulted in a novel synthesis scheme that we call the parallel pyramid synthesis protocol, the development of a suit of computational tools to minimize and quantify errors in the synthesized DNA sequence, and experimental proof of this technique. The modeling consists of three interrelated modules: the bioinformatics code which determines the specifics of parallel pyramid synthesis for a given chain of long DNA, the thermodynamics code which tracks the products of DNA hybridization and polymerase extension during the later steps in the process, and the kinetics model which examines the temporal and spatial processes during one thermocycle. Most importantly, we conducted the first successful syntheses of a gene using small starting oligomers (tetramers). The synthesized sequence, 813 base pairs long, contained a 725 base pair gene, modified green fluorescent protein (mGFP), which has been shown to be a functional gene by cloning into cells and observing its green fluorescent product.

  17. Temporal encoding in a nervous system.

    Directory of Open Access Journals (Sweden)

    Zane N Aldworth

    2011-05-01

    Full Text Available We examined the extent to which temporal encoding may be implemented by single neurons in the cercal sensory system of the house cricket Acheta domesticus. We found that these neurons exhibit a greater-than-expected coding capacity, due in part to an increased precision in brief patterns of action potentials. We developed linear and non-linear models for decoding the activity of these neurons. We found that the stimuli associated with short-interval patterns of spikes (ISIs of 8 ms or less could be predicted better by second-order models as compared to linear models. Finally, we characterized the difference between these linear and second-order models in a low-dimensional subspace, and showed that modification of the linear models along only a few dimensions improved their predictive power to parity with the second order models. Together these results show that single neurons are capable of using temporal patterns of spikes as fundamental symbols in their neural code, and that they communicate specific stimulus distributions to subsequent neural structures.

  18. Comparative genomics of Shiga toxin encoding bacteriophages

    Directory of Open Access Journals (Sweden)

    Smith Darren L

    2012-07-01

    Full Text Available Abstract Background Stx bacteriophages are responsible for driving the dissemination of Stx toxin genes (stx across their bacterial host range. Lysogens carrying Stx phages can cause severe, life-threatening disease and Stx toxin is an integral virulence factor. The Stx-bacteriophage vB_EcoP-24B, commonly referred to as Ф24B, is capable of multiply infecting a single bacterial host cell at a high frequency, with secondary infection increasing the rate at which subsequent bacteriophage infections can occur. This is biologically unusual, therefore determining the genomic content and context of Ф24B compared to other lambdoid Stx phages is important to understanding the factors controlling this phenomenon and determining whether they occur in other Stx phages. Results The genome of the Stx2 encoding phage, Ф24B was sequenced and annotated. The genomic organisation and general features are similar to other sequenced Stx bacteriophages induced from Enterohaemorrhagic Escherichia coli (EHEC, however Ф24B possesses significant regions of heterogeneity, with implications for phage biology and behaviour. The Ф24B genome was compared to other sequenced Stx phages and the archetypal lambdoid phage, lambda, using the Circos genome comparison tool and a PCR-based multi-loci comparison system. Conclusions The data support the hypothesis that Stx phages are mosaic, and recombination events between the host, phages and their remnants within the same infected bacterial cell will continue to drive the evolution of Stx phage variants and the subsequent dissemination of shigatoxigenic potential.

  19. Genes Encoding Enzymes Involved in Ethanol Metabolism

    Science.gov (United States)

    Hurley, Thomas D.; Edenberg, Howard J.

    2012-01-01

    The effects of beverage alcohol (ethanol) on the body are determined largely by the rate at which it and its main breakdown product, acetaldehyde, are metabolized after consumption. The main metabolic pathway for ethanol involves the enzymes alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH). Seven different ADHs and three different ALDHs that metabolize ethanol have been identified. The genes encoding these enzymes exist in different variants (i.e., alleles), many of which differ by a single DNA building block (i.e., single nucleotide polymorphisms [SNPs]). Some of these SNPs result in enzymes with altered kinetic properties. For example, certain ADH1B and ADH1C variants that are commonly found in East Asian populations lead to more rapid ethanol breakdown and acetaldehyde accumulation in the body. Because acetaldehyde has harmful effects on the body, people carrying these alleles are less likely to drink and have a lower risk of alcohol dependence. Likewise, an ALDH2 variant with reduced activity results in acetaldehyde buildup and also has a protective effect against alcoholism. In addition to affecting drinking behaviors and risk for alcoholism, ADH and ALDH alleles impact the risk for esophageal cancer. PMID:23134050

  20. Temporal encoding in a nervous system.

    Science.gov (United States)

    Aldworth, Zane N; Dimitrov, Alexander G; Cummins, Graham I; Gedeon, Tomáš; Miller, John P

    2011-05-01

    We examined the extent to which temporal encoding may be implemented by single neurons in the cercal sensory system of the house cricket Acheta domesticus. We found that these neurons exhibit a greater-than-expected coding capacity, due in part to an increased precision in brief patterns of action potentials. We developed linear and non-linear models for decoding the activity of these neurons. We found that the stimuli associated with short-interval patterns of spikes (ISIs of 8 ms or less) could be predicted better by second-order models as compared to linear models. Finally, we characterized the difference between these linear and second-order models in a low-dimensional subspace, and showed that modification of the linear models along only a few dimensions improved their predictive power to parity with the second order models. Together these results show that single neurons are capable of using temporal patterns of spikes as fundamental symbols in their neural code, and that they communicate specific stimulus distributions to subsequent neural structures.

  1. Encoding complex values using two DLP spatial light modulators

    Science.gov (United States)

    Becker, Michael F.; Wu, Sih-Ying; Liang, Jinyang

    2013-03-01

    We present a method to encode complex values into three or four quantized complex values for wavefront modulation using two digital micromirror devices (DMDs). This encoding offers advantages to eliminate the twin image or suppress the zero order diffraction as well to improve hologram fidelity. The optical architecture utilizes a Michelson interferometer with a DMD in Littrow configuration replacing the mirrors to combine the two holograms with the desired phase shift. System performance was examined using numerical simulations and experimental measurements to explore different encoding methods for hologram reconstruction. Both ZOD and conjugate image suppression were demonstrated for different encoding schemes.

  2. Method for high-speed Manchester encoded optical signal generation

    DEFF Research Database (Denmark)

    Zhang, Jianfeng; Chi, Nan; Holm-Nielsen, Pablo Villanueva

    2004-01-01

    A method for high-speed Manchester encoded optical signal generation is proposed and demonstrated with a specially configured electro-optical modulator. A 10 Gb/s Manchester encoded optical signal was generated, and its bit-error-ratio (BER) performance was evaluated.......A method for high-speed Manchester encoded optical signal generation is proposed and demonstrated with a specially configured electro-optical modulator. A 10 Gb/s Manchester encoded optical signal was generated, and its bit-error-ratio (BER) performance was evaluated....

  3. Improved reader for magnetically-encoded ID cards

    Science.gov (United States)

    Wu, T. T.

    1979-01-01

    Hybrid demodulator in electronic card reader for magnetically encoded identification cards, accommodates variations in insertion speeds, yet is simpler and less expensive than equivalent all-digital circuits.

  4. Encoded cell grating array in anti-counterfeit technology

    Institute of Scientific and Technical Information of China (English)

    Zhongyu Chen; N. K. Bao; Po S. Chung

    2005-01-01

    @@ The dot matrix hologram (DMH) has been widely used in anti-counterfeiting label. With the same technology and cell array configuration, we can encode to the incidence beam. These codes can be some image matrix grating with different grating gap and different grating orientation. When the multi-level phase diffractive grating is etched, the incidence beam on the cell appears as an encoding image. When the encoded grating and DMH are used in the same label synchronously, the technology of multi-encoded grating array enhances the anti-counterfeit ability.

  5. Double image encryption based on phase-amplitude mixed encoding and multistage phase encoding in gyrator transform domains

    Science.gov (United States)

    Wang, Qu; Guo, Qing; Lei, Liang

    2013-06-01

    We present a novel method for double image encryption that is based on amplitude-phase mixed encoding and multistage random phase encoding in gyrator transform (GT) domains. In the amplitude-phase mixed encoding operation, a random binary distribution matrix is defined to mixed encode two primitive images to a single complex-valued image, which is then encrypted into a stationary white noise distribution by the multistage phase encoding with GTs. Compared with the earlier methods that uses fully phase encoding, the proposed method reduces the difference between two primitive images in key space and sensitivity to the GT orders. The primitive images can be recovered exactly by applying correct keys with initial conditions of chaotic system, the GT orders and the pixel scrambling operation. Numerical simulations demonstrate that the proposed scheme has considerably high security level and certain robustness against data loss and noise disturbance.

  6. Brassinosteroid signal transduction: An emerging picture

    Institute of Scientific and Technical Information of China (English)

    WANG Qiaomei; MA Ligeng

    2003-01-01

    Steroid hormones play essential roles in animal growth and development. Steroid signaling in animal system is focused on the direct gene regulation response mediated by its nuclear receptors. Recently, steroid hormones are also found in plants. Identification of BRI1 - a critical component of the plasma-membrane steroid receptor complex, and the related signal transduction pathway mediated by the membrane receptor have revealed an elementary picture of BR signaling from the cell surface perception to the activation of BR-responsive nuclear genes.

  7. Olfactory bulb encoding during learning under anesthesia

    Science.gov (United States)

    Nicol, Alister U.; Sanchez-Andrade, Gabriela; Collado, Paloma; Segonds-Pichon, Anne; Kendrick, Keith M.

    2014-01-01

    Neural plasticity changes within the olfactory bulb are important for olfactory learning, although how neural encoding changes support new associations with specific odors and whether they can be investigated under anesthesia, remain unclear. Using the social transmission of food preference olfactory learning paradigm in mice in conjunction with in vivo microdialysis sampling we have shown firstly that a learned preference for a scented food odor smelled on the breath of a demonstrator animal occurs under isofluorane anesthesia. Furthermore, subsequent exposure to this cued odor under anesthesia promotes the same pattern of increased release of glutamate and gamma-aminobutyric acid (GABA) in the olfactory bulb as previously found in conscious animals following olfactory learning, and evoked GABA release was positively correlated with the amount of scented food eaten. In a second experiment, multiarray (24 electrodes) electrophysiological recordings were made from olfactory bulb mitral cells under isofluorane anesthesia before, during and after a novel scented food odor was paired with carbon disulfide. Results showed significant increases in overall firing frequency to the cued-odor during and after learning and decreases in response to an uncued odor. Analysis of patterns of changes in individual neurons revealed that a substantial proportion (>50%) of them significantly changed their response profiles during and after learning with most of those previously inhibited becoming excited. A large number of cells exhibiting no response to the odors prior to learning were either excited or inhibited afterwards. With the uncued odor many previously responsive cells became unresponsive or inhibited. Learning associated changes only occurred in the posterior part of the olfactory bulb. Thus olfactory learning under anesthesia promotes extensive, but spatially distinct, changes in mitral cell networks to both cued and uncued odors as well as in evoked glutamate and GABA

  8. Olfactory bulb encoding during learning under anaesthesia

    Directory of Open Access Journals (Sweden)

    Alister U Nicol

    2014-06-01

    Full Text Available Neural plasticity changes within the olfactory bulb are important for olfactory learning, although how neural encoding changes support new associations with specific odours and whether they can be investigated under anaesthesia, remain unclear. Using the social transmission of food preference olfactory learning paradigm in mice in conjunction with in vivo microdialysis sampling we have shown firstly that a learned preference for a scented food odour smelled on the breath of a demonstrator animal occurs under isofluorane anaesthesia. Furthermore, subsequent exposure to this cued odour under anaesthesia promotes the same pattern of increased release of glutamate and GABA in the olfactory bulb as previously found in conscious animals following olfactory learning, and evoked GABA release was positively correlated with the amount of scented food eaten. In a second experiment, multiarray (24 electrodes electrophysiological recordings were made from olfactory bulb mitral cells under isofluorane anaesthesia before, during and after a novel scented food odour was paired with carbon disulfide. Results showed significant increases in overall firing frequency to the cued-odour during and after learning and decreases in response to an uncued odour. Analysis of patterns of changes in individual neurons revealed that a substantial proportion (>50% of them significantly changed their response profiles during and after learning with most of those previously inhibited becoming excited. A large number of cells exhibiting no response to the odours prior to learning were either excited or inhibited afterwards. With the uncued odour many previously responsive cells became unresponsive or inhibited. Learning associated changes only occurred in the posterior part of the olfactory bulb. Thus olfactory learning under anaesthesia promotes extensive, but spatially distinct, changes in mitral cell networks to both cued and uncued odours as well as in evoked glutamate and

  9. What physics is encoded in Maxwell's equations?

    Science.gov (United States)

    Kosyakov, B. P.

    2005-08-01

    We reconstruct Maxwell's equations showing that a major part of the information encoded in them is taken from topological properties of spacetime, and the residual information, divorced from geometry, which represents the physical contents of electrodynamics, %these equations, translates into four assumptions:(i) locality; (ii) linearity; %of the dynamical law; (iii) identity of the charge-source and the charge-coupling; and (iv) lack of magnetic monopoles. However, a closer inspection of symmetries peculiar to electrodynamics shows that these assumptions may have much to do with geometry. Maxwell's equations tell us that we live in a three-dimensional space with trivial (Euclidean) topology; time is a one-dimensional unidirectional and noncompact continuum; and spacetime is endowed with a light cone structure readable in the conformal invariance of electrodynamics. Our geometric feelings relate to the fact that Maxwell's equations are built in our brain, hence our space and time orientation, our visualization and imagination capabilities are ensured by perpetual instinctive processes of solving Maxwell's equations. People are usually agree in their observations of angle relations, for example, a right angle is never confused with an angle slightly different from right. By contrast, we may disagree in metric issues, say, a colour-blind person finds the light wave lengths quite different from those found by a man with normal vision. This lends support to the view that conformal invariance of Maxwell's equations is responsible for producing our notion of space. Assuming that our geometric intuition is guided by our innate realization of electrodynamical laws, some abnormal mental phenomena, such as clairvoyance, may have a rational explanation.

  10. Neutron encoded labeling for peptide identification.

    Science.gov (United States)

    Rose, Christopher M; Merrill, Anna E; Bailey, Derek J; Hebert, Alexander S; Westphall, Michael S; Coon, Joshua J

    2013-05-21

    Metabolic labeling of cells using heavy amino acids is most commonly used for relative quantitation; however, partner mass shifts also detail the number of heavy amino acids contained within the precursor species. Here, we use a recently developed metabolic labeling technique, NeuCode (neutron encoding) stable isotope labeling with amino acids in cell culture (SILAC), which produces precursor partners spaced ~40 mDa apart to enable amino acid counting. We implement large scale counting of amino acids through a program, "Amino Acid Counter", which determines the most likely combination of amino acids within a precursor based on NeuCode SILAC partner spacing and filters candidate peptide sequences during a database search using this information. Counting the number of lysine residues for precursors selected for MS/MS decreases the median number of candidate sequences from 44 to 14 as compared to an accurate mass search alone (20 ppm). Furthermore, the ability to co-isolate and fragment NeuCode SILAC partners enables counting of lysines in product ions, and when the information is used, the median number of candidates is reduced to 7. We then demonstrate counting leucine in addition to lysine results in a 6-fold decrease in search space, 43 to 7, when compared to an accurate mass search. We use this scheme to analyze a nanoLC-MS/MS experiment and demonstrate that accurate mass plus lysine and leucine counting reduces the number of candidate sequences to one for ~20% of all precursors selected, demonstrating an ability to identify precursors without MS/MS analysis.

  11. Stress as a mnemonic filter: Interactions between medial temporal lobe encoding processes and post-encoding stress.

    Science.gov (United States)

    Ritchey, Maureen; McCullough, Andrew M; Ranganath, Charan; Yonelinas, Andrew P

    2017-01-01

    Acute stress has been shown to modulate memory for recently learned information, an effect attributed to the influence of stress hormones on medial temporal lobe (MTL) consolidation processes. However, little is known about which memories will be affected when stress follows encoding. One possibility is that stress interacts with encoding processes to selectively protect memories that had elicited responses in the hippocampus and amygdala, two MTL structures important for memory formation. There is limited evidence for interactions between encoding processes and consolidation effects in humans, but recent studies of consolidation in rodents have emphasized the importance of encoding "tags" for determining the impact of consolidation manipulations on memory. Here, we used functional magnetic resonance imaging in humans to test the hypothesis that the effects of post-encoding stress depend on MTL processes observed during encoding. We found that changes in stress hormone levels were associated with an increase in the contingency of memory outcomes on hippocampal and amygdala encoding responses. That is, for participants showing high cortisol reactivity, memories became more dependent on MTL activity observed during encoding, thereby shifting the distribution of recollected events toward those that had elicited relatively high activation. Surprisingly, this effect was generally larger for neutral, compared to emotionally negative, memories. The results suggest that stress does not uniformly enhance memory, but instead selectively preserves memories tagged during encoding, effectively acting as mnemonic filter. © 2016 Wiley Periodicals, Inc.

  12. Multiple channel secure communication using chaotic system encoding

    Energy Technology Data Exchange (ETDEWEB)

    Miller, S.L.

    1996-12-31

    fA new method to encrypt signals using chaotic systems has been developed that offers benefits over conventional chaotic encryption methods. The method simultaneously encodes multiple plaintext streams using a chaotic system; a key is required to extract the plaintext from the chaotic cipertext. A working prototype demonstrates feasibility of the method by simultaneously encoding and decoding multiple audio signals using electrical circuits.

  13. Review of Random Phase Encoding in Volume Holographic Storage

    Directory of Open Access Journals (Sweden)

    Wei-Chia Su

    2012-09-01

    Full Text Available Random phase encoding is a unique technique for volume hologram which can be applied to various applications such as holographic multiplexing storage, image encryption, and optical sensing. In this review article, we first review and discuss diffraction selectivity of random phase encoding in volume holograms, which is the most important parameter related to multiplexing capacity of volume holographic storage. We then review an image encryption system based on random phase encoding. The alignment of phase key for decryption of the encoded image stored in holographic memory is analyzed and discussed. In the latter part of the review, an all-optical sensing system implemented by random phase encoding and holographic interconnection is presented.

  14. Power-optimal encoding for low-power address bus

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    This paper presented a novel bus encoding method to reduce the switching activity on address buses and hence reduce power dissipation. Dynamic-sorting encoding (DSE) method reduces the power dissipation of address bus based on the dynamic reordering of the modified offset address bus lines. This method reorders the ten least significant bits of offset address according to the range of offset address, and the optimal sorting pattern is transmitted through the high bits of address bus without the need for redundant bus lines. The experimental results using an instruction set simulator and SPEC2000 benchmarks show that DSE method can reduce signal transitions on the address bus by 88.2%, and the actual overhead of the encoder circuit is estimated after encoder is designed and synthesized in 0.18-μm CMOS technology. The results show that DSE method outperforms the low-power encoding schemes presented in the past.

  15. What is a "good" encoding of guarded choice?

    DEFF Research Database (Denmark)

    Nestmann, Uwe

    2000-01-01

    The pi-calculus with synchronous output and mixed-guarded choices is strictly more expressive than the pi-calculus with asynchronous output and no choice. This result was recently proved by C. Palamidessi and, as a corollary, she showed that there is no fully compositional encoding from the former...... into the latter that preserves divergence-freedom and symmetries. This paper argues that there are nevertheless "good" encodings between these calculi. In detail, we present a series of encodings for languages with (1) input-guarded choice, (2) both input and output-guarded choice, and (3) mixed-guarded choice......, and investigate them with respect to compositionality and divergence-freedom. The first and second encoding satisfy all of the above criteria, but various "good" candidates for the third encoding-inspired by an existing distributed implementation-invalidate one or the other criterion, While essentially confirming...

  16. Encoding of multi-alphabet sources by binary arithmetic coding

    Science.gov (United States)

    Guo, Muling; Oka, Takahumi; Kato, Shigeo; Kajiwara, Hiroshi; Kawamura, Naoto

    1998-12-01

    In case of encoding a multi-alphabet source, the multi- alphabet symbol sequence can be encoded directly by a multi- alphabet arithmetic encoder, or the sequence can be first converted into several binary sequences and then each binary sequence is encoded by binary arithmetic encoder, such as the L-R arithmetic coder. Arithmetic coding, however, requires arithmetic operations for each symbol and is computationally heavy. In this paper, a binary representation method using Huffman tree is introduced to reduce the number of arithmetic operations, and a new probability approximation for L-R arithmetic coding is further proposed to improve the coding efficiency when the probability of LPS (Least Probable Symbol) is near 0.5. Simulation results show that our proposed scheme has high coding efficacy and can reduce the number of coding symbols.

  17. Incidental and intentional encoding in young and elderly adults.

    Science.gov (United States)

    Téllez-Alanís, Bernarda; Cansino, Selene

    2004-08-06

    Event-related potentials (ERPs) were recorded in young and elderly adults during the performance of an incidental encoding task (subjects were unexpectedly given a recognition test) followed by an intentional task (subjects expected the recognition test). Both tasks consisted of an encoding stage in which subjects classified words (natural/artificial) and a recognition stage in which they indicated whether the words were old (presented during the encoding stage) or new. In both groups and tasks, the ERPs, during encoding, differed as a function of subsequent recognition: the old words correctly recognized generated greater amplitude potentials than the incorrect ones. The memory processes expressed by these ERPs are preserved in elderly adults, independently of whether the information is incidentally or intentionally encoded.

  18. High-resolution MRI encoding using radiofrequency phase gradients.

    Science.gov (United States)

    Sharp, Jonathan C; King, Scott B; Deng, Qunli; Volotovskyy, Vyacheslav; Tomanek, Boguslaw

    2013-11-01

    Although MRI offers highly diagnostic medical imagery, patient access to this modality worldwide is very limited when compared with X-ray or ultrasound. One reason for this is the expense and complexity of the equipment used to generate the switched magnetic fields necessary for MRI encoding. These field gradients are also responsible for intense acoustic noise and have the potential to induce nerve stimulation. We present results with a new MRI encoding principle which operates entirely without the use of conventional B0 field gradients. This new approach--'Transmit Array Spatial Encoding' (TRASE)--uses only the resonant radiofrequency (RF) field to produce Fourier spatial encoding equivalent to conventional MRI. k-space traversal (image encoding) is achieved by spin refocusing with phase gradient transmit fields in spin echo trains. A transmit coil array, driven by just a single transmitter channel, was constructed to produce four phase gradient fields, which allows the encoding of two orthogonal spatial axes. High-resolution two-dimensional-encoded in vivo MR images of hand and wrist were obtained at 0.2 T. TRASE exploits RF field phase gradients, and offers the possibility of very low-cost diagnostics and novel experiments exploiting unique capabilities, such as imaging without disturbance of the main B0 magnetic field. Lower field imaging (imaging are favorable application domains as, in both cases, it is technically easier to achieve the short RF pulses desirable for long echo trains, and also to limit RF power deposition. As TRASE is simply an alternative mechanism (and technology) of moving through k space, there are many close analogies between it and conventional B0 -encoded techniques. TRASE is compatible with both B0 gradient encoding and parallel imaging, and so hybrid sequences containing all three spatial encoding approaches are possible.

  19. Small-molecule discovery from DNA-encoded chemical libraries.

    Science.gov (United States)

    Kleiner, Ralph E; Dumelin, Christoph E; Liu, David R

    2011-12-01

    Researchers seeking to improve the efficiency and cost effectiveness of the bioactive small-molecule discovery process have recently embraced selection-based approaches, which in principle offer much higher throughput and simpler infrastructure requirements compared with traditional small-molecule screening methods. Since selection methods benefit greatly from an information-encoding molecule that can be readily amplified and decoded, several academic and industrial groups have turned to DNA as the basis for library encoding and, in some cases, library synthesis. The resulting DNA-encoded synthetic small-molecule libraries, integrated with the high sensitivity of PCR and the recent development of ultra high-throughput DNA sequencing technology, can be evaluated very rapidly for binding or bond formation with a target of interest while consuming minimal quantities of material and requiring only modest investments of time and equipment. In this tutorial review we describe the development of two classes of approaches for encoding chemical structures and reactivity with DNA: DNA-recorded library synthesis, in which encoding and library synthesis take place separately, and DNA-directed library synthesis, in which DNA both encodes and templates library synthesis. We also describe in vitro selection methods used to evaluate DNA-encoded libraries and summarize successful applications of these approaches to the discovery of bioactive small molecules and novel chemical reactivity.

  20. High-Efficient Parallel CAVLC Encoders on Heterogeneous Multicore Architectures

    Directory of Open Access Journals (Sweden)

    H. Y. Su

    2012-04-01

    Full Text Available This article presents two high-efficient parallel realizations of the context-based adaptive variable length coding (CAVLC based on heterogeneous multicore processors. By optimizing the architecture of the CAVLC encoder, three kinds of dependences are eliminated or weaken, including the context-based data dependence, the memory accessing dependence and the control dependence. The CAVLC pipeline is divided into three stages: two scans, coding, and lag packing, and be implemented on two typical heterogeneous multicore architectures. One is a block-based SIMD parallel CAVLC encoder on multicore stream processor STORM. The other is a component-oriented SIMT parallel encoder on massively parallel architecture GPU. Both of them exploited rich data-level parallelism. Experiments results show that compared with the CPU version, more than 70 times of speedup can be obtained for STORM and over 50 times for GPU. The implementation of encoder on STORM can make a real-time processing for 1080p @30fps and GPU-based version can satisfy the requirements for 720p real-time encoding. The throughput of the presented CAVLC encoders is more than 10 times higher than that of published software encoders on DSP and multicore platforms.

  1. pENCODE: a plant encyclopedia of DNA elements.

    Science.gov (United States)

    Lane, Amanda K; Niederhuth, Chad E; Ji, Lexiang; Schmitz, Robert J

    2014-01-01

    ENCODE projects exist for many eukaryotes, including humans, but as of yet no defined project exists for plants. A plant ENCODE would be invaluable to the research community and could be more readily produced than its metazoan equivalents by capitalizing on the preexisting infrastructure provided from similar projects. Collecting and normalizing plant epigenomic data for a range of species will facilitate hypothesis generation, cross-species comparisons, annotation of genomes, and an understanding of epigenomic functions throughout plant evolution. Here, we discuss the need for such a project, outline the challenges it faces, and suggest ways forward to build a plant ENCODE.

  2. Optimal encoding and decoding of a spin direction

    CERN Document Server

    Bagán, E; Brey, A; Muñoz-Tàpia, R; Tarrach, Rolf

    2001-01-01

    For a system of N spins 1/2 there are quantum states that can encode a direction in an intrinsic way. Information on this direction can later be decoded by means of a quantum measurement. We present here the optimal encoding and decoding procedure using the fidelity as a figure of merit. We compute the maximal fidelity and prove that it is directly related to the largest zeroes of the Legendre and Jacobi polynomials. We show that this maximal fidelity approaches unity quadratically in 1/N. We also discuss this result in terms of the dimension of the encoding Hilbert space.

  3. Differentially-Enhanced Sideband Imaging via Radio-frequency Encoding

    CERN Document Server

    Fard, A M; Jalali, B

    2015-01-01

    We present a microscope paradigm that performs differential interference imaging with high sensitivity via optical amplification and radio-frequency (RF) heterodyne detection. This method, termed differentially-enhanced sideband imaging via radio-frequency encoding (DESIRE), uniquely exploits frequency-to-space mapping technique to encode the image of an object onto the RF sidebands of an illumination beam. As a proof-of-concept, we show validation experiment by implementing radio frequency (f = 15 GHz) phase modulation in conjunction with spectrally-encoded laser scanning technique to acquire one-dimensional image of a barcode-like object using a commercial RF spectrum analyzer.

  4. Integrated source and channel encoded digital communications system design study

    Science.gov (United States)

    Huth, G. K.

    1974-01-01

    Studies on the digital communication system for the direct communication links from ground to space shuttle and the links involving the Tracking and Data Relay Satellite (TDRS). Three main tasks were performed:(1) Channel encoding/decoding parameter optimization for forward and reverse TDRS links,(2)integration of command encoding/decoding and channel encoding/decoding; and (3) modulation coding interface study. The general communication environment is presented to provide the necessary background for the tasks and to provide an understanding of the implications of the results of the studies.

  5. Wavelength-encoded OCDMA system using opto-VLSI processors.

    Science.gov (United States)

    Aljada, Muhsen; Alameh, Kamal

    2007-07-01

    We propose and experimentally demonstrate a 2.5 Gbits/sper user wavelength-encoded optical code-division multiple-access encoder-decoder structure based on opto-VLSI processing. Each encoder and decoder is constructed using a single 1D opto-very-large-scale-integrated (VLSI) processor in conjunction with a fiber Bragg grating (FBG) array of different Bragg wavelengths. The FBG array spectrally and temporally slices the broadband input pulse into several components and the opto-VLSI processor generates codewords using digital phase holograms. System performance is measured in terms of the autocorrelation and cross-correlation functions as well as the eye diagram.

  6. Encoding of electrophysiology and other signals in MR images

    DEFF Research Database (Denmark)

    Hanson, Lars G; Lund, Torben E; Hanson, Christian G

    2007-01-01

    to the "magstripe" technique used for encoding of soundtracks in motion pictures, the electrical signals are in this way encoded as artifacts appearing in the MR images or spectra outside the region of interest. The encoded signals are subsequently reconstructed from the signal recorded by the scanner. RESULTS......PURPOSE: To develop a gradient insensitive, generic technique for recording of non-MR signals by use of surplus scanner bandwidth. MATERIALS AND METHODS: Relatively simple battery driven hardware is used to transform one or more signals into radio waves detectable by the MR scanner. Similar...

  7. Sin/cosine encoder interpolation methods: encoder to digital tracking converters for rate and position loop controllers

    Science.gov (United States)

    Jenkins, Steven T.; Hilkert, J. M.

    2008-04-01

    Pointing and tracking applications usually require relative gimbal angles to be measured for reporting and controlling the line-of-sight angular position. Depending on the application, angular resolution and/or accuracy might jointly or independently determine the angle transducer requirements. In the past decade, encoders have been increasingly taking the place of inductive devices where the measurement of angles over a wide range is required. This is primarily due to the fact that encoders are now achieving very high resolution in smaller sizes than was previously possible. These advances in resolution are primarily due to improved encoder disk and detector technology along with developments in interpolation techniques. Measurement accuracy, on the other hand, is primarily determined by mounting and bearing eccentricity as it is with all angular measurement devices. For very demanding accuracy requirements, some type of calibration of the assembled system may be the only solution, in which case transducer repeatability is paramount. This paper describes a unique encoder-to-digital tracking converter concept for improving interpolation of optical encoders. The new method relies on Fraunhofer diffraction models to correct the non-ideal sin/cos outputs of the encoder detectors. Diffraction model concepts are used in the interpolation filters to predict the phase of non-ideal sin and cosine encoder outputs. The new method also minimizes many of the open loop pre-processing requirements and assumptions that limit interpolation accuracy and rate loop noise performance in ratiometric tracking converter designs.

  8. The mitochondrial genome encodes abundant small noncoding RNAs

    Institute of Scientific and Technical Information of China (English)

    Seungil Ro; Hsiu-Yen Ma; Chanjae Park; Nicole Ortogero; Rui Song; Grant W Hennig; Huili Zheng

    2013-01-01

    Small noncoding RNAs identified thus far are all encoded by the nuclear genome.Here,we report that the murine and human mitochondriai genomes encode thousands of small noncoding RNAs,which are predominantly derived from the sense transcripts of the mitochondrial genes (host genes),and we termed these small RNAs mitochondrial genome-encoded small RNAs (mitosRNAs).DICER inactivation affected,but did not completely abolish mitosRNA production.MitosRNAs appear to be products of currently unidentified mitochondrial ribonucleases.Overexpression of mitosRNAs enhanced expression levels of their host genes in vitro,and dysregulated mitosRNA expression was generally associated with aberrant mitochondrial gene expression in vivo.Our data demonstrate that in addition to 37 known mitochondrial genes,the mammalian mitochondrial genome also encodes abundant mitosRNAs,which may play an important regulatory role in the control of mitochondrial gene expression in the cell.

  9. Universal Quantum Computing with Arbitrary Continuous-Variable Encoding

    Science.gov (United States)

    Lau, Hoi-Kwan; Plenio, Martin B.

    2016-09-01

    Implementing a qubit quantum computer in continuous-variable systems conventionally requires the engineering of specific interactions according to the encoding basis states. In this work, we present a unified formalism to conduct universal quantum computation with a fixed set of operations but arbitrary encoding. By storing a qubit in the parity of two or four qumodes, all computing processes can be implemented by basis state preparations, continuous-variable exponential-swap operations, and swap tests. Our formalism inherits the advantages that the quantum information is decoupled from collective noise, and logical qubits with different encodings can be brought to interact without decoding. We also propose a possible implementation of the required operations by using interactions that are available in a variety of continuous-variable systems. Our work separates the "hardware" problem of engineering quantum-computing-universal interactions, from the "software" problem of designing encodings for specific purposes. The development of quantum computer architecture could hence be simplified.

  10. Discoveries and functions of virus-encoded MicroRNAs

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou 730046, ChinaVirus-encoded microRNAs (miRNAs) are a new kind of miRNAs that regulate the expression of target gene in host cells or viruses through inducing cleavage of mRNA, repressing translation, etc., and change the processes of host cells or replicate viruses to escape or resist immune surveillance of host and protect viruses themselves. It has become a hot topic to discover viral genes encoding miRNAs and their target genes, and to identify their functions. This review provides background information on the history of virally encoded miRNAs including their genomic distribution, functions and mechanisms.In addition, we discuss the similarities and differences between virus- and host-encoded miRNAs, the future directions of researches in viral miRNAs and their applications in diseases control and therapy.

  11. Current Density Imaging through Acoustically Encoded Magnetometry: A Theoretical Exploration

    CERN Document Server

    Sheltraw, Daniel J

    2014-01-01

    The problem of determining a current density confined to a volume from measurements of the magnetic field it produces exterior to that volume is known to have non-unique solutions. To uniquely determine the current density, or the non-silent components of it, additional spatial encoding of the electric current is needed. In biological systems such as the brain and heart, which generate electric current associated with normal function, a reliable means of generating such additional encoding, on a spatial and temporal scale meaningful to the study of such systems, would be a boon for research. This paper explores a speculative method by which the required additional encoding might be accomplished, on the time scale associated with the propagation of sound across the volume of interest, by means of the application of a radially encoding pulsed acoustic spherical wave.

  12. Two Genes Encoding Uracil Phosphoribosyltransferase Are Present in Bacillus subtilis

    DEFF Research Database (Denmark)

    Martinussen, Jan; Glaser, Philippe; Andersen, Paal S.

    1995-01-01

    Uracil phosphoribosyltransferase (UPRTase) catalyzes the key reaction in the salvage of uracil in many microorganisms. Surprisingly, two genes encoding UPRTase activity were cloned from Bacillus subtilis by complementation of an Escherichia coli mutant. The genes were sequenced, and the putative...

  13. Universal Quantum Computing with Arbitrary Continuous-Variable Encoding.

    Science.gov (United States)

    Lau, Hoi-Kwan; Plenio, Martin B

    2016-09-02

    Implementing a qubit quantum computer in continuous-variable systems conventionally requires the engineering of specific interactions according to the encoding basis states. In this work, we present a unified formalism to conduct universal quantum computation with a fixed set of operations but arbitrary encoding. By storing a qubit in the parity of two or four qumodes, all computing processes can be implemented by basis state preparations, continuous-variable exponential-swap operations, and swap tests. Our formalism inherits the advantages that the quantum information is decoupled from collective noise, and logical qubits with different encodings can be brought to interact without decoding. We also propose a possible implementation of the required operations by using interactions that are available in a variety of continuous-variable systems. Our work separates the "hardware" problem of engineering quantum-computing-universal interactions, from the "software" problem of designing encodings for specific purposes. The development of quantum computer architecture could hence be simplified.

  14. A user's guide to the encyclopedia of DNA elements (ENCODE).

    Science.gov (United States)

    2011-04-01

    The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

  15. The Sulfolobicin Genes of Sulfolobus acidocaldarius Encode Novel Antimicrobial Proteins

    NARCIS (Netherlands)

    Ellen, Albert F.; Rohulya, Olha V.; Fusetti, Fabrizia; Wagner, Michaela; Albers, Sonja-Verena; Driessen, Arnold J. M.

    2011-01-01

    Crenarchaea, such as Sulfolobus acidocaldarius and Sulfolobus tokodaii, produce antimicrobial proteins called sulfolobicins. These antimicrobial proteins inhibit the growth of closely related species. Here we report the identification of the sulfolobicin-encoding genes in S. acidocaldarius. The acti

  16. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Spodsberg, Nikolaj

    2016-12-13

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  17. Encoding Speed and Memory Span in Dyslexic Children

    Science.gov (United States)

    Spring, Carl

    1976-01-01

    Evaluated with 14 dyslexic and 14 normal boys (all 6-12 years old) was the relationship between slow speech-motor encoding to the transfer of information from short-term to long-term memory. (Author/DB)

  18. Isolated menthone reductase and nucleic acid molecules encoding same

    Science.gov (United States)

    Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L

    2013-04-23

    The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

  19. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu; Tang, Lan; Henriksen, Svend Hostgaard Bang

    2016-05-17

    The present invention provides isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also provides nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  20. Polypeptides having cellobiohydrolase activitiy and polynucleotides encoding same

    Science.gov (United States)

    Liu, Ye; Tang, Lan; Duan, Junxin

    2015-12-15

    The present invention provides isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also provides nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  1. Hybrid polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Science.gov (United States)

    Liu, Ye; Shaghasi, Tarana

    2016-11-01

    The present invention provides hybrid polypeptides having cellobiohydrolase activity. The present invention also provides polynucleotides encoding the hybrid polypeptides; nucleic acid constructs, vectors and host cells comprising the polynucleotides; and processes of using the hybrid polypeptides.

  2. Dual-pharmacophore DNA-encoded chemical libraries.

    Science.gov (United States)

    Scheuermann, Jörg; Neri, Dario

    2015-06-01

    In contrast to single-pharmacophore DNA-encoded libraries, where only one chemical moiety is linked to DNA, dual-pharmacophore DNA-encoded chemical libraries feature the display of two independent small-molecules in close proximity. This, in principle, allows to explore adjacent epitopes on a pharmaceutical target of choice and hence the discovery of simultaneously binding pairs of fragments, by virtue of the chelate effect.

  3. Theory of multisource crosstalk reduction by phase-encoded statics

    KAUST Repository

    Schuster, Gerard T.

    2011-03-01

    Formulas are derived that relate the strength of the crosstalk noise in supergather migration images to the variance of time, amplitude and polarity shifts in encoding functions. A supergather migration image is computed by migrating an encoded supergather, where the supergather is formed by stacking a large number of encoded shot gathers. Analysis reveals that for temporal source static shifts in each shot gather, the crosstalk noise is exponentially reduced with increasing variance of the static shift and the square of source frequency. This is not too surprising because larger time shifts lead to less correlation between traces in different shot gathers, and so should tend to reduce the crosstalk noise. Analysis also reveals that combining both polarity and time statics is a superior encoding strategy compared to using either polarity statics or time statics alone. Signal-to-noise (SNR) estimates show that for a standard migration image and for an image computed by migrating a phase-encoded supergather; here, G is the number of traces in a shot gather, I is the number of stacking iterations in the supergather and S is the number of encoded/blended shot gathers that comprise the supergather. If the supergather can be uniformly divided up into Q unique sub-supergathers, then the resulting SNR of the final image is, which means that we can enhance image quality but at the expense of Q times more cost. The importance of these formulas is that they provide a precise understanding between different phase encoding strategies and image quality. Finally, we show that iterative migration of phase-encoded supergathers is a special case of passive seismic interferometry. We suggest that the crosstalk noise formulas can be helpful in designing optimal strategies for passive seismic interferometry and efficient extraction of Green\\'s functions from simulated supergathers. © 2011 The Authors Geophysical Journal International © 2011 RAS.

  4. Information Encoding on a Pseudo Random Noise Radar Waveform

    Science.gov (United States)

    2013-03-01

    PSEUDO RANDOM NOISE RADAR WAVEFORM THESIS Joshua A. Hardin, Captain, USAF AFIT-ENG-13-M-22 DEPARTMENT OF THE AIR FORCE AIR...protection in the United States. AFIT-ENG-13-M-22 INFORMATION ENCODING ON A PSEUDO RANDOM NOISE RADAR WAVEFORM THESIS Presented to the Faculty...INFORMATION ENCODING ON A PSEUDO RANDOM NOISE RADAR WAVEFORM I. Introduction 1.1 Problem Description Navigation requires knowledge of current

  5. 20 years of DNA-encoded chemical libraries.

    Science.gov (United States)

    Mannocci, Luca; Leimbacher, Markus; Wichert, Moreno; Scheuermann, Jörg; Neri, Dario

    2011-12-28

    The identification of specific binding molecules is a central problem in chemistry, biology and medicine. Therefore, technologies, which facilitate ligand discovery, may substantially contribute to a better understanding of biological processes and to drug discovery. DNA-encoded chemical libraries represent a new inexpensive tool for the fast and efficient identification of ligands to target proteins of choice. Such libraries consist of collections of organic molecules, covalently linked to a unique DNA tag serving as an amplifiable identification bar code. DNA-encoding enables the in vitro selection of ligands by affinity capture at sub-picomolar concentrations on virtually any target protein of interest, in analogy to established selection methodologies like antibody phage display. Multiple strategies have been investigated by several academic and industrial laboratories for the construction of DNA-encoded chemical libraries comprising up to millions of DNA-encoded compounds. The implementation of next generation high-throughput sequencing enabled the rapid identification of binding molecules from DNA-encoded libraries of unprecedented size. This article reviews the development of DNA-encoded library technology and its evolution into a novel drug discovery tool, commenting on challenges, perspectives and opportunities for the different experimental approaches.

  6. Secret key rates for an encoded quantum repeater

    Science.gov (United States)

    Bratzik, Sylvia; Kampermann, Hermann; Bruß, Dagmar

    2014-03-01

    We investigate secret key rates for the quantum repeater using encoding [L. Jiang et al., Phys. Rev. A 79, 032325 (2009), 10.1103/PhysRevA.79.032325] and compare them to the standard repeater scheme by Briegel, Dür, Cirac, and Zoller. The former scheme has the advantage of a minimal consumption of classical communication. We analyze the trade-off in the secret key rate between the communication time and the required resources. For this purpose we introduce an error model for the repeater using encoding which allows for input Bell states with a fidelity smaller than one, in contrast to the model given by L. Jiang et al. [Phys. Rev. A 79, 032325 (2009), 10.1103/PhysRevA.79.032325]. We show that one can correct additional errors in the encoded connection procedure of this repeater and develop a suitable decoding algorithm. Furthermore, we derive the rate of producing entangled pairs for the quantum repeater using encoding and give the minimal parameter values (gate quality and initial fidelity) for establishing a nonzero secret key. We find that the generic quantum repeater is optimal regarding the secret key rate per memory per second and show that the encoded quantum repeater using the simple three-qubit repetition code can even have an advantage with respect to the resources compared to other recent quantum repeater schemes with encoding.

  7. Conjugative botulinum neurotoxin-encoding plasmids in Clostridium botulinum.

    Directory of Open Access Journals (Sweden)

    Kristin M Marshall

    Full Text Available BACKGROUND: Clostridium botulinum produces seven distinct serotypes of botulinum neurotoxins (BoNTs. The genes encoding different subtype neurotoxins of serotypes A, B, F and several dual neurotoxin-producing strains have been shown to reside on plasmids, suggesting that intra- and interspecies transfer of BoNT-encoding plasmids may occur. The objective of the present study was to determine whether these C. botulinum BoNT-encoding plasmids are conjugative. METHODOLOGY/PRINCIPAL FINDINGS: C. botulinum BoNT-encoding plasmids pBotCDC-A3 (strain CDC-A3, pCLJ (strain 657Ba and pCLL (strain Eklund 17B were tagged with the erythromycin resistance marker (Erm using the ClosTron mutagenesis system by inserting a group II intron into the neurotoxin genes carried on these plasmids. Transfer of the tagged plasmids from the donor strains CDC-A3, 657Ba and Eklund 17B to tetracycline-resistant recipient C. botulinum strains was evaluated in mating experiments. Erythromycin and tetracycline resistant transconjugants were isolated from donor:recipient mating pairs tested. Transfer of the plasmids to the transconjugants was confirmed by pulsed-field gel electrophoresis (PFGE and Southern hybridizations. Transfer required cell-to-cell contact and was DNase resistant. This indicates that transfer of these plasmids occurs via a conjugation mechanism. CONCLUSIONS/SIGNIFICANCE: This is the first evidence supporting conjugal transfer of native botulinum neurotoxin-encoding plasmids in C. botulinum, and provides a probable mechanism for the lateral distribution of BoNT-encoding plasmids to other C. botulinum strains. The potential transfer of C. botulinum BoNT-encoding plasmids to other bacterial hosts in the environment or within the human intestine is of great concern for human pathogenicity and necessitates further characterization of these plasmids.

  8. Holistic random encoding for imaging through multimode fibers.

    Science.gov (United States)

    Jang, Hwanchol; Yoon, Changhyeong; Chung, Euiheon; Choi, Wonshik; Lee, Heung-No

    2015-03-01

    The input numerical aperture (NA) of multimode fiber (MMF) can be effectively increased by placing turbid media at the input end of the MMF. This provides the potential for high-resolution imaging through the MMF. While the input NA is increased, the number of propagation modes in the MMF and hence the output NA remains the same. This makes the image reconstruction process underdetermined and may limit the quality of the image reconstruction. In this paper, we aim to improve the signal to noise ratio (SNR) of the image reconstruction in imaging through MMF. We notice that turbid media placed in the input of the MMF transforms the incoming waves into a better format for information transmission and information extraction. We call this transformation as holistic random (HR) encoding of turbid media. By exploiting the HR encoding, we make a considerable improvement on the SNR of the image reconstruction. For efficient utilization of the HR encoding, we employ sparse representation (SR), a relatively new signal reconstruction framework when it is provided with a HR encoded signal. This study shows for the first time to our knowledge the benefit of utilizing the HR encoding of turbid media for recovery in the optically underdetermined systems where the output NA of it is smaller than the input NA for imaging through MMF.

  9. Brain activity underlying encoding and retrieval of source memory.

    Science.gov (United States)

    Cansino, Selene; Maquet, Pierre; Dolan, Raymond J; Rugg, Michael D

    2002-10-01

    Neural activity elicited during the encoding and retrieval of source information was investigated with event-related functional magnetic resonance imaging (efMRI). During encoding, 17 subjects performed a natural/artificial judgement on pictures of common objects which were presented randomly in one of the four quadrants of the display. At retrieval, old pictures were mixed with new ones and subjects judged whether each picture was new or old and, if old, indicated in which quadrant it was presented at encoding. During encoding, study items that were later recognized and assigned a correct source judgement elicited greater activity than recognized items given incorrect judgements in a variety of regions, including right lateral occipital and left prefrontal cortex. At retrieval, regions showing greater activity for recognized items given correct versus incorrect source judgements included the right hippocampal formation and the left prefrontal cortex. These findings indicate a role for these regions in the encoding and retrieval of episodic information beyond that required for simple item recognition.

  10. Functional neural networks underlying semantic encoding of associative memories.

    Science.gov (United States)

    Crespo-Garcia, M; Cantero, J L; Pomyalov, A; Boccaletti, S; Atienza, M

    2010-04-15

    Evidence suggests that theta oscillations recruit distributed cortical representations to improve associative encoding under semantically congruent conditions. Here we show that positive effects of semantic context on encoding and retrieval of associations are mediated by changes in the coupling pattern between EEG theta sources. During successful encoding of semantically congruent face-location associations, the right superior parietal lobe showed enhanced theta phase synchronization with other regions within the lateral posterior parietal lobe (PPL) and left medial temporal lobe (MTL). However, functional coordination involving the inferior parietal lobe was higher in the incongruent condition. These results suggest a differential engagement of top-down and bottom-up mechanisms during encoding of semantically congruent and incongruent episodic associations, respectively. Although retrieval processes operated on a similar neural network, the main difference with the study phase was the larger amount of functional links shown by the lateral prefrontal cortex with regions of the MTL and PPL. All together, these results suggest that theta oscillations mediate, at least partially, the positive effect of semantic congruence on associative memory by (i) optimizing top-down attentional mechanisms through enhanced theta phase synchronization between dorsal regions of the PPL and MTL and (ii) by adjusting the control of automatic attention to sensory and contextual information reactivated in the MTL through functional connections with the inferior parietal lobe during both encoding and retrieval processes.

  11. Early remodeling of the neocortex upon episodic memory encoding.

    Science.gov (United States)

    Bero, Adam W; Meng, Jia; Cho, Sukhee; Shen, Abra H; Canter, Rebecca G; Ericsson, Maria; Tsai, Li-Huei

    2014-08-12

    Understanding the mechanisms by which long-term memories are formed and stored in the brain represents a central aim of neuroscience. Prevailing theory suggests that long-term memory encoding involves early plasticity within hippocampal circuits, whereas reorganization of the neocortex is thought to occur weeks to months later to subserve remote memory storage. Here we report that long-term memory encoding can elicit early transcriptional, structural, and functional remodeling of the neocortex. Parallel studies using genome-wide RNA sequencing, ultrastructural imaging, and whole-cell recording in wild-type mice suggest that contextual fear conditioning initiates a transcriptional program in the medial prefrontal cortex (mPFC) that is accompanied by rapid expansion of the synaptic active zone and postsynaptic density, enhanced dendritic spine plasticity, and increased synaptic efficacy. To address the real-time contribution of the mPFC to long-term memory encoding, we performed temporally precise optogenetic inhibition of excitatory mPFC neurons during contextual fear conditioning. Using this approach, we found that real-time inhibition of the mPFC inhibited activation of the entorhinal-hippocampal circuit and impaired the formation of long-term associative memory. These findings suggest that encoding of long-term episodic memory is associated with early remodeling of neocortical circuits, identify the prefrontal cortex as a critical regulator of encoding-induced hippocampal activation and long-term memory formation, and have important implications for understanding memory processing in healthy and diseased brain states.

  12. Genetically-encoded biosensors for monitoring cellular stress in bioprocessing.

    Science.gov (United States)

    Polizzi, Karen M; Kontoravdi, Cleo

    2015-02-01

    With the current wealth of transcriptomic data, it is possible to design genetically-encoded biosensors for the detection of stress responses and apply these to high-throughput bioprocess development and monitoring of cellular health. Such biosensors can sense extrinsic factors such as nutrient or oxygen deprivation and shear stress, as well as intrinsic stress factors like oxidative damage and unfolded protein accumulation. Alongside, there have been developments in biosensing hardware and software applicable to the field of genetically-encoded biosensors in the near future. This review discusses the current state-of-the-art in biosensors for monitoring cultures during biological manufacturing and the future challenges for the field. Connecting the individual achievements into a coherent whole will enable the application of genetically-encoded biosensors in industry.

  13. DENSE: Displacement Encoding with Stimulated Echoes in Cardiac Functional MRI

    Science.gov (United States)

    Aletras, Anthony H.; Ding, Shujun; Balaban, Robert S.; Wen, Han

    1999-03-01

    Displacement encoding with stimulated echoes (DENSE) was developed for high-resolution myocardial displacement mapping. Pixel phase is modulated by myocardial displacement and data spatial resolution is limited only by pixel size. 2D displacement vector maps were generated for the systolic action in canines with 0.94 × 1.9 mm nominal in-plane resolution and 2.3 mm/π displacement encoding. A radial strain of 0.208 was measured across the free left ventricular wall over 105 ms during systole. DENSE displacement maps require small first-order gradient moments for encoding. DENSE magnitude images exhibit black-blood contrast which allows for better myocardial definition and reduced motion-related artifacts.

  14. Feedback-Based Collaborative Secrecy Encoding over Binary Symmetric Channels

    CERN Document Server

    Amariucai, George

    2009-01-01

    In this paper we propose a feedback scheme for transmitting secret messages between two legitimate parties, over an eavesdropped communication link. Relative to Wyner's traditional encoding scheme \\cite{wyner1}, our feedback-based encoding often yields larger rate-equivocation regions and achievable secrecy rates. More importantly, by exploiting the channel randomness inherent in the feedback channels, our scheme achieves a strictly positive secrecy rate even when the eavesdropper's channel is less noisy than the legitimate receiver's channel. All channels are modeled as binary and symmetric (BSC). We demonstrate the versatility of our feedback-based encoding method by using it in three different configurations: the stand-alone configuration, the mixed configuration (when it combines with Wyner's scheme \\cite{wyner1}), and the reversed configuration. Depending on the channel conditions, significant improvements over Wyner's secrecy capacity can be observed in all configurations.

  15. Encoding techniques for complex information structures in connectionist systems

    Science.gov (United States)

    Barnden, John; Srinivas, Kankanahalli

    1990-01-01

    Two general information encoding techniques called relative position encoding and pattern similarity association are presented. They are claimed to be a convenient basis for the connectionist implementation of complex, short term information processing of the sort needed in common sense reasoning, semantic/pragmatic interpretation of natural language utterances, and other types of high level cognitive processing. The relationships of the techniques to other connectionist information-structuring methods, and also to methods used in computers, are discussed in detail. The rich inter-relationships of these other connectionist and computer methods are also clarified. The particular, simple forms are discussed that the relative position encoding and pattern similarity association techniques take in the author's own connectionist system, called Conposit, in order to clarify some issues and to provide evidence that the techniques are indeed useful in practice.

  16. Multiresolutional encoding and decoding in embedded image and video coders

    Science.gov (United States)

    Xiong, Zixiang; Kim, Beong-Jo; Pearlman, William A.

    1998-07-01

    We address multiresolutional encoding and decoding within the embedded zerotree wavelet (EZW) framework for both images and video. By varying a resolution parameter, one can obtain decoded images at different resolutions from one single encoded bitstream, which is already rate scalable for EZW coders. Similarly one can decode video sequences at different rates and different spatial and temporal resolutions from one bitstream. Furthermore, a layered bitstream can be generated with multiresolutional encoding, from which the higher resolution layers can be used to increase the spatial/temporal resolution of the images/video obtained from the low resolution layer. In other words, we have achieved full scalability in rate and partial scalability in space and time. This added spatial/temporal scalability is significant for emerging multimedia applications such as fast decoding, image/video database browsing, telemedicine, multipoint video conferencing, and distance learning.

  17. Broadcast Channels with Confidential Messages by Randomness Constrained Stochastic Encoder

    CERN Document Server

    Watanabe, Shun

    2012-01-01

    In coding schemes for the wire-tap channel or the broadcast channels with confidential messages, it is well known that the sender needs to use a stochastic encoding to avoid the information about the transmitted confidential message to be leaked to an eavesdropper. In this paper, it is investigated that the trade-off between the rate of the random number to realize the stochastic encoding and the rates of the common, private, and confidential messages. For the direct theorem, the superposition coding scheme for the wire-tap channel recently proposed by Chia and El Gamal is employed, and its strong security is proved. The matching converse theorem is also established. Our result clarifies that a combination of the ordinary stochastic encoding and the channel prefixing by the channel simulation is suboptimal.

  18. Selection for Genes Encoding Secreted Proteins and Receptors

    Science.gov (United States)

    Klein, Robert D.; Gu, Qimin; Goddard, Audrey; Rosenthal, Arnon

    1996-07-01

    Extracellular proteins play an essential role in the formation, differentiation, and maintenance of multicellular organisms. Despite that, the systematic identification of genes encoding these proteins has not been possible. We describe here a highly efficient method to isolate genes encoding secreted and membrane-bound proteins by using a single-step selection in yeast. Application of this method, termed signal peptide selection, to various tissues yielded 559 clones that appear to encode known or novel extracellular proteins. These include members of the transforming growth factor and epidermal growth factor protein families, endocrine hormones, tyrosine kinase receptors, serine/threonine kinase receptors, seven transmembrane receptors, cell adhesion molecules, extracellular matrix proteins, plasma proteins, and ion channels. The eventual identification of most, or all, extracellular signaling molecules will advance our understanding of fundamental biological processes and our ability to intervene in disease states.

  19. Phonetic feature encoding in human superior temporal gyrus.

    Science.gov (United States)

    Mesgarani, Nima; Cheung, Connie; Johnson, Keith; Chang, Edward F

    2014-02-28

    During speech perception, linguistic elements such as consonants and vowels are extracted from a complex acoustic speech signal. The superior temporal gyrus (STG) participates in high-order auditory processing of speech, but how it encodes phonetic information is poorly understood. We used high-density direct cortical surface recordings in humans while they listened to natural, continuous speech to reveal the STG representation of the entire English phonetic inventory. At single electrodes, we found response selectivity to distinct phonetic features. Encoding of acoustic properties was mediated by a distributed population response. Phonetic features could be directly related to tuning for spectrotemporal acoustic cues, some of which were encoded in a nonlinear fashion or by integration of multiple cues. These findings demonstrate the acoustic-phonetic representation of speech in human STG.

  20. Nucleic acids encoding antifungal polypeptides and uses thereof

    Science.gov (United States)

    Altier, Daniel J.; Ellanskaya, I. A.; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K; Schepers, Eric; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-11-02

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  1. Atmospheric effects on Quaternary polarization encoding for free space communication

    Science.gov (United States)

    Soorat, Ram; Vudayagiri, Ashok

    2016-10-01

    We have simulated atmospheric effects such as fog and smoke in laboratory environment to simulate depolarisation due to atmospheric effects during a free space optical communi- cation. This has been used to study noise in two components of quaternary encoding for polarization shift keying. Individual components of a Quaternary encoding, such as vertical and horizontal as well as 45$^\\circ$ and 135$^\\circ$ , are tested separately and indicates that the depo- larization effects are different for these two situation. However, due to a differential method used to extract information bits, the protocol shows extremely low bit error rates. The information obtained is useful during deployment of a fully functional Quaternary encoded PolSK scheme in free space.

  2. Phonetic Feature Encoding in Human Superior Temporal Gyrus

    Science.gov (United States)

    Mesgarani, Nima; Cheung, Connie; Johnson, Keith; Chang, Edward F.

    2015-01-01

    During speech perception, linguistic elements such as consonants and vowels are extracted from a complex acoustic speech signal. The superior temporal gyrus (STG) participates in high-order auditory processing of speech, but how it encodes phonetic information is poorly understood. We used high-density direct cortical surface recordings in humans while they listened to natural, continuous speech to reveal the STG representation of the entire English phonetic inventory. At single electrodes, we found response selectivity to distinct phonetic features. Encoding of acoustic properties was mediated by a distributed population response. Phonetic features could be directly related to tuning for spectrotemporal acoustic cues, some of which were encoded in a nonlinear fashion or by integration of multiple cues. These findings demonstrate the acoustic-phonetic representation of speech in human STG. PMID:24482117

  3. Effect of Encoding Method on the Distribution of Cardiac Arrhythmias

    CERN Document Server

    Mora, Luis A

    2011-01-01

    This paper presents the evaluation of the effect of the method of ECG signal encoding, based on nonlinear characteristics such as information entropy and Lempel-Ziv complexity, on the distribution of cardiac arrhythmias. Initially proposed a procedure electrocardiographic gating to compensate for errors inherent in the process of filtering segments. For the evaluation of distributions and determine which of the different encoding methods produces greater separation between different kinds of arrhythmias studied (AFIB, AFL, SVTA, VT, Normal's), use a function based on the dispersion of the elements on the centroid of its class, the result being that the best encoding for the entire system is through the method of threshold value for a ternary code with E = 1 / 12.

  4. Information quality measurement of medical encoding support based on usability.

    Science.gov (United States)

    Puentes, John; Montagner, Julien; Lecornu, Laurent; Cauvin, Jean-Michel

    2013-12-01

    Medical encoding support systems for diagnoses and medical procedures are an emerging technology that begins to play a key role in billing, reimbursement, and health policies decisions. A significant problem to exploit these systems is how to measure the appropriateness of any automatically generated list of codes, in terms of fitness for use, i.e. their quality. Until now, only information retrieval performance measurements have been applied to estimate the accuracy of codes lists as quality indicator. Such measurements do not give the value of codes lists for practical medical encoding, and cannot be used to globally compare the quality of multiple codes lists. This paper defines and validates a new encoding information quality measure that addresses the problem of measuring medical codes lists quality. It is based on a usability study of how expert coders and physicians apply computer-assisted medical encoding. The proposed measure, named ADN, evaluates codes Accuracy, Dispersion and Noise, and is adapted to the variable length and content of generated codes lists, coping with limitations of previous measures. According to the ADN measure, the information quality of a codes list is fully represented by a single point, within a suitably constrained feature space. Using one scheme, our approach is reliable to measure and compare the information quality of hundreds of codes lists, showing their practical value for medical encoding. Its pertinence is demonstrated by simulation and application to real data corresponding to 502 inpatient stays in four clinic departments. Results are compared to the consensus of three expert coders who also coded this anonymized database of discharge summaries, and to five information retrieval measures. Information quality assessment applying the ADN measure showed the degree of encoding-support system variability from one clinic department to another, providing a global evaluation of quality measurement trends.

  5. Negative affect promotes encoding of and memory for details at the expense of the gist: affect, encoding, and false memories.

    Science.gov (United States)

    Storbeck, Justin

    2013-01-01

    I investigated whether negative affective states enhance encoding of and memory for item-specific information reducing false memories. Positive, negative, and neutral moods were induced, and participants then completed a Deese-Roediger-McDermott (DRM) false-memory task. List items were presented in unique spatial locations or unique fonts to serve as measures for item-specific encoding. The negative mood conditions had more accurate memories for item-specific information, and they also had fewer false memories. The final experiment used a manipulation that drew attention to distinctive information, which aided learning for DRM words, but also promoted item-specific encoding. For the condition that promoted item-specific encoding, false memories were reduced for positive and neutral mood conditions to a rate similar to that of the negative mood condition. These experiments demonstrated that negative affective cues promote item-specific processing reducing false memories. People in positive and negative moods encode events differently creating different memories for the same event.

  6. Straight to the point: how people encode linear discontinuations

    Directory of Open Access Journals (Sweden)

    Rodrigo I. Mora

    2012-12-01

    Full Text Available Spatial discontinuations, as those found in cities and buildings, are everyday events. But, how do we encode and classify such misalignments? This is the topic of this paper. Twenty participants were asked to classify a total of 51 icons showing an upward-moving line being misaligned to the right, left and straight down. The results show that subjects were very sensitive to slight discontinuations occurring to vertical lines and that there was not exact symmetry between the left and right axis, meaning that the pieces slightly misaligned to the left were encoded differently than those misaligned to the right

  7. Design and Synthesis of Biaryl DNA-Encoded Libraries.

    Science.gov (United States)

    Ding, Yun; Franklin, G Joseph; DeLorey, Jennifer L; Centrella, Paolo A; Mataruse, Sibongile; Clark, Matthew A; Skinner, Steven R; Belyanskaya, Svetlana

    2016-10-10

    DNA-encoded library technology (ELT) is a powerful tool for the discovery of new small-molecule ligands to various protein targets. Here we report the design and synthesis of biaryl DNA-encoded libraries based on the scaffold of 5-formyl 3-iodobenzoic acid. Three reactions on DNA template, acylation, Suzuki-Miyaura coupling and reductive amination, were applied in the library synthesis. The three cycle library of 3.5 million diversity has delivered potent hits for phosphoinositide 3-kinase α (PI3Kα).

  8. Multiple genes encode the major surface glycoprotein of Pneumocystis carinii

    DEFF Research Database (Denmark)

    Kovacs, J A; Powell, F; Edman, J C;

    1993-01-01

    this antigen is a good candidate for development as a vaccine to prevent or control P. carinii infection. We have cloned and sequenced seven related but unique genes encoding the major surface glycoprotein of rat P. carinii. Partial amino acid sequencing confirmed the identity of these genes. Based on Southern...... hydrophobic region at the carboxyl terminus. The presence of multiple related msg genes encoding the major surface glycoprotein of P. carinii suggests that antigenic variation is a possible mechanism for evading host defenses. Further characterization of this family of genes should allow the development...

  9. Mosaic tetracycline resistance genes encoding ribosomal protection proteins.

    Science.gov (United States)

    Warburton, Philip J; Amodeo, Nina; Roberts, Adam P

    2016-12-01

    First reported in 2003, mosaic tetracycline resistance genes are a subgroup of the genes encoding ribosomal protection proteins (RPPs). They are formed when two or more RPP-encoding genes recombine resulting in a functional chimera. To date, the majority of mosaic genes are derived from sections of three RPP genes, tet(O), tet(W) and tet(32), with others comprising tet(M) and tet(S). In this first review of mosaic genes, we report on their structure, diversity and prevalence, and suggest that these genes may be responsible for an under-reported contribution to tetracycline resistance in bacteria.

  10. Toward Better Genetically Encoded Sensors of Membrane Potential.

    Science.gov (United States)

    Storace, Douglas; Sepehri Rad, Masoud; Kang, BokEum; Cohen, Lawrence B; Hughes, Thom; Baker, Bradley J

    2016-05-01

    Genetically encoded optical sensors of cell activity are powerful tools that can be targeted to specific cell types. This is especially important in neuroscience because individual brain regions can include a multitude of different cell types. Optical imaging allows for simultaneous recording from numerous neurons or brain regions. Optical signals of membrane potential are useful because membrane potential changes are a direct sign of both synaptic and action potentials. Here we describe recent improvements in the in vitro and in vivo signal size and kinetics of genetically encoded voltage indicators (GEVIs) and discuss their relationship to alternative sensors of neural activity.

  11. Modified 8×8 quantization table and Huffman encoding steganography

    Science.gov (United States)

    Guo, Yongning; Sun, Shuliang

    2014-10-01

    A new secure steganography, which is based on Huffman encoding and modified quantized discrete cosine transform (DCT) coefficients, is provided in this paper. Firstly, the cover image is segmented into 8×8 blocks and modified DCT transformation is applied on each block. Huffman encoding is applied to code the secret image before embedding. DCT coefficients are quantized by modified quantization table. Inverse DCT(IDCT) is conducted on each block. All the blocks are combined together and the steg image is finally achieved. The experiment shows that the proposed method is better than DCT and Mahender Singh's in PSNR and Capacity.

  12. Signal Encoding and Telemetry Systems for Space Vehicles.

    Science.gov (United States)

    1983-05-01

    first application in which this design encoder was flown on two Brazilian Sonda III rockets. These encoders were programmed for the following operating...State University (OSU). The depletion sensing vehicles will be Sonda III rockets and will be instrumented by Northeastern University. The experiments...Preamp. Gain 400 Polarization Loss 3 dB Safety Factor 3 dB Xmtr. Power 3, 5 or 8 W RESULTS Xmtr. Power CNR at IF 3 watts 9.7 dB 5 12.0 8 14.0 Sonda III

  13. pTAR-Encoded Proteins in Plasmid Partitioning

    OpenAIRE

    Kalnin, Kirill; Stegalkina, Svetlana; Yarmolinsky, Michael

    2000-01-01

    Partition cassettes, essential for the segregational stability of low-copy-number bacterial plasmids, typically encode two autoregulated proteins and an adjacent cis-acting centromere analog to which one or perhaps both proteins bind. The diminutive partition region of pTAR of Agrobacterium spp. was reported to be exceptional, encoding only a single protein, ParA (D. R. Gallie and C. I. Kado, J. Mol. Biol. 193:465–478, 1987). However, resequencing of the region revealed two small downstream g...

  14. Identification and Function of MicroRNAs Encoded by Herpesviruses

    Institute of Scientific and Technical Information of China (English)

    Zhi-qing Bai; Xiu-fen Lei; Lin-ding Wang; Shou-jiang Gao

    2008-01-01

    MicroRNAs (miRNAs) play important roles in eukaryotes,plants and some viruses.It is increasingly clear that miRNAs-encoded by viruses can affect the viral life cycle and host physiology.Viral miRNAs could repress the innate and adaptive host immunity,modulate cellular signaling pathways,and regulate the expression of cellular and viral genes.These functions facilitate viral acute and persistent infections,and have profound effects on the host cell survival and disease progression.Here,we discuss the miRNAs encoded by herpesviruses,and their regulatory roles involved in virus-host interactions.

  15. Accelerated radial Fourier-velocity encoding using compressed sensing

    Energy Technology Data Exchange (ETDEWEB)

    Hilbert, Fabian; Han, Dietbert [Wuerzburg Univ. (Germany). Inst. of Radiology; Wech, Tobias; Koestler, Herbert [Wuerzburg Univ. (Germany). Inst. of Radiology; Wuerzburg Univ. (Germany). Comprehensive Heart Failure Center (CHFC)

    2014-10-01

    Purpose:Phase Contrast Magnetic Resonance Imaging (MRI) is a tool for non-invasive determination of flow velocities inside blood vessels. Because Phase Contrast MRI only measures a single mean velocity per voxel, it is only applicable to vessels significantly larger than the voxel size. In contrast, Fourier Velocity Encoding measures the entire velocity distribution inside a voxel, but requires a much longer acquisition time. For accurate diagnosis of stenosis in vessels on the scale of spatial resolution, it is important to know the velocity distribution of a voxel. Our aim was to determine velocity distributions with accelerated Fourier Velocity Encoding in an acquisition time required for a conventional Phase Contrast image. Materials and Methods:We imaged the femoral artery of healthy volunteers with ECG - triggered, radial CINE acquisition. Data acquisition was accelerated by undersampling, while missing data were reconstructed by Compressed Sensing. Velocity spectra of the vessel were evaluated by high resolution Phase Contrast images and compared to spectra from fully sampled and undersampled Fourier Velocity Encoding. By means of undersampling, it was possible to reduce the scan time for Fourier Velocity Encoding to the duration required for a conventional Phase Contrast image. Results:Acquisition time for a fully sampled data set with 12 different Velocity Encodings was 40 min. By applying a 12.6 - fold retrospective undersampling, a data set was generated equal to 3:10 min acquisition time, which is similar to a conventional Phase Contrast measurement. Velocity spectra from fully sampled and undersampled Fourier Velocity Encoded images are in good agreement and show the same maximum velocities as compared to velocity maps from Phase Contrast measurements. Conclusion: Compressed Sensing proved to reliably reconstruct Fourier Velocity Encoded data. Our results indicate that Fourier Velocity Encoding allows an accurate determination of the velocity

  16. Learning from Number Board Games: You Learn What You Encode

    Science.gov (United States)

    Laski, Elida V.; Siegler, Robert S.

    2014-01-01

    We tested the hypothesis that encoding the numerical-spatial relations in a number board game is a key process in promoting learning from playing such games. Experiment 1 used a microgenetic design to examine the effects on learning of the type of counting procedure that children use. As predicted, having kindergartners count-on from their current…

  17. Observers as Internal Models for Remote Tracking via Encoded Information

    NARCIS (Netherlands)

    Isidori, Alberto; Marconi, Lorenzo; De Persis, Claudio; Gilles, Ernst Dieter; Graichen, Knut; Meurer, Thomas

    2005-01-01

    In this paper, we consider a servomechanism problem in which the command and control functions are distributed in space, and hence the system consists of different components linked by a communication channel of finite capacity. The desired control goal is achieved by designing appropriate encoders,

  18. Error Locked Encoder and Decoder for Nanomemory Application

    Directory of Open Access Journals (Sweden)

    Y. Sharath

    2014-03-01

    Full Text Available Memory cells have been protected from soft errors for more than a decade; due to the increase in soft error rate in logic circuits, the encoder and decoder circuitry around the memory blocks have become susceptible to soft errors as well and must also be protected. We introduce a new approach to design fault-secure encoder and decoder circuitry for memory designs. The key novel contribution of this paper is identifying and defining a new class of error-correcting codes whose redundancy makes the design of fault-secure detectors (FSD particularly simple. We further quantify the importance of protecting encoder and decoder circuitry against transient errors, illustrating a scenario where the system failure rate (FIT is dominated by the failure rate of the encoder and decoder. We prove that Euclidean Geometry Low-Density Parity-Check (EG-LDPC codes have the fault-secure detector capability. Using some of the smaller EG-LDPC codes, we can tolerate bit or nanowire defect rates of 10% and fault rates of 10-18 upsets/device/cycle, achieving a FIT rate at or below one for the entire memory system and a memory density of 1011 bit/cm with nanowire pitch of 10 nm for memory blocks of 10 Mb or larger. Larger EG-LDPC codes can achieve even higher reliability and lower area overhead.

  19. False memory and importance: can we prioritize encoding without consequence?

    Science.gov (United States)

    Bui, Dung C; Friedman, Michael C; McDonough, Ian M; Castel, Alan D

    2013-10-01

    Given the large amount of information that we encounter, we often must prioritize what information we attempt to remember. Although critical for everyday functioning, relatively little research has focused on how people prioritize the encoding of information. Recent research has shown that people can and do selectively remember information assigned with higher, relative to lower, importance. However, the mechanisms underlying this prioritization process and the consequences of these processes are still not well understood. In the present study, we sought to better understand these prioritization processes and whether implementing these processes comes at the cost of memory accuracy, by increasing false memories. We used a modified form of the Deese/Roediger-McDermott (DRM) paradigm, in which participants studied DRM lists, with each list paired with low, medium, or high point values. In Experiment 1, encoding higher values led to more false memories than did encoding lower values, possibly because prioritizing information enhanced relational processing among high-value words. In Experiment 2, disrupting relational processing selectively reduced false memories for high-value words. Finally, in Experiment 3, facilitating relational processing selectively increased false memories for low-value words. These findings suggest that while prioritizing information can enhance true memory, this process concomitantly increases false memories. Furthermore, the mechanism underlying these prioritization processes depends on the ability to successfully engage in relational processing. Thus, how we prioritize the encoding of incoming information can come at a cost in terms of accurate memory.

  20. Neural Activity during Encoding Predicts False Memories Created by Misinformation

    Science.gov (United States)

    Okado, Yoko; Stark, Craig E. L.

    2005-01-01

    False memories are often demonstrated using the misinformation paradigm, in which a person's recollection of a witnessed event is altered after exposure to misinformation about the event. The neural basis of this phenomenon, however, remains unknown. The authors used fMRI to investigate encoding processes during the viewing of an event and…

  1. Superior Memorizers Employ Different Neural Networks for Encoding and Recall

    Directory of Open Access Journals (Sweden)

    Johannes eMallow

    2015-09-01

    Full Text Available Superior memorizers often employ the method of loci (MoL to memorize large amounts of information. The method of loci, known since ancient times, relies on a complex process where information to be memorized is bound to landmarks along mental routes in a previously memorized environment. However, fMRI data on groups of trained superior memorizer are rare. Based on the memorizing strategy reported by superior memorizers we developed a scheme of the processes successively employed during memorizing and recalling digits and relate these to brain activation that is specific for the encoding and recall period. In the examined superior memorizers several regions, suggested to be involved in mental navigation and digit-to-word processing, were specifically activated during encoding: bilateral early visual cortex, retrosplenial cortex, left parahippocampus, left visual cortex, and left superior parietal cortex. Although the scheme suggests that some steps during encoding and recall seem to be analog, none of the encoding areas were specifically activated during the recall. Instead, we found strong activation in left anterior superior temporal gyrus, which we relate to recalling the sequential order of the digits, and right motor cortex that may be related to reciting the digits.

  2. Optimization of encoding gradients for MR-ARFI.

    Science.gov (United States)

    Chen, Jing; Watkins, Ron; Pauly, Kim Butts

    2010-04-01

    MR acoustic radiation force imaging provides a promising method to monitor therapeutic ultrasound treatments. By measuring the displacement induced by the acoustic radiation force, MR acoustic radiation force imaging can locate the focal spot, without a significant temperature rise. In this work, the encoding gradient for MR acoustic radiation force imaging is optimized to achieve an enhanced accuracy and precision of the displacement measurement. By analyzing the sources of artifacts, bulk motion and eddy currents are shown to introduce errors to the measurement, and heavy diffusion-weighting is shown to result in noisy displacement maps. To eliminate these problems, a new encoding scheme is proposed, which utilizes a pair of bipolar gradients. Improved precision is achieved with robustness against bulk motion and background phase distortion, and improved accuracy is achieved with reduced diffusion-weighting and optimized encoding pulse width. The experiment result shows that the signal-to-noise ratio can be enhanced by more than 2-fold. These significant improvements are obtained at no cost of scan time or encoding sensitivity, enabling the detection of a displacement less than 0.l microm in a gel phantom with MR acoustic radiation force imaging.

  3. Drug discovery with DNA-encoded chemical libraries.

    Science.gov (United States)

    Buller, Fabian; Mannocci, Luca; Scheuermann, Jörg; Neri, Dario

    2010-09-15

    DNA-encoded chemical libraries represent a novel avenue for the facile discovery of small molecule ligands against target proteins of biological or pharmaceutical importance. Library members consist of small molecules covalently attached to unique DNA fragments that serve as amplifiable identification barcodes. This encoding allows the in vitro selection of ligands at subpicomolar concentrations from large library populations by affinity capture on a target protein of interest, in analogy to established technologies for the selection of binding polypeptides (e.g., antibodies). Different library formats have been explored by various groups, allowing the construction of chemical libraries comprising up to millions of DNA-encoded compounds. Libraries before and after selection have been characterized by PCR amplification of the DNA codes and subsequent relative quantification of library members using high-throughput sequencing. The most enriched compounds have then been further analyzed in biological assays, in the presence or in the absence of linked DNA. This article reviews experimental strategies used for the construction of DNA-encoded chemical libraries, revealing how selection, decoding, and hit validation technologies have been used for drug discovery programs.

  4. Selective memories: infants' encoding is enhanced in selection via suppression.

    Science.gov (United States)

    Markant, Julie; Amso, Dima

    2013-11-01

    The present study examined the hypothesis that inhibitory visual selection mechanisms play a vital role in memory by limiting distractor interference during item encoding. In Experiment 1a we used a modified spatial cueing task in which 9-month-old infants encoded multiple category exemplars in the contexts of an attention orienting mechanism involving suppression (i.e. inhibition of return, IOR) versus one that does not (i.e. facilitation). At test, infants in the IOR condition showed both item-specific learning and abstraction of broader category information. In contrast, infants in the facilitation condition did not discriminate across novel and familiar test items. Experiment 1b confirmed that the learning observed in the IOR condition was specific to spatial cueing of attention and was not due to timing differences across the IOR and facilitation conditions. In Experiment 2, we replicated the results of Experiment 1, using a within-subjects design to explicitly examine learning and memory encoding in the context of concurrent suppression. These data show that developing inhibitory selective attention enhances efficacy of memory encoding for subsequent retrieval. Furthermore, these results highlight the importance of considering interactions between developing attention and memory systems.

  5. Area Efficient Turbo Encoder for Wireless Applications on FPGA

    Directory of Open Access Journals (Sweden)

    Mansi Rastogi

    2014-03-01

    Full Text Available Error control is the major insistence in today’s wireless communication systems. In this era parallel concatenated convolutional codes known as turbo codes plays a crucial role. These codes have been chosen as error control approach for various wireless applications such as UMTS (Universal Mobile Telecommunication System,DVB (Digital Video Broadcasting etc. In this paper an area efficient turbo encoder (2, 1, 3 is proposed to suffice the elevated demand of miniaturization in future wireless communication. The proposed design is simulated using matlab and synthesized on Xilinx Virtex-2p (xc2vp30-ff896-5 FPGA. During simulation the proposed design is compared with the matlab model of RSC encoder. The performance of proposed Turbo encoder will be compared for FPGAs in terms of number of slices, number of slice Flip-flops and the number of registers. The Synthesis results show a 7% improvement in the utilized no. of slices and slice flip-flop. So an area efficient, cost effective Parallel Concatenated Convolutional Code Encoder has been proposed in this paper

  6. Generalized non-separable two-dimensional Dammann encoding method

    Science.gov (United States)

    Yu, Junjie; Zhou, Changhe; Zhu, Linwei; Lu, Yancong; Wu, Jun; Jia, Wei

    2017-01-01

    We generalize for the first time, to the best of our knowledge, the Dammann encoding method into non-separable two-dimensional (2D) structures for designing various pure-phase Dammann encoding gratings (DEGs). For examples, three types of non-separable 2D DEGs, including non-separable binary Dammann vortex gratings, non-separable binary distorted Dammann gratings, and non-separable continuous-phase cubic gratings, are designed theoretically and demonstrated experimentally. Correspondingly, it is shown that 2D square arrays of optical vortices with topological charges proportional to the diffraction orders, focus spots shifting along both transversal and axial directions with equal spacings, and Airy-like beams with controllable orientation for each beam, are generated in symmetry or asymmetry by these three DEGs, respectively. Also, it is shown that a more complex-shaped array of modulated beams could be achieved by this non-separable 2D Dammann encoding method, which will be a big challenge for those conventional separable 2D Dammann encoding gratings. Furthermore, the diffractive efficiency of the gratings can be improved around ∼10% when the non-separable structure is applied, compared with their conventional separable counterparts. Such improvement in the efficiency should be of high significance for some specific applications.

  7. Motion Detection, Letter Position Encoding, and Single Word Reading.

    Science.gov (United States)

    Cornelissen, P. L.; Hansen, P. C.

    1998-01-01

    A study involving 48 undergraduates found a link between motion detection and letter-position encoding and a positive relationship, albeit a nonlinear one, between motion detection threshold and the likelihood of making letter errors. This result held when age, IQ, reading age, and phonological awareness were taken into account. (CR)

  8. Spatio-Temporal Encoding in Medical Ultrasound Imaging

    DEFF Research Database (Denmark)

    Gran, Fredrik

    2005-01-01

    In this dissertation two methods for spatio-temporal encoding in medical ultrasound imaging are investigated. The first technique is based on a frequency division approach. Here, the available spectrum of the transducer is divided into a set of narrow bands. A waveform is designed for each band...

  9. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Schnorr, Kirk; Kramer, Randall

    2016-08-09

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  10. EGVII endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel [Los Gatos, CA; Goedegebuur, Frits [Vlaardingen, NL; Ward, Michael [San Francisco, CA; Yao, Jian [Sunnyvale, CA

    2012-02-14

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  11. EGVI endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2010-10-12

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  12. EGVII endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2009-05-05

    The present invention provides an endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  13. EGVI endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2010-10-05

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  14. Polypeptides having endoglucanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Paul [Carnation, WA; Lopez de Leon, Alfredo [Davis, CA; Rey, Micheal [Davis, CA; Ding, Hanshu [Davis, CA; Vlasenko, Elena [Davis, CA

    2012-02-21

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  15. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Paul (Carnation, WA); Golightly, Elizabeth (Reno, NV)

    2011-06-14

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  16. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly (Elk Grove, CA); Harris, Paul (Carnation, WA); Lopez De Leon, Alfredo (Davis, CA); Merino, Sandra (West Sacremento, CA)

    2007-05-22

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  17. Polypeptides having beta-glucosidase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Paul (Carnation, WA); Golightly, Elizabeth (Reno, NV)

    2007-07-17

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  18. Polypeptides having endoglucanase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Paul (Carnation, WA); Lopez de Leon, Alfredo (Davis, CA); Rey, Michael (Davis, CA); Ding, Hanshu (Davis, CA); Vlasenko, Elena (Davis, CA)

    2010-11-02

    The present invention relates to isolated polypeptides having endoglucanase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  19. Polynucleotides encoding polypeptides having beta-glucosidase activity

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Paul (Carnation, WA); Golightly, Elizabeth (Reno, NV)

    2010-03-02

    The present invention relates to isolated polypeptides having beta-glucosidase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  20. An algebra for the analysis of object encoding.

    Science.gov (United States)

    Tyler, Christopher W; Likova, Lora T

    2010-04-15

    The encoding of the objects from the world around us is one of the major topics of cognitive psychology, yet the principles of object coding in the human brain remain unresolved. Beyond referring to the particular features commonly associated with objects, our ability to categorize and discuss objects in detailed linguistic propositions implies that we have access to generic concepts of each object category with well-specified boundaries between them. Consideration of the nature of generic object concepts reveals that they must have the structure of a probabilistic list array specifying the Bayesian prior on all possible features that the object can possess, together with mutual covariance matrices among the features. Generic object concepts must also be largely context independent for propositions to have communicable meaning. Although, there is good evidence for local feature processing in the occipital lobe and specific responses for a few basic object categories in the posterior temporal lobe, the encoding of the generic object concepts remains obscure. We analyze the conceptual underpinnings of the study of object encoding, draw some necessary clarifications in relation to its modality-specific and amodal aspects, and propose an analytic algebra with specific reference to functional Magnetic Resonance Imaging approaches to the issue of how generic (amodal) object concepts are encoded in the human brain.

  1. Encoding color information for visual tracking: Algorithms and benchmark.

    Science.gov (United States)

    Liang, Pengpeng; Blasch, Erik; Ling, Haibin

    2015-12-01

    While color information is known to provide rich discriminative clues for visual inference, most modern visual trackers limit themselves to the grayscale realm. Despite recent efforts to integrate color in tracking, there is a lack of comprehensive understanding of the role color information can play. In this paper, we attack this problem by conducting a systematic study from both the algorithm and benchmark perspectives. On the algorithm side, we comprehensively encode 10 chromatic models into 16 carefully selected state-of-the-art visual trackers. On the benchmark side, we compile a large set of 128 color sequences with ground truth and challenge factor annotations (e.g., occlusion). A thorough evaluation is conducted by running all the color-encoded trackers, together with two recently proposed color trackers. A further validation is conducted on an RGBD tracking benchmark. The results clearly show the benefit of encoding color information for tracking. We also perform detailed analysis on several issues, including the behavior of various combinations between color model and visual tracker, the degree of difficulty of each sequence for tracking, and how different challenge factors affect the tracking performance. We expect the study to provide the guidance, motivation, and benchmark for future work on encoding color in visual tracking.

  2. A Novel Image Data Hiding Scheme with Diamond Encoding

    Directory of Open Access Journals (Sweden)

    Wu Hsien-Chu

    2009-01-01

    Full Text Available A novel data hiding scheme in digital images with the diamond encoding by pixel value adjustment is proposed. The proposed method is the extension of the exploiting modification direction (EMD embedding scheme. First, the process of embedding partitions the cover image into nonoverlapping blocks of two consecutive pixels and transforms the secret messages to a series of -ary digits. For each block, the diamond encoding technique is applied to calculate the diamond characteristic value, and one secret -ary digit is concealed into the diamond characteristic value. The diamond characteristic value is modified to secret digit and it can be obtained by adjusting pixel values in a block. This scheme is designed in such a way that the distortion of each block after diamond encoding is never out of the embedding parameter , and the block capacity is equal to . The diamond encoding provides an easy way to produce a more perceptible result than those yielded by simple least-significant-bit substitution methods. The embedded secret data can be extracted without the original cover image. Experimental results have demonstrated that the proposed method is capable of hiding more secret data while keeping the stego-image quality degradation imperceptible.

  3. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Ye; Tang, Lan; Duan, Junxin

    2017-02-07

    The present invention relates to isolated polypeptides having cellobiohydrolase activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  4. Polypeptides having cellobiohydrolase activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Stringer, Mary Ann; McBrayer, Brett

    2016-11-29

    The present invention relates to isolated polypeptides having cellobiohydrolase activity, catalytic domains, and cellulose binding domains and polynucleotides encoding the polypeptides, catalytic domains, and cellulose binding domains. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides, catalytic domains, or cellulose binding domains.

  5. EGVII endoglucanase and nucleic acids encoding the same

    Energy Technology Data Exchange (ETDEWEB)

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-11-11

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  6. Amount of Postcue Encoding Predicts Amount of Directed Forgetting

    Science.gov (United States)

    Pastotter, Bernhard; Bauml, Karl-Heinz

    2010-01-01

    In list-method directed forgetting, participants are cued to intentionally forget a previously studied list (List 1) before encoding a subsequently presented list (List 2). Compared with remember-cued participants, forget-cued participants typically show impaired recall of List 1 and improved recall of List 2, referred to as List 1 forgetting and…

  7. Forgetting from Working Memory: Does Novelty Encoding Matter?

    Science.gov (United States)

    Plancher, Gaen; Barrouillet, Pierre

    2013-01-01

    The sources of forgetting in working memory remain the matter of intense debate. According to the SOB model (serial order in a box; Farrell & Lewandowsky, 2002), forgetting in complex span tasks does not result from temporal decay but from interference produced by the encoding of distractors that are superimposed over memory items onto a composite…

  8. Verb Inflections in Agrammatic Aphasia: Encoding of Tense Features

    Science.gov (United States)

    Faroqi-Shah, Yasmeen; Thompson, Cynthia K.

    2007-01-01

    Across most languages, verbs produced by agrammatic aphasic individuals are frequently marked by syntactically and semantically inappropriate inflectional affixes, such as "Last night, I walking home." As per language production models, verb inflection errors in English agrammatism could arise from three potential sources: encoding the verbs'…

  9. Relationships between grammatical encoding and decoding : an experimental psycholinguistic study

    NARCIS (Netherlands)

    Olsthoorn, Nomi Maria

    2007-01-01

    Although usually considered distinct processes, grammatical encoding and decoding have many theoretical and empirical commonalities. In two series of experiments relationships between the two processes are explored. The first series uses a dual task (edited reading aloud (ERA)) paradigm to test the

  10. Fast Fractal Image Encoding Using an Improved Search Scheme

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    As fractal image encoding algorithms can yield high-resolution reconstructed images at very high compression ratio, and therefore, have a great potential for improving the efficiency of image storage and image transmission. However, the baseline fractal encoding algorithm requires a great deal of time to complete the best matching search between the range and domain blocks, which greatly limits practical applications of the algorithm. In order to solve this problem, a necessary condition of the best matching search based on an image feature is proposed in this paper. The proposed method can reduce the search space significantly and excludes the most inappropriate domain blocks for each range block before carrying out the best matching search. Experimental results show that the proposed algorithm can produce good quality reconstructed images and requires much less time than the baseline encoding algorithm. Specifically, the new algorithm can speed up encoding by about 85 times with a loss of just 3 dB in the peak signal to noise ratio (PSNR), and yields compression ratios close to 34.

  11. Polypeptides having cellulolytic enhancing activity and polynucleotides encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yu; Duan, Junxin; Tang, Lan; Wu, Wenping

    2016-06-14

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods of producing and using the polypeptides.

  12. Robust EPI Nyquist ghost elimination via spatial and temporal encoding.

    Science.gov (United States)

    Hoge, W Scott; Tan, Huan; Kraft, Robert A

    2010-12-01

    Nyquist ghosts are an inherent artifact in echo planar imaging acquisitions. An approach to robustly eliminate Nyquist ghosts is presented that integrates two previous Nyquist ghost correction techniques: temporal domain encoding (phase labeling for additional coordinate encoding: PLACE and spatial domain encoding (phased array ghost elimination: PAGE). Temporal encoding modulates the echo planar imaging acquisition trajectory from frame to frame, enabling one to interleave data to remove inconsistencies that occur between sampling on positive and negative gradient readouts. With PLACE, one can coherently combine the interleaved data to cancel residual Nyquist ghosts. If the level of ghosting varies significantly from image to image, however, the signal cancellation that occurs with PLACE can adversely affect SNR-sensitive applications such as perfusion imaging with arterial spin labeling. This work proposes integrating PLACE into a PAGE-based reconstruction process to yield significantly better Nyquist ghost correction that is more robust than PLACE or PAGE alone. The robustness of this method is demonstrated in the presence of magnetic field drift with an in-vivo arterial spin labeling perfusion experiment.

  13. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2016-08-09

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  14. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2014-09-30

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  15. Nucleus-encoded periplastid-targeted EFL in chlorarachniophytes.

    Science.gov (United States)

    Gile, Gillian H; Keeling, Patrick J

    2008-09-01

    Chlorarachniophytes are cercozoan amoeboflagellates that acquired photosynthesis by enslaving a green alga, which has retained a highly reduced nucleus called a nucleomorph. The nucleomorph lacks many genes necessary for its own maintenance and expression, suggesting that some genes have been moved to the host nucleus and their products are now targeted back to the periplastid compartment (PPC), the reduced eukaryotic cytoplasm of the endosymbiont. Protein trafficking in chlorarachniophytes is therefore complex, including nucleus-encoded plastid-targeted proteins, nucleomorph-encoded plastid-targeted proteins, and nucleus-encoded periplastid-targeted proteins. A major gap in our understanding of this system is the PPC-targeted proteins because none have been described in any chlorarachniophytes. Here we describe the first such protein, the GTPase EFL. EFL was characterized from 7 chlorarachniophytes, and 2 distinct types were found. One is related to foraminiferan EFL and lacks an amino-terminal extension. The second, distantly related, type encodes an amino-terminal extension consisting of a signal peptide followed by sequence sharing many characteristics with transit peptides from nucleus-encoded plastid-targeted proteins and which we conclude is most likely PPC targeted. Western blotting with antibodies specific to putative host and PPC-targeted EFL from the chlorarachniophytes Bigelowiella natans and Gymnochlora stellata is consistent with posttranslational cleavage of the leaders from PPC-targeted proteins. Immunolocalization of both proteins in B. natans confirmed the cytosolic location of the leaderless EFL and a distinct localization pattern for the PPC-targeted protein but could not rule out a plastid location (albeit very unlikely). We sought other proteins with a similar leader and identified a eukaryotic translation initiation factor 1 encoding a bipartite extension with the same properties. Transit peptide sequences were characterized from all 3

  16. A MPEG-4 encoder based on TMS320C6416

    Science.gov (United States)

    Li, Gui-ju; Liu, Wei-ning

    2013-08-01

    Engineering and products need to achieve real-time video encoding by DSP, but the high computational complexity and huge amount of data requires that system has high data throughput. In this paper, a real-time MPEG-4 video encoder is designed based on TMS320C6416 platform. The kernel is the DSP of TMS320C6416T and FPGA chip f as the organization and management of video data. In order to control the flow of input and output data. Encoded stream is output using the synchronous serial port. The system has the clock frequency of 1GHz and has up to 8000 MIPS speed processing capacity when running at full speed. Due to the low coding efficiency of MPEG-4 video encoder transferred directly to DSP platform, it is needed to improve the program structure, data structures and algorithms combined with TMS320C6416T characteristics. First: Design the image storage architecture by balancing the calculation spending, storage space cost and EDMA read time factors. Open up a more buffer in memory, each buffer cache 16 lines of video data to be encoded, reconstruction image and reference image including search range. By using the variable alignment mode of the DSP, modifying the definition of structure variables and change the look-up table which occupy larger space with a direct calculation array to save memory space. After the program structure optimization, the program code, all variables, buffering buffers and the interpolation image including the search range can be placed in memory. Then, as to the time-consuming process modules and some functions which are called many times, the corresponding modules are written in parallel assembly language of TMS320C6416T which can increase the running speed. Besides, the motion estimation algorithm is improved by using a cross-hexagon search algorithm, The search speed can be increased obviously. Finally, the execution time, signal-to-noise ratio and compression ratio of a real-time image acquisition sequence is given. The experimental

  17. [Immunoglobulin genes encoding antibodies directed to oncodevelopmental carbohydrate antigens].

    Science.gov (United States)

    Zenita, K; Yago, K; Fujimoto, E; Kannagi, R

    1990-07-01

    We investigated the immunoglobulin genes which encode the variable region of the monoclonal antibodies directed to the onco-developmental carbohydrate antigens such SSEA-1, fucosyl SSEA-1, SSEA-3 and SSEA-4. The VH region of these antibodies was preferentially encoded by the gene members of the X24, VH7183 and Q52 families, the families which are known to be located at the 3'-end region of the murine germ line VH gene. This result is interesting particularly when considering that the members of the 3'-end VH families are known to be preferentially expressed in embryonic B lymphocytes by an intrinsic genetic program. The comparative study of the nucleic acid sequences of mRNAs encoding these antibodies and the sequences of the corresponding germ line VH genes disclosed that the sequences encoding the antibodies contain no mutation from the germ line VH genes, or contain only a few somatic mutations, which are thought to be insignificant for the reactivity of the antibodies to the nominal antigens. These results imply that some of the embryonic B lymphocytes that express the unmutated germ line VH genes of the 3'-end families can be reactive with embryonic carbohydrate antigens, albeit rearranged with appropriate D-JH gene segments, and coupled with proper light chains. The VH region of the syngenic monoclonal anti-idiotypic antibodies directed to these anti-carbohydrate antibodies were also encoded preferentially by the members of the 3'-end VH families. We propose here that a part of the virgin embryonic B lymphocytes, which express the antibody encoded by the gene members of the 3'-end VH families at the cell surface, will be stimulated by the embryonic carbohydrate antigens which are abundantly present in the internal milieu of the embryo. The clonally expanded B lymphocytes, in turn, will facilitate the proliferation of other populations of embryonic B lymphocytes expressing the corresponding anti-idiotypic antibodies, which are also encoded by the gene members

  18. Molecular chaperones encoded by a reduced nucleus: the cryptomonad nucleomorph.

    Science.gov (United States)

    Archibald, J M; Cavalier-Smith, T; Maier, U; Douglas, S

    2001-06-01

    Molecular chaperones mediate the correct folding of nascent or denatured proteins and are found in both the organelles and cytoplasm of eukaryotic cells. Cryptomonad algae are unusual in possessing an extra cytoplasmic compartment (the periplastid space), the result of having engulfed and retained a photosynthetic eukaryote. Within the periplastid space is a diminutive nucleus (the nucleomorph) that encodes mostly genes for its own expression as well as a few needed by the plastid. Two plastid-encoded chaperones (GroEL and DnaK) and a nucleomorph-encoded chaperone (Cpn60) have been reported from the cryptomonad, Guillardia theta. Here we analyse G. theta nucleomorph genes for members of the cytosolic HSP70 and HSP90 families of molecular chaperones, a heat shock transcription factor (HSF), and all eight subunits of the group II chaperonin, CCT. These are presumably all active in the periplastid space, assisting in the maturation of polypeptides required by the cell; we propose a central role for them also in the structure and assembly of a putative relict mitotic apparatus. Curiously, none of the genes for co-chaperones of HSP70, HSP90, or CCT have been detected in the nucleomorph genome; they are either not needed or are encoded in the host nuclear genome and targeted back into the periplastid space. Endoplasmic reticulum (ER) homologs of HSP70 and HSP90 are also not present. Striking differences in the degree of conservation of the various nucleomorph-encoded molecular chaperones were observed. While the G. theta HSP70 and HSP90 homologs are well conserved, each of the eight CCT subunits (alpha, beta, gamma, delta, epsilon, eta, theta, and zeta) is remarkably divergent. Such differences are likely evidence for reduced/different functional constraints on the various molecular chaperones functioning in the periplastid space.

  19. Identification and validation of human papillomavirus encoded microRNAs.

    Directory of Open Access Journals (Sweden)

    Kui Qian

    Full Text Available We report here identification and validation of the first papillomavirus encoded microRNAs expressed in human cervical lesions and cell lines. We established small RNA libraries from ten human papillomavirus associated cervical lesions including cancer and two human papillomavirus harboring cell lines. These libraries were sequenced using SOLiD 4 technology. We used the sequencing data to predict putative viral microRNAs and discovered nine putative papillomavirus encoded microRNAs. Validation was performed for five candidates, four of which were successfully validated by qPCR from cervical tissue samples and cell lines: two were encoded by HPV 16, one by HPV 38 and one by HPV 68. The expression of HPV 16 microRNAs was further confirmed by in situ hybridization, and colocalization with p16INK4A was established. Prediction of cellular target genes of HPV 16 encoded microRNAs suggests that they may play a role in cell cycle, immune functions, cell adhesion and migration, development, and cancer. Two putative viral target sites for the two validated HPV 16 miRNAs were mapped to the E5 gene, one in the E1 gene, two in the L1 gene and one in the LCR region. This is the first report to show that papillomaviruses encode their own microRNA species. Importantly, microRNAs were found in libraries established from human cervical disease and carcinoma cell lines, and their expression was confirmed in additional tissue samples. To our knowledge, this is also the first paper to use in situ hybridization to show the expression of a viral microRNA in human tissue.

  20. Semantic congruence reverses effects of sleep restriction on associative encoding.

    Science.gov (United States)

    Alberca-Reina, Esther; Cantero, Jose L; Atienza, Mercedes

    2014-04-01

    Encoding and memory consolidation are influenced by factors such as sleep and congruency of newly learned information with prior knowledge (i.e., schema). However, only a few studies have examined the contribution of sleep to enhancement of schema-dependent memory. Based on previous studies showing that total sleep deprivation specifically impairs hippocampal encoding, and that coherent schemas reduce the hippocampal consolidation period after learning, we predict that sleep loss in the pre-training night will mainly affect schema-unrelated information whereas sleep restriction in the post-training night will have similar effects on schema-related and unrelated information. Here, we tested this hypothesis by presenting participants with face-face associations that could be semantically related or unrelated under different sleep conditions: normal sleep before and after training, and acute sleep restriction either before or after training. Memory was tested one day after training, just after introducing an interference task, and two days later, without any interference. Significant results were evident on the second retesting session. In particular, sleep restriction before training enhanced memory for semantically congruent events in detriment of memory for unrelated events, supporting the specific role of sleep in hippocampal memory encoding. Unexpectedly, sleep restriction after training enhanced memory for both related and unrelated events. Although this finding may suggest a poorer encoding during the interference task, this hypothesis should be specifically tested in future experiments. All together, the present results support a framework in which encoding processes seem to be more vulnerable to sleep loss than consolidation processes.

  1. Task-selective memory effects for successfully implemented encoding strategies.

    Directory of Open Access Journals (Sweden)

    Eric D Leshikar

    Full Text Available Previous behavioral evidence suggests that instructed strategy use benefits associative memory formation in paired associate tasks. Two such effective encoding strategies--visual imagery and sentence generation--facilitate memory through the production of different types of mediators (e.g., mental images and sentences. Neuroimaging evidence suggests that regions of the brain support memory reflecting the mental operations engaged at the time of study. That work, however, has not taken into account self-reported encoding task success (i.e., whether participants successfully generated a mediator. It is unknown, therefore, whether task-selective memory effects specific to each strategy might be found when encoding strategies are successfully implemented. In this experiment, participants studied pairs of abstract nouns under either visual imagery or sentence generation encoding instructions. At the time of study, participants reported their success at generating a mediator. Outside of the scanner, participants further reported the quality of the generated mediator (e.g., images, sentences for each word pair. We observed task-selective memory effects for visual imagery in the left middle occipital gyrus, the left precuneus, and the lingual gyrus. No such task-selective effects were observed for sentence generation. Intriguingly, activity at the time of study in the left precuneus was modulated by the self-reported quality (vividness of the generated mental images with greater activity for trials given higher ratings of quality. These data suggest that regions of the brain support memory in accord with the encoding operations engaged at the time of study.

  2. Human germline antibody gene segments encode polyspecific antibodies.

    Science.gov (United States)

    Willis, Jordan R; Briney, Bryan S; DeLuca, Samuel L; Crowe, James E; Meiler, Jens

    2013-04-01

    Structural flexibility in germline gene-encoded antibodies allows promiscuous binding to diverse antigens. The binding affinity and specificity for a particular epitope typically increase as antibody genes acquire somatic mutations in antigen-stimulated B cells. In this work, we investigated whether germline gene-encoded antibodies are optimal for polyspecificity by determining the basis for recognition of diverse antigens by antibodies encoded by three VH gene segments. Panels of somatically mutated antibodies encoded by a common VH gene, but each binding to a different antigen, were computationally redesigned to predict antibodies that could engage multiple antigens at once. The Rosetta multi-state design process predicted antibody sequences for the entire heavy chain variable region, including framework, CDR1, and CDR2 mutations. The predicted sequences matched the germline gene sequences to a remarkable degree, revealing by computational design the residues that are predicted to enable polyspecificity, i.e., binding of many unrelated antigens with a common sequence. The process thereby reverses antibody maturation in silico. In contrast, when designing antibodies to bind a single antigen, a sequence similar to that of the mature antibody sequence was returned, mimicking natural antibody maturation in silico. We demonstrated that the Rosetta computational design algorithm captures important aspects of antibody/antigen recognition. While the hypervariable region CDR3 often mediates much of the specificity of mature antibodies, we identified key positions in the VH gene encoding CDR1, CDR2, and the immunoglobulin framework that are critical contributors for polyspecificity in germline antibodies. Computational design of antibodies capable of binding multiple antigens may allow the rational design of antibodies that retain polyspecificity for diverse epitope binding.

  3. Fast Packet Classification Using Multi-Dimensional Encoding

    Science.gov (United States)

    Huang, Chi Jia; Chen, Chien

    Internet routers need to classify incoming packets quickly into flows in order to support features such as Internet security, virtual private networks and Quality of Service (QoS). Packet classification uses information contained in the packet header, and a predefined rule table in the routers. Packet classification of multiple fields is generally a difficult problem. Hence, researchers have proposed various algorithms. This study proposes a multi-dimensional encoding method in which parameters such as the source IP address, destination IP address, source port, destination port and protocol type are placed in a multi-dimensional space. Similar to the previously best known algorithm, i.e., bitmap intersection, multi-dimensional encoding is based on the multi-dimensional range lookup approach, in which rules are divided into several multi-dimensional collision-free rule sets. These sets are then used to form the new coding vector to replace the bit vector of the bitmap intersection algorithm. The average memory storage of this encoding is Θ (L · N · log N) for each dimension, where L denotes the number of collision-free rule sets, and N represents the number of rules. The multi-dimensional encoding practically requires much less memory than bitmap intersection algorithm. Additionally, the computation needed for this encoding is as simple as bitmap intersection algorithm. The low memory requirement of the proposed scheme means that it not only decreases the cost of packet classification engine, but also increases the classification performance, since memory represents the performance bottleneck in the packet classification engine implementation using a network processor.

  4. Tape measuring system using linear encoder and digital camera

    Science.gov (United States)

    Eom, Tae Bong; Jeong, Don Young; Kim, Myung Soon; Kim, Jae Wan; Kim, Jong Ahn

    2013-04-01

    We have designed and constructed the calibration system of line standards such as tape and rule for the secondary calibration laboratories. The system consists of the main body with linear stage and linear encoder, the optical microscope with digital camera, and the computer. The base of the system is a aluminum profile with 2.9 m length, 0.09 m height and 0.18 m width. The linear stage and the linear encoder are fixed on the aluminum profile. The micro-stage driven by micrometer is fixed on the carriage of the long linear stage, and the optical microscope with digital camera and the tablet PC are on the this stage. The linear encoder counts the moving distance of the linear stage with resolution of 1 μm and its counting value is transferred to the tablet PC. The image of the scale mark of the tape is captured by the CCD camera of optical microscope and transferred to the PC through USB interface. The computer automatically determines the center of the scale mark by image processing technique and at the same time reads the moving distance of the linear stage. As a result, the computer can calculate the interval between the scale marks of the tape. In order to achieve the high accuracy, the linear encoder should be calibrated using the laser interferometer or the rigid steel rule. This calibration data of the linear encoder is stored at the computer and the computer corrects the reading value of the linear encoder. In order to determine the center of the scale mark, we use three different algorithms. First, the image profile over specified threshold level is fitted in even order polynomial and the axis of the polynomial is used as the center of the line. Second, the left side and right side areas at the center of the image profile are calculated so that two areas are same. Third, the left and right edges of the image profile are determined at every intensity level of the image and the center of the graduation is calculated as an average of the centers of the left

  5. The encoding complexity of two dimensional range minimum data structures

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Brodnik, Andrej; Davoodi, Pooya

    2013-01-01

    In the two-dimensional range minimum query problem an input matrix A of dimension m ×n, m ≤ n, has to be preprocessed into a data structure such that given a query rectangle within the matrix, the position of a minimum element within the query range can be reported. We consider the space complexity...... of the encoding variant of the problem where queries have access to the constructed data structure but can not access the input matrix A, i.e. all information must be encoded in the data structure. Previously it was known how to solve the problem with space O(mn min {m,logn}) bits (and with constant query time...

  6. Proteins encoded near the adenovirus late messenger RNA leader segments

    Energy Technology Data Exchange (ETDEWEB)

    Lewis, J.B.; Anderson, C.W.

    1983-01-01

    Small fragments of adenovirus 2 DNA cloned into the single-strand phage M13 were used to select adenoviral messenger RNAs transcribed from the R-strand between map positions 16 and 30. Cell-free translation of these mRNAs produced proteins of 13.5K, 13.6K, and 11.5K, respectively encoded between the first and second segments of the tripartite major late leader, within the ''i''-leader segment, and immediately preceding the third leader segment. Partial sequence analysis of the 13.6K protein is consistent with the hypothesis that it is encoded within the i-leader segment.

  7. Novel selection methods for DNA-encoded chemical libraries.

    Science.gov (United States)

    Chan, Alix I; McGregor, Lynn M; Liu, David R

    2015-06-01

    Driven by the need for new compounds to serve as biological probes and leads for therapeutic development and the growing accessibility of DNA technologies including high-throughput sequencing, many academic and industrial groups have begun to use DNA-encoded chemical libraries as a source of bioactive small molecules. In this review, we describe the technologies that have enabled the selection of compounds with desired activities from these libraries. These methods exploit the sensitivity of in vitro selection coupled with DNA amplification to overcome some of the limitations and costs associated with conventional screening methods. In addition, we highlight newer techniques with the potential to be applied to the high-throughput evaluation of DNA-encoded chemical libraries.

  8. Practical Programming with Higher-Order Encodings and Dependent Types

    DEFF Research Database (Denmark)

    Poswolsky, Adam; Schürmann, Carsten

    2008-01-01

    Higher-order abstract syntax (HOAS) refers to the technique of representing variables of an object-language using variables of a meta-language. The standard first-order alternatives force the programmer to deal with superficial concerns such as substitutions, whose implementation is often routine......, tedious, and error-prone. In this paper, we describe the underlying calculus of Delphin. Delphin is a fully implemented functional-programming language supporting reasoning over higher-order encodings and dependent types, while maintaining the benefits of HOAS. More specifically, just as representations...... utilizing HOAS free the programmer from concerns of handling explicit contexts and substitutions, our system permits programming over such encodings without making these constructs explicit, leading to concise and elegant programs. To this end our system distinguishes bindings of variables intended...

  9. Power calculation of linear and angular incremental encoders

    Science.gov (United States)

    Prokofev, Aleksandr V.; Timofeev, Aleksandr N.; Mednikov, Sergey V.; Sycheva, Elena A.

    2016-04-01

    Automation technology is constantly expanding its role in improving the efficiency of manufacturing and testing processes in all branches of industry. More than ever before, the mechanical movements of linear slides, rotary tables, robot arms, actuators, etc. are numerically controlled. Linear and angular incremental photoelectric encoders measure mechanical motion and transmit the measured values back to the control unit. The capabilities of these systems are undergoing continual development in terms of their resolution, accuracy and reliability, their measuring ranges, and maximum speeds. This article discusses the method of power calculation of linear and angular incremental photoelectric encoders, to find the optimum parameters for its components, such as light emitters, photo-detectors, linear and angular scales, optical components etc. It analyzes methods and devices that permit high resolutions in the order of 0.001 mm or 0.001°, as well as large measuring lengths of over 100 mm. In linear and angular incremental photoelectric encoders optical beam is usually formulated by a condenser lens passes through the measuring unit changes its value depending on the movement of a scanning head or measuring raster. Past light beam is converting into an electrical signal by the photo-detecter's block for processing in the electrical block. Therefore, for calculating the energy source is a value of the desired value of the optical signal at the input of the photo-detecter's block, which reliably recorded and processed in the electronic unit of linear and angular incremental optoelectronic encoders. Automation technology is constantly expanding its role in improving the efficiency of manufacturing and testing processes in all branches of industry. More than ever before, the mechanical movements of linear slides, rotary tables, robot arms, actuators, etc. are numerically controlled. Linear and angular incremental photoelectric encoders measure mechanical motion and

  10. Compression of surface myoelectric signals using MP3 encoding.

    Science.gov (United States)

    Chan, Adrian D C

    2011-01-01

    The potential of MP3 compression of surface myoelectric signals is explored in this paper. MP3 compression is a perceptual-based encoder scheme, used traditionally to compress audio signals. The ubiquity of MP3 compression (e.g., portable consumer electronics and internet applications) makes it an attractive option for remote monitoring and telemedicine applications. The effects of muscle site and contraction type are examined at different MP3 encoding bitrates. Results demonstrate that MP3 compression is sensitive to the myoelectric signal bandwidth, with larger signal distortion associated with myoelectric signals that have higher bandwidths. Compared to other myoelectric signal compression techniques reported previously (embedded zero-tree wavelet compression and adaptive differential pulse code modulation), MP3 compression demonstrates superior performance (i.e., lower percent residual differences for the same compression ratios).

  11. Encoded diffractive optics for full-spectrum computational imaging

    Science.gov (United States)

    Heide, Felix; Fu, Qiang; Peng, Yifan; Heidrich, Wolfgang

    2016-09-01

    Diffractive optical elements can be realized as ultra-thin plates that offer significantly reduced footprint and weight compared to refractive elements. However, such elements introduce severe chromatic aberrations and are not variable, unless used in combination with other elements in a larger, reconfigurable optical system. We introduce numerically optimized encoded phase masks in which different optical parameters such as focus or zoom can be accessed through changes in the mechanical alignment of a ultra-thin stack of two or more masks. Our encoded diffractive designs are combined with a new computational approach for self-calibrating imaging (blind deconvolution) that can restore high-quality images several orders of magnitude faster than the state of the art without pre-calibration of the optical system. This co-design of optics and computation enables tunable, full-spectrum imaging using thin diffractive optics.

  12. Bacillus caldolyticus prs gene encoding phosphoribosyl-diphosphate synthase

    DEFF Research Database (Denmark)

    Krath, Britta N.; Hove-Jensen, Bjarne

    1996-01-01

    The prs gene, encoding phosphoribosyl-diphosphate (PRPP) synthase, as well as the flanking DNA sequences were cloned and sequenced from the Gram-positive thermophile, Bacillus caldolyticus. Comparison with the homologous sequences from the mesophile, Bacillus subtilis, revealed a gene (gca......D) encoding N-acetylglucosamine-1-phosphate uridyltransferase upstream of prs, and a gene homologous to ctc downstream of prs. cDNA synthesis with a B. caldolyticus gcaD-prs-ctc-specified mRNA as template, followed by amplification utilising the polymerase chain reaction indicated that the three genes are co......-transcribed. Comparison of amino acid sequences revealed a high similarity among PRPP synthases across a wide phylogenetic range. An E. coli strain harbouring the B. caldolyticus prs gene in a multicopy plasmid produced PRPP synthase activity 33-fold over the activity of a haploid B. caldolyticus strain. B. caldolyticus...

  13. Bus Encoder for Crosstalk Avoidance in RLC Modeled Interconnects

    Directory of Open Access Journals (Sweden)

    G. Nagendra Babu

    2012-02-01

    Full Text Available Most of the encoding methods proposed in recent years have dealt with only RC modeled VLSI interconnects. For deep sub micron technologies (DSM, on-chip inductive effects have increased due to faster clock speeds, smaller signal rise times and longer length of on-chip interconnects. All these issues raise the concern for cross talk, propagation delay and power dissipation of overall. Therefore, this research work introduces an efficient Bus Encoder using Bus Inverting (BI method. The proposed design dramatically reduces both cross talk and power dissipation in RLC modeled interconnects which makes it suitable for current high-speed low-power VLSI interconnects. The proposed model demonstrates an overall reduction of power dissipation and cross talk induced delay by 55.43% and 45.87%, respectively.

  14. Optical-spectrum-encoded analog-to-digital converter

    Institute of Scientific and Technical Information of China (English)

    LIAO Xiao-jun; YANG Ya-pei

    2007-01-01

    A novel optical-spectrum-encoded (OSE) analog-to-digital converter (ADC) is proposed in this letter. To simply exemplify the conversion idea, a 5-bit device structure consisted of Fabry-Perot interferometers (FPI) is analyzed and numerically simulated. The dependence of peak-transmission wavelength on modulation voltage in an electro-optical FPI and the dependence of transmitted power on incident light wavelength in an FPI are discussed and utilized to implement OSEADC.A linearly tunable mode-locked laser, as a voltage-wavelength transformer and a sampler, and chirped grating FPIs, as an encoder array, can be used to obtain much greater sampling rate and bit-resolution.

  15. Screening and identification of virus-encoded RNA silencing suppressors.

    Science.gov (United States)

    Karjee, Sumona; Islam, Mohammad Nurul; Mukherjee, Sunil K

    2008-01-01

    RNA silencing, including RNA interference, is a novel method of gene regulation and one of the potent host-defense mechanisms against the viruses. In the course of evolution, the viruses have encoded proteins with the potential to suppress the host RNA silencing mechanism as a counterdefense strategy. The virus-encoded RNA silencing suppressors (RSSs) can serve as important biological tools to dissect the detailed RNA silencing pathways and also to evolve the antiviral strategies. Screening and identification of the RSSs are indeed of utmost significance in the field of plant biotechnology. We describe two Green Fluorescent Protein (GFP) reporter-based plant assay systems that rely on two different principles, namely reversal of silencing and enhancement of rolling circle replication (RCR) of geminiviral replicon. These proof-of-concept examples and assay systems could be used to screen various plant, animal, and insect viral ORFs for identification of the RSS activities.

  16. A Note on Encodings of Phylogenetic Networks of Bounded Level

    CERN Document Server

    Gambette, Philippe

    2009-01-01

    Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees, such networks canonically induce collections of phylogenetic trees, clusters, and triplets, respectively. Thus it is not surprising that many network approaches aim to reconstruct a phylogenetic network from such collections. Related to the well-studied perfect phylogeny problem, the following question is of fundamental importance in this context: When does one of the above collections encode (i.e. uniquely describe) the network that induces it? In this note, we present a complete answer to this question for the special case of a level-1 (phylogenetic) network by characterizing those level-1 networks for which an encoding in terms of one (or equivalently all) of the above collections exists. Given that this type of network forms the first layer of the rich hierarchy of lev...

  17. Transduction and encoding sensory information by skin mechanoreceptors.

    Science.gov (United States)

    Hao, Jizhe; Bonnet, Caroline; Amsalem, Muriel; Ruel, Jérôme; Delmas, Patrick

    2015-01-01

    Physical contact with the external world occurs through specialized neural structures called mechanoreceptors. Cutaneous mechanoreceptors provide information to the central nervous system (CNS) about touch, pressure, vibration, and skin stretch. The physiological function of these mechanoreceptors is to convert physical forces into neuronal signals. Key questions concern the molecular identity of the mechanoelectric transducer channels and the mechanisms by which the physical parameters of the mechanical stimulus are encoded into patterns of action potentials (APs). Compelling data indicate that the biophysical traits of mechanosensitive channels combined with the collection of voltage-gated channels are essential to describe the nature of the stimulus. Recent research also points to a critical role of the auxiliary cell-nerve ending communication in encoding stimulus properties. This review describes the characteristics of ion channels responsible for translating mechanical stimuli into the neural codes that underlie touch perception and pain.

  18. Aeromonas phages encode tRNAs for their overused codons.

    Science.gov (United States)

    Prabhakaran, Ramanandan; Chithambaram, Shivapriya; Xia, Xuhua

    2014-01-01

    The GC-rich bacterial species, Aeromonas salmonicida, is parasitised by both GC-rich phages (Aeromonas phages - phiAS7 and vB_AsaM-56) and GC-poor phages (Aeromonas phages - 25, 31, 44RR2.8t, 65, Aes508, phiAS4 and phiAS5). Both the GC-rich Aeromonas phage phiAS7 and Aeromonas phage vB_AsaM-56 have nearly identical codon usage bias as their host. While all the remaining seven GC-poor Aeromonas phages differ dramatically in codon usage from their GC-rich host. Here, we investigated whether tRNA encoded in the genome of Aeromonas phages facilitate the translation of phage proteins. We found that tRNAs encoded in the phage genome correspond to synonymous codons overused in the phage genes but not in the host genes.

  19. Encoded diffractive optics for full-spectrum computational imaging

    KAUST Repository

    Heide, Felix

    2016-09-16

    Diffractive optical elements can be realized as ultra-thin plates that offer significantly reduced footprint and weight compared to refractive elements. However, such elements introduce severe chromatic aberrations and are not variable, unless used in combination with other elements in a larger, reconfigurable optical system. We introduce numerically optimized encoded phase masks in which different optical parameters such as focus or zoom can be accessed through changes in the mechanical alignment of a ultra-thin stack of two or more masks. Our encoded diffractive designs are combined with a new computational approach for self-calibrating imaging (blind deconvolution) that can restore high-quality images several orders of magnitude faster than the state of the art without pre-calibration of the optical system. This co-design of optics and computation enables tunable, full-spectrum imaging using thin diffractive optics.

  20. Neurophysiology of successful encoding and retrieval of source memory.

    Science.gov (United States)

    Cansino, Selene; Trejo-Morales, Patricia

    2008-03-01

    Event-related potentials were recorded during encoding, to identify whether brain activity predicts subsequent retrieval of spatial source information, and during retrieval, to investigate the neural correlates of successful and unsuccessful spatial context recollection. The amplitude registered during encoding for study items that were later recognized and assigned a correct source judgment was more positive than the amplitude for recognized items given incorrect source judgments; this difference started 480 msec poststimulus, predominantly at central and anterior sites. During retrieval, the waveform was more positive from 250 to 1,600 msec poststimulus when the brain had retrieved episodic information successfully than when it had failed. These findings indicate that brain electrical activity recorded during the first presentation of an item within its context predicts the subsequent retrieval of the specific spatial context. During retrieval, brain activity differed quantitatively at anterior sites and qualitatively at posterior sites according to the accuracy of source memory.

  1. High nucleosome occupancy is encoded at human regulatory sequences.

    Directory of Open Access Journals (Sweden)

    Desiree Tillo

    Full Text Available Active eukaryotic regulatory sites are characterized by open chromatin, and yeast promoters and transcription factor binding sites (TFBSs typically have low intrinsic nucleosome occupancy. Here, we show that in contrast to yeast, DNA at human promoters, enhancers, and TFBSs generally encodes high intrinsic nucleosome occupancy. In most cases we examined, these elements also have high experimentally measured nucleosome occupancy in vivo. These regions typically have high G+C content, which correlates positively with intrinsic nucleosome occupancy, and are depleted for nucleosome-excluding poly-A sequences. We propose that high nucleosome preference is directly encoded at regulatory sequences in the human genome to restrict access to regulatory information that will ultimately be utilized in only a subset of differentiated cells.

  2. Digital encoding and detection of voiceband data signals

    Science.gov (United States)

    Koneru, R. R.

    1980-12-01

    The codecs considered for investigation are Pulse Code Modulation (PCM), Differential PCM, and Delta Modulation operating at bit rates from 16 to 64 kb/sec. A central result of this study was the identification and evaluation of sampling phase differential effect present in a digital encoding system when sampling clock is not synchronous with an integral multiple of the data modern bit clock. PSK voiceband data signals are allowed to pass through these codecs that are designed for speech or data input signals. Digital encoders considered for investigation are ranked using the above performance metrics. Performance results of these coders are fully discussed and analyzed. Recognition algorithm for voiceband data, speech, and silence signals is developed for complete automation in digital channel efficiency models to achieve the optimum system performance. Pattern recognition approaches are sought to formulate and solve this problem. Maximum likelihood estimation procedure with recursive implementation of algorithm is developed.

  3. Assessment of a DNA Vaccine Encoding Burkholderia pseudomallei Bacterioferritin

    Science.gov (United States)

    2007-08-01

    bacterioferritin gene from Brucella abortus, when delivered to mice as a DNA vaccine, evokes a potent Th1 immune response, including strong IFN-γ...blocking buffer containing goat anti-mouse IgG alkaline phosphatase conjugate (Sigma) at a dilution of 1:30000 for 1hr at room temperature. Following...Walravens, and J. J. Letesson. 2001. Induction of immune response in BALB/c mice with a DNA vaccine encoding bacterioferritin or P39 of Brucella

  4. Encoding Lexicalized Tree Adjoining Grammars with a Nonmonotonic Inheritance Hierarchy

    CERN Document Server

    Evans, R; Weir, D; Evans, Roger; Gazdar, Gerald; Weir, David

    1995-01-01

    This paper shows how DATR, a widely used formal language for lexical knowledge representation, can be used to define an LTAG lexicon as an inheritance hierarchy with internal lexical rules. A bottom-up featural encoding is used for LTAG trees and this allows lexical rules to be implemented as covariation constraints within feature structures. Such an approach eliminates the considerable redundancy otherwise associated with an LTAG lexicon.

  5. Dissociating Distractor-Filtering at Encoding and During Maintenance

    OpenAIRE

    McNab, Fiona; Dolan, Raymond J.

    2014-01-01

    The effectiveness of distractor-filtering is a potentially important determinant of working memory capacity (WMC). However, a distinction between the contributions of distractor-filtering at WM encoding as opposed to filtering during maintenance has not been made and the assumption is that these rely on the same mechanism. Within 2 experiments, 1 conducted in the laboratory with 21 participants, and the other played as a game on smartphones (n = 3,247) we measure WMC without distractors, and ...

  6. Soybean phytase and nucleic acid encoding the same

    OpenAIRE

    1999-01-01

    Isolated soybean phytase polypeptides and isolated nucleic acids encoding soybean phytases are provided. The invention is also directed to nucleic acid expression constructs, vectors, and host cells comprising the isolated soybean phytase nucleic acids, as well as methods for producing recombinant and non-recombinant purified soybean phytase. The invention also relates to transgenic plants expressing the soybean phytase, particularly expression under seed-specific expression control elements.

  7. Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same

    Science.gov (United States)

    Croteau, Rodney Bruce; Burke, Charles Cullen

    2008-06-24

    In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

  8. Fractional topological phase on spatially encoded photonic qudits

    CERN Document Server

    Khoury, A Z; Marques, B; Matoso, A; Pádua, S

    2013-01-01

    We discuss the appearance of fractional topological phases on cyclic evolutions of entangled qudits encoded on photonic degrees of freedom. We show how the spatial correlations between photons generated by spontaneous parametric down conversion can be used to evidence the multiple topological phases acquired by entangled qudits and the role played by the Hilbert space dimension. A realistic experimental proposal is presented with numerical predictions of the expected results.

  9. Junk DNA-Encoded Antigens in Ovarian Cancer

    Science.gov (United States)

    2014-10-01

    SUBTITLE Junk DNA-Encoded Antigens in Ovarian Cancer 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-13-1-0359 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR...ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER The Johns Hopkins University School of Medicine 733 North Broadway, Suite 117 ...recombinase inactivates homozygous floxed alleles of p53 and Rb1. We also increased our understanding of aberrant ORF1p long interspersed element -1

  10. Structure of the gene encoding columbid annexin Icp35.

    Science.gov (United States)

    Hitti, Y S; Horseman, N D

    1991-07-22

    The cp35 gene, encoding an annexin I (AnxI) cropsac 35-kDa protein (cp35) from the pigeon, consists of 13 exons and twelve introns. The borders of exons 2-13 were mapped by comparison with the known cDNA sequence. A 5-kb sequence containing exons 1, 2, and 3, and 1.4 kb of 5'-flanking DNA, is presented. The transcription start point was mapped by S1 nuclease protection. The region of the cp35 mRNA sequence, which we had previously shown to be profoundly different from mammalian anxI, is located in the first half of exon 3. Whereas human anxI is known to be single copy, Southern analysis of pigeon genomic DNA and genomic clones demonstrated multiple anxI genes in the pigeon, diverging significantly in their 5'-termini. Pigeon vimentin, on the other hand, is encoded by a single-copy gene as it is in other birds and mammals. These experiments have demonstrated that the cp35 mRNA is transcribed from its individual gene and is not a product of alternative processing of the pigeon homolog of mammalian anxI. We speculate that the diversification of anxI genes in Columbid birds allowed the recruitment of one of these genes (cp35) for unique regulation by prolactin in the absence of post-translational regulation via residues encoded by exons 2 and 3.

  11. Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs.

    Science.gov (United States)

    Cervera, Amelia; De la Peña, Marcos

    2014-11-01

    Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

  12. DNA Compatible Multistep Synthesis and Applications to DNA Encoded Libraries.

    Science.gov (United States)

    Satz, Alexander Lee; Cai, Jianping; Chen, Yi; Goodnow, Robert; Gruber, Felix; Kowalczyk, Agnieszka; Petersen, Ann; Naderi-Oboodi, Goli; Orzechowski, Lucja; Strebel, Quentin

    2015-08-19

    Complex mixtures of DNA encoded small molecules may be readily interrogated via high-throughput sequencing. These DNA encoded libraries (DELs) are commonly used to discover molecules that interact with pharmaceutically relevant proteins. The chemical diversity displayed by the library is key to successful discovery of potent, novel, and drug-like chemical matter. The small molecule moieties of DELs are generally synthesized though a multistep process, and each chemical step is accomplished while it is simultaneously attached to an encoding DNA oligomer. Hence, library chemical diversity is often limited to DNA compatible synthetic reactions. Herein, protocols for 24 reactions are provided that have been optimized for high-throughput production of DELs. These protocols detail the multistep synthesis of benzimidazoles, imidazolidinones, quinazolinones, isoindolinones, thiazoles, and imidazopyridines. Additionally, protocols are provided for a diverse range of useful chemical reactions including BOC deprotection (under pH neutral conditions), carbamylation, and Sonogashira coupling. Last, step-by-step protocols for synthesizing functionalized DELs from trichloronitropyrimidine and trichloropyrimidine scaffolds are detailed.

  13. Compressed Domain H.264 Baseline Encoder in Video Transcoding Architecture

    Directory of Open Access Journals (Sweden)

    P. Essaki Muthu

    2014-08-01

    Full Text Available With the growth of technology, there is an increase in the number of networks, types of devices and different content representation formats as a result of which interoperability between different systems and networks is gaining in importance. Video transcoding is the process of converting video from one format to another. H.264/AVC, developed by the Joint Video Team (JVT, is new standard which fulfils significant coding efficiency, simple syntax specifications and seamless integration of video coding into all current protocols and multiple architectures. The research work presented in this paper is carrying out compressed domain video encoding through integer transform in compliance with H.264 Standard in the transcoding pipeline. The core forward transform or H.264 Transform (HT and inverse transform are analysed and adopted in this paper. The complete encoder has been demonstrated with the help of three different types of input video sequences. This paper analysed different metrics/parameters involved in encoding. This research work proposed the method of computing the complexity. It has also been proposed that the combination of Quality, File size and Complexity shall be used as one of the important metrics to evaluate the video processing.

  14. Mixed noise removal by weighted encoding with sparse nonlocal regularization.

    Science.gov (United States)

    Jiang, Jielin; Zhang, Lei; Yang, Jian

    2014-06-01

    Mixed noise removal from natural images is a challenging task since the noise distribution usually does not have a parametric model and has a heavy tail. One typical kind of mixed noise is additive white Gaussian noise (AWGN) coupled with impulse noise (IN). Many mixed noise removal methods are detection based methods. They first detect the locations of IN pixels and then remove the mixed noise. However, such methods tend to generate many artifacts when the mixed noise is strong. In this paper, we propose a simple yet effective method, namely weighted encoding with sparse nonlocal regularization (WESNR), for mixed noise removal. In WESNR, there is not an explicit step of impulse pixel detection; instead, soft impulse pixel detection via weighted encoding is used to deal with IN and AWGN simultaneously. Meanwhile, the image sparsity prior and nonlocal self-similarity prior are integrated into a regularization term and introduced into the variational encoding framework. Experimental results show that the proposed WESNR method achieves leading mixed noise removal performance in terms of both quantitative measures and visual quality.

  15. Learning Spatiotemporally Encoded Pattern Transformations in Structured Spiking Neural Networks.

    Science.gov (United States)

    Gardner, Brian; Sporea, Ioana; Grüning, André

    2015-12-01

    Information encoding in the nervous system is supported through the precise spike timings of neurons; however, an understanding of the underlying processes by which such representations are formed in the first place remains an open question. Here we examine how multilayered networks of spiking neurons can learn to encode for input patterns using a fully temporal coding scheme. To this end, we introduce a new supervised learning rule, MultilayerSpiker, that can train spiking networks containing hidden layer neurons to perform transformations between spatiotemporal input and output spike patterns. The performance of the proposed learning rule is demonstrated in terms of the number of pattern mappings it can learn, the complexity of network structures it can be used on, and its classification accuracy when using multispike-based encodings. In particular, the learning rule displays robustness against input noise and can generalize well on an example data set. Our approach contributes to both a systematic understanding of how computations might take place in the nervous system and a learning rule that displays strong technical capability.

  16. Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding.

    Directory of Open Access Journals (Sweden)

    Chao Huang

    2016-06-01

    Full Text Available Neural processing rests on the intracellular transformation of information as synaptic inputs are translated into action potentials. This transformation is governed by the spike threshold, which depends on the history of the membrane potential on many temporal scales. While the adaptation of the threshold after spiking activity has been addressed before both theoretically and experimentally, it has only recently been demonstrated that the subthreshold membrane state also influences the effective spike threshold. The consequences for neural computation are not well understood yet. We address this question here using neural simulations and whole cell intracellular recordings in combination with information theoretic analysis. We show that an adaptive spike threshold leads to better stimulus discrimination for tight input correlations than would be achieved otherwise, independent from whether the stimulus is encoded in the rate or pattern of action potentials. The time scales of input selectivity are jointly governed by membrane and threshold dynamics. Encoding information using adaptive thresholds further ensures robust information transmission across cortical states i.e. decoding from different states is less state dependent in the adaptive threshold case, if the decoding is performed in reference to the timing of the population response. Results from in vitro neural recordings were consistent with simulations from adaptive threshold neurons. In summary, the adaptive spike threshold reduces information loss during intracellular information transfer, improves stimulus discriminability and ensures robust decoding across membrane states in a regime of highly correlated inputs, similar to those seen in sensory nuclei during the encoding of sensory information.

  17. An encoding methodology for medical knowledge using SNOMED CT ontology

    Directory of Open Access Journals (Sweden)

    Shaker El-Sappagh

    2016-07-01

    Full Text Available Knowledge-Intensive Case Based Reasoning (KI-CBR systems mainly depend on ontology. Using ontology as domain knowledge supports the implementation of semantically-intelligent case retrieval algorithms. The case-based knowledge must be encoded with the same concepts of the domain ontology. Standard medical ontologies, such as SNOMED CT (SCT, can play the role of domain ontology to enhance case representation and retrieval. This study has three stages. First, we propose an encoding methodology using SCT. Second, this methodology is used to encode the case-based knowledge. Third, all the used SCT concepts are collected in a reference set, and an OWL2 ontology of 550 pre-coordinated concepts is proposed. A diabetes diagnosis is chosen as a case study of our proposed framework. SCT is used to provide a pre-coordination concept coverage of ∼75% for diabetes diagnosis terms. Whereas, the uncovered concepts in SCT are proposed. The resulting OWL2 ontology will be used as domain knowledge representation in diabetes diagnosis CBR systems. The proposed framework is tested by using 60 real cases.

  18. Bioinformatics analysis and detection of gelatinase encoded gene in Lysinibacillussphaericus

    Science.gov (United States)

    Repin, Rul Aisyah Mat; Mutalib, Sahilah Abdul; Shahimi, Safiyyah; Khalid, Rozida Mohd.; Ayob, Mohd. Khan; Bakar, Mohd. Faizal Abu; Isa, Mohd Noor Mat

    2016-11-01

    In this study, we performed bioinformatics analysis toward genome sequence of Lysinibacillussphaericus (L. sphaericus) to determine gene encoded for gelatinase. L. sphaericus was isolated from soil and gelatinase species-specific bacterium to porcine and bovine gelatin. This bacterium offers the possibility of enzymes production which is specific to both species of meat, respectively. The main focus of this research is to identify the gelatinase encoded gene within the bacteria of L. Sphaericus using bioinformatics analysis of partially sequence genome. From the research study, three candidate gene were identified which was, gelatinase candidate gene 1 (P1), NODE_71_length_93919_cov_158.931839_21 which containing 1563 base pair (bp) in size with 520 amino acids sequence; Secondly, gelatinase candidate gene 2 (P2), NODE_23_length_52851_cov_190.061386_17 which containing 1776 bp in size with 591 amino acids sequence; and Thirdly, gelatinase candidate gene 3 (P3), NODE_106_length_32943_cov_169.147919_8 containing 1701 bp in size with 566 amino acids sequence. Three pairs of oligonucleotide primers were designed and namely as, F1, R1, F2, R2, F3 and R3 were targeted short sequences of cDNA by PCR. The amplicons were reliably results in 1563 bp in size for candidate gene P1 and 1701 bp in size for candidate gene P3. Therefore, the results of bioinformatics analysis of L. Sphaericus resulting in gene encoded gelatinase were identified.

  19. Copyright Protection of Color Imaging Using Robust-Encoded Watermarking

    Directory of Open Access Journals (Sweden)

    M. Cedillo-Hernandez

    2015-04-01

    Full Text Available In this paper we present a robust-encoded watermarking method applied to color images for copyright protection, which presents robustness against several geometric and signal processing distortions. Trade-off between payload, robustness and imperceptibility is a very important aspect which has to be considered when a watermark algorithm is designed. In our proposed scheme, previously to be embedded into the image, the watermark signal is encoded using a convolutional encoder, which can perform forward error correction achieving better robustness performance. Then, the embedding process is carried out through the discrete cosine transform domain (DCT of an image using the image normalization technique to accomplish robustness against geometric and signal processing distortions. The embedded watermark coded bits are extracted and decoded using the Viterbi algorithm. In order to determine the presence or absence of the watermark into the image we compute the bit error rate (BER between the recovered and the original watermark data sequence. The quality of the watermarked image is measured using the well-known indices: Peak Signal to Noise Ratio (PSNR, Visual Information Fidelity (VIF and Structural Similarity Index (SSIM. The color difference between the watermarked and original images is obtained by using the Normalized Color Difference (NCD measure. The experimental results show that the proposed method provides good performance in terms of imperceptibility and robustness. The comparison among the proposed and previously reported methods based on different techniques is also provided.

  20. New Complexity Scalable MPEG Encoding Techniques for Mobile Applications

    Directory of Open Access Journals (Sweden)

    Stephan Mietens

    2004-03-01

    Full Text Available Complexity scalability offers the advantage of one-time design of video applications for a large product family, including mobile devices, without the need of redesigning the applications on the algorithmic level to meet the requirements of the different products. In this paper, we present complexity scalable MPEG encoding having core modules with modifications for scalability. The interdependencies of the scalable modules and the system performance are evaluated. Experimental results show scalability giving a smooth change in complexity and corresponding video quality. Scalability is basically achieved by varying the number of computed DCT coefficients and the number of evaluated motion vectors but other modules are designed such they scale with the previous parameters. In the experiments using the “Stefan” sequence, the elapsed execution time of the scalable encoder, reflecting the computational complexity, can be gradually reduced to roughly 50% of its original execution time. The video quality scales between 20 dB and 48 dB PSNR with unity quantizer setting, and between 21.5 dB and 38.5 dB PSNR for different sequences targeting 1500 kbps. The implemented encoder and the scalability techniques can be successfully applied in mobile systems based on MPEG video compression.

  1. Neural modeling of episodic memory: encoding, retrieval, and forgetting.

    Science.gov (United States)

    Wang, Wenwen; Subagdja, Budhitama; Tan, Ah-Hwee; Starzyk, Janusz A

    2012-10-01

    This paper presents a neural model that learns episodic traces in response to a continuous stream of sensory input and feedback received from the environment. The proposed model, based on fusion adaptive resonance theory (ART) network, extracts key events and encodes spatio-temporal relations between events by creating cognitive nodes dynamically. The model further incorporates a novel memory search procedure, which performs a continuous parallel search of stored episodic traces. Combined with a mechanism of gradual forgetting, the model is able to achieve a high level of memory performance and robustness, while controlling memory consumption over time. We present experimental studies, where the proposed episodic memory model is evaluated based on the memory consumption for encoding events and episodes as well as recall accuracy using partial and erroneous cues. Our experimental results show that: 1) the model produces highly robust performance in encoding and recalling events and episodes even with incomplete and noisy cues; 2) the model provides enhanced performance in a noisy environment due to the process of forgetting; and 3) compared with prior models of spatio-temporal memory, our model shows a higher tolerance toward noise and errors in the retrieval cues.

  2. Holistic random encoding for imaging through multimode fibers

    CERN Document Server

    Jang, Hwanchol; Chung, Euiheon; Choi, Wonshik; Lee, Heung-No

    2015-01-01

    The input numerical aperture (NA) of multimode fiber (MMF) can be effectively increased by placing turbid media at the input end of the MMF. This provides the potential for high-resolution imaging through the MMF. While the input NA is increased, the number of propagation modes in the MMF and hence the output NA remains the same. This makes the image reconstruction process underdetermined and may limit the quality of the image reconstruction. In this paper, we aim to improve the signal to noise ratio (SNR) of the image reconstruction in imaging through MMF. We notice that turbid media placed in the input of the MMF transforms the incoming waves into a better format for information transmission and information extraction. We call this transformation as holistic random (HR) encoding of turbid media. By exploiting the HR encoding, we make a considerable improvement on the SNR of the image reconstruction. For efficient utilization of the HR encoding, we employ sparse representation (SR), a relatively new signal r...

  3. Strain correction in interleaved strain-encoded (SENC) cardiac MR

    Science.gov (United States)

    Motaal, Abdallah G.; Osman, Nael F.

    2010-03-01

    The strain encoding (SENC) technique directly encodes regional strain of the heart into the acquired MR images and produces two images with two different tunings so that longitudinal strain, on the short-axis view, or circumferential strain on the long-axis view, are measured. Interleaving acquisition is used to shorten the acquisition time of the two tuned images by 50%, but it suffers from errors in the strain calculations due to inter-tunings motion of the heart. In this work, we propose a method to correct for the inter-tunings motion by estimating the motion-induced shift in the spatial frequency of the encoding pattern, which depends on the strain rate. Numerical data was generated to test the proposed method and real images of human subjects were used for validation. The proposed method corrected the measured strain values so they became nearly identical to the original ones. The results show an improvement in strain calculations so as to relax the imaging constraints on spatial and temporal resolutions and improve image quality.

  4. The effects of molecular diffusion in spatially encoded magnetic resonance imaging

    Science.gov (United States)

    Marhabaie, Sina; Bodenhausen, Geoffrey; Pelupessy, Philippe

    2016-12-01

    In spatially encoded MRI, the signal is acquired sequentially for different coordinates. In particular for single-scan acquisitions in inhomogeneous fields, spatially encoded methods improve the image quality compared to traditional k-space encoding. Previously, much attention has been paid in order to homogenize T2 losses across the sample. In this work, we investigate the effects of diffusion on the image quality in spatially encoded MRI. We show that losses due to diffusion are often not uniform along the spatially encoded dimension, and how to adapt spatially encoded sequences in order to obtain uniformly diffusion-weighted images.

  5. Research on a novel orientation algorithm of single-ring absolute photoelectric shaft encoder

    Institute of Scientific and Technical Information of China (English)

    CHEN Yun

    2007-01-01

    A novel single-ring absolute optical shaft encoder is designed by studying the encoding principle of traditional absolute optical shaft encoder in this paper. The description of the orientation algorithm of the encoder is specified,and an example for explaining the orientation arithmetic is given,which indicates that the theory of the encoder works. The visual interface to acquire signals of CCD is shown with VB,which provides reliable foundation to process data. The effective factors of measurement precision of the encoder are analyzed.

  6. Transmit Array Spatial Encoding (TRASE) using broadband WURST pulses for RF spatial encoding in inhomogeneous B0 fields

    Science.gov (United States)

    Stockmann, Jason P.; Cooley, Clarissa Z.; Guerin, Bastien; Rosen, Matthew S.; Wald, Lawrence L.

    2016-07-01

    Transmit Array Spatial Encoding (TRASE) is a promising new MR encoding method that uses transmit RF (B1+) phase gradients over the field-of-view to perform Fourier spatial encoding. Acquisitions use a spin echo train in which the transmit coil phase ramp is modulated to jump from one k-space point to the next. This work extends the capability of TRASE by using swept radiofrequency (RF) pulses and a quadratic phase removal method to enable TRASE where it is arguably most needed: portable imaging systems with inhomogeneous B0 fields. The approach is particularly well-suited for portable MR scanners where (a) inhomogeneous B0 fields are a byproduct of lightweight magnet design, (b) heavy, high power-consumption gradient coil systems are a limitation to siting the system in non-conventional locations and (c) synergy with the use of spin echo trains is required to overcome intra-voxel dephasing (short T2∗) in the inhomogeneous field. TRASE does not use a modulation of the B0 field to encode, but it does suffer from secondary effects of the inhomogeneous field. Severe artifacts arise in TRASE images due to off-resonance effects when the RF pulse does not cover the full bandwidth of spin resonances in the imaging FOV. Thus, for highly inhomogeneous B0 fields, the peak RF power needed for high-bandwidth refocusing hard pulses becomes very expensive, in addition to requiring RF coils that can withstand thousands of volts. In this work, we use swept WURST RF pulse echo trains to achieve TRASE imaging in a highly inhomogeneous magnetic field (ΔB0/B0 ∼ 0.33% over the sample). By accurately exciting and refocusing the full bandwidth of spins, the WURST pulses eliminate artifacts caused by the limited bandwidth of the hard pulses used in previous realizations of TRASE imaging. We introduce a correction scheme to remove the unwanted quadratic phase modulation caused by the swept pulses. Also, a phase alternation scheme is employed to mitigate artifacts caused by mixture of

  7. Multi-DOF Incremental Optical Encoder with Laser Wavelength Compensation

    Directory of Open Access Journals (Sweden)

    Cha'o-Kuang Chen

    2013-09-01

    Full Text Available This study used a reflective diffraction grating as the medium to develop a multi-DOF incremental optical encoder for motion stage. The optical encoder can measure three angular displacements, roll, yaw and pitch of the motion stage simultaneously, as well as the horizontal straightness and linear displacement, summed to five DOF errors of motion stage by only using the positive and negative first-order diffracted light. The grating diffraction theory, Doppler effect, and optical interference technique were used. Two quadrant photodetectors were used to measure the changes in three-dimensional space of diffraction direction of diffracted light, in order to construct a multi-DOF incremental optical encoder. Considering the working stability of a laser diode and preventing the influence of the zeroth-order diffracted light returning to the laser diode, an additional optical isolation system was designed and a wavelength variation monitoring module was created. The compensation for the light source wavelength variation could be 0.001 nm. The multi-DOF verification results showed that the roll error is ±0.7/60 arcsec, the standard deviation is 0.025 arcsec; the yaw error is ±0.7/30 arcsec, the standard deviation is 0.05 arcsec; the pitch error is ±0.8/90 arcsec, the standard deviation is 0.18 arcsec, the horizontal straightness error is ±0.5/250 μm, the standard deviation is 0.05 μm and the linear displacement error is ±1/20000 μm, the standard deviation is 12 nm.

  8. Structure and function of a cyanophage-encoded peptide deformylase.

    Science.gov (United States)

    Frank, Jeremy A; Lorimer, Don; Youle, Merry; Witte, Pam; Craig, Tim; Abendroth, Jan; Rohwer, Forest; Edwards, Robert A; Segall, Anca M; Burgin, Alex B

    2013-06-01

    Bacteriophages encode auxiliary metabolic genes that support more efficient phage replication. For example, cyanophages carry several genes to maintain host photosynthesis throughout infection, shuttling the energy and reducing power generated away from carbon fixation and into anabolic pathways. Photodamage to the D1/D2 proteins at the core of photosystem II necessitates their continual replacement. Synthesis of functional proteins in bacteria requires co-translational removal of the N-terminal formyl group by a peptide deformylase (PDF). Analysis of marine metagenomes to identify phage-encoded homologs of known metabolic genes found that marine phages carry PDF genes, suggesting that their expression during infection might benefit phage replication. We identified a PDF homolog in the genome of Synechococcus cyanophage S-SSM7. Sequence analysis confirmed that it possesses the three absolutely conserved motifs that form the active site in PDF metalloproteases. Phylogenetic analysis placed it within the Type 1B subclass, most closely related to the Arabidopsis chloroplast PDF, but lacking the C-terminal α-helix characteristic of that group. PDF proteins from this phage and from Synechococcus elongatus were expressed and characterized. The phage PDF is the more active enzyme and deformylates the N-terminal tetrapeptides from D1 proteins more efficiently than those from ribosomal proteins. Solution of the X-ray/crystal structures of those two PDFs to 1.95 Å resolution revealed active sites identical to that of the Type 1B Arabidopsis chloroplast PDF. Taken together, these findings show that many cyanophages encode a PDF with a D1 substrate preference that adds to the repertoire of genes used by phages to maintain photosynthetic activities.

  9. Genetically encoded cleavable protein photo-cross-linker.

    Science.gov (United States)

    Lin, Shixian; He, Dan; Long, Teng; Zhang, Shuai; Meng, Rong; Chen, Peng R

    2014-08-27

    We have developed a genetically encoded, selenium-based cleavable photo-cross-linker that allows for the separation of bait and prey proteins after protein photo-cross-linking. We have further demonstrated the efficient capture of the in situ generated selenenic acid on the cleaved prey proteins. Our strategy involves tagging the selenenic acid with an alkyne-containing dimethoxyaniline molecule and subsequently labeling with an azide-bearing fluorophore or biotin probe. This cleavage-and-capture after protein photo-cross-linking strategy allows for the efficient capture of prey proteins that are readily accessible by two-dimensional gel-based proteomics and mass spectrometry analysis.

  10. Optimal Encoding of Data in Data Transmission Channels

    Directory of Open Access Journals (Sweden)

    Silviu Draghici

    2013-01-01

    Full Text Available This paper aims to present the methods of achieving an optimal encoding in the data communication channels. After a short description of the communication channel and of the data communication channel types, follow briefly a few notions of the data channel enthropy, information, transinformation, with their properties, definitions and mathematical relations connecting them. Chapter 2 presents the concept of optimal code, following a detailed description (using two suggestive examples of the two main methods used to obtain an optimal code: Shannon-Fano and Huffman.

  11. Chemical Biology Probes from Advanced DNA-encoded Libraries.

    Science.gov (United States)

    Salamon, Hazem; Klika Škopić, Mateja; Jung, Kathrin; Bugain, Olivia; Brunschweiger, Andreas

    2016-02-19

    The identification of bioactive compounds is a crucial step toward development of probes for chemical biology studies. Screening of DNA-encoded small molecule libraries (DELs) has emerged as a validated technology to interrogate vast chemical space. DELs consist of chimeric molecules composed of a low-molecular weight compound that is conjugated to a DNA identifier tag. They are screened as pooled libraries using selection to identify "hits." Screening of DELs has identified numerous bioactive compounds. Some of these molecules were instrumental in gaining a deeper understanding of biological systems. One of the main challenges in the field is the development of synthesis methodology for DELs.

  12. Target searching based on modified implicit ROI encoding scheme

    Institute of Scientific and Technical Information of China (English)

    Bai Xu; Zhang Zhongzhao

    2008-01-01

    An EBCOT-based method is proposed to reduce the priority of background coefficients in the ROI code block without compromising algorithm complexity.The region of interest is encoded to a higher quality level than background,and the target searching time in video-guided penetrating missile can be shortened.Three kinds of coding schemes based on EBCOT are discussed.Experimental results demonstrate that the proposed method shows higher compression efficiency,lower complexity,and good reconstructed ROI image quality in the lower channel capacity.

  13. The sulfolobicin genes of Sulfolobus acidocaldarius encode novel antimicrobial proteins.

    Science.gov (United States)

    Ellen, Albert F; Rohulya, Olha V; Fusetti, Fabrizia; Wagner, Michaela; Albers, Sonja-Verena; Driessen, Arnold J M

    2011-09-01

    Crenarchaea, such as Sulfolobus acidocaldarius and Sulfolobus tokodaii, produce antimicrobial proteins called sulfolobicins. These antimicrobial proteins inhibit the growth of closely related species. Here we report the identification of the sulfolobicin-encoding genes in S. acidocaldarius. The active sulfolobicin comprises two proteins that are equipped with a classical signal sequence. These proteins are secreted by the cells and found to be membrane vesicle associated. Gene inactivation studies demonstrate that both proteins are required for the bacteriostatic antimicrobial activity. Sulfolobicins constitute a novel class of antimicrobial proteins without detectable homology to any other protein.

  14. Quantum key distribution based on phase encoding and polarization measurement

    CERN Document Server

    Ma, H Q; Zhao, J L; Ma, Hai-Qiang; Wu, Ling-An; Zhao, Jian-Ling

    2007-01-01

    A one-way quantum key distribution scheme based on intrinsically stable Faraday-mirror type Michelson interferometers with four-port polarizing beampslitters has been demonstrated which can compensate for birefringence effects automatically. The encoding is performed with phase modulators, but decoding is accomplished through measurement of the polarization state of Bob's photons. An extinction ratio of about 30dB was maintained for several hours over 50km of fiber at 1310nm without any adjustment to the setup, which shows its good potential for practical systems

  15. AIdentification of encoding proteins related to SARS-CoV

    Institute of Scientific and Technical Information of China (English)

    MEI Hu; SUN Lili; ZHOU Yuan; XIONG Qing; LI Zhiliang

    2004-01-01

    By sampling 100 encoding proteins from SARS-coronavirus (SARS-CoV, NC 004718) and other six coronaviruses and selecting 23 variables through stepwise multiple regression (SMR) from 172 variables, the multiple linear regression (MLR) model was established with good results of the quantitative modelling correlation coefficient R2 = 0.645 and the cross-validation correlation coefficient 0.375. After removing 4 outliers, the quantitative modelling and cross-validation correlation coefficients were R2 = 0.743 and R2CV=0.543, respectively.

  16. Model Checking Event-B by Encoding into Alloy

    CERN Document Server

    Matos, Paulo J

    2008-01-01

    As systems become ever more complex, verification becomes more main stream. Event-B and Alloy are two formal specification languages based on fairly different methodologies. While Event-B uses theorem provers to prove that invariants hold for a given specification, Alloy uses a SAT-based model finder. In some settings, Event-B invariants may not be proved automatically, and so the often difficult step of interactive proof is required. One solution for this problem is to validate invariants with model checking. This work studies the encoding of Event-B machines and contexts to Alloy in order to perform temporal model checking with Alloy's SAT-based engine.

  17. [Mutations in the gene encoding filaggrin cause ichthyosis vulgaris].

    Science.gov (United States)

    Prasad, Sumangali Chandra; Rasmussen, Kirsten; Bygum, Anette

    2011-02-14

    Ichthyosis vulgaris is a common genetic skin disorder with an estimated prevalence of 1:250 caused by mutations in the gene encoding filaggrin. This disorder manifests itself within the first year of life and is clinically characterized by dry, scaly skin, keratosis pilaris, palmar hyperlinearity and atopic manifestations. Patients with a severe phenotype are homozygous or compound heterozygous for the mutations, whereas heterozygous patients show mild disease, suggesting semidominant inheritance with incomplete penetrance. We present a patient with classic severe ichthyosis vulgaris, atopic eczema and two loss-of-function mutations.

  18. Identification and use of genes encoding amatoxin and phallotoxin

    Energy Technology Data Exchange (ETDEWEB)

    Hallen, Heather E.; Walton, Jonathan D.; Luo, Hong; Scott-Craig, John S.

    2016-12-13

    The present invention relates to compositions and methods comprising genes and peptides associated with cyclic peptide toxins and toxin production in mushrooms. In particular, the present invention relates to using genes and proteins from Amanita species encoding Amanita peptides, specifically relating to amatoxins and phallotoxins. In a preferred embodiment, the present invention also relates to methods for detecting Amanita peptide toxin genes for identifying Amanita peptide-producing mushrooms and for diagnosing suspected cases of mushroom poisoning. Further, the present inventions relate to providing kits for diagnosing and monitoring suspected cases of mushroom poisoning in patients.

  19. Design of output voltage waveform on magnetic encoder

    Energy Technology Data Exchange (ETDEWEB)

    Shi Yu E-mail: shiyu_aaa@163.com; Zhang Huaiwu; Jiang Xiangdong; Wen Qiye; Han Baoshan

    2004-11-01

    A novel design model based on slant multi-phase filter (SMPF) theory is presented. By the theory nth harmonic voltage (n=2nd, 3rd and 4th...(V)) can be reduced easily. Magnetic encoder with sinusoidal output voltage waveform has been developed and sinusoidal output waveform can be easily improved. The minimum of distortion factor was observed when the difference of slant phase is 2{pi}3. This result agrees with SMPF theory value {phi}=4.904 deg. (p=0.8 mm, l=3 mm, {delta}{theta}=2{pi}3]. This result can be widely used in magnetoresistive sensor fields.

  20. Recent Advances in Development of Genetically Encoded Fluorescent Sensors.

    Science.gov (United States)

    Sanford, Lynn; Palmer, Amy

    2017-01-01

    Genetically encoded fluorescent sensors are essential tools in modern biological research, and recent advances in fluorescent proteins (FPs) have expanded the scope of sensor design and implementation. In this review we compare different sensor platforms, including Förster resonance energy transfer (FRET) sensors, fluorescence-modulated single FP-based sensors, translocation sensors, complementation sensors, and dimerization-based sensors. We discuss elements of sensor design and engineering for each platform, including the incorporation of new types of FPs and sensor screening techniques. Finally, we summarize the wide range of sensors in the literature, exploring creative new sensor architectures suitable for different applications.

  1. Direct Pathogenic Effects of HERV-encoded Proteins

    DEFF Research Database (Denmark)

    Hansen, Dorte Tranberg; Møller-Larsen, Anné; Petersen, Thor;

    and the possible direct pathogenic effects of HERV-encoded Env proteins on the CNS. Methods: Construction and characterization of a panel of recombinant Env-proteins is initiated and their pathogenic potential will be investigated: Fusiogenic potential analyzed by flow cytometry and confocal microscopy. Analysis...... of Env-induced apoptosis/necrosis in CNS cells will be performed by both DNA fragmentation ELISA and qPCR. Furthermore, the cellular localization of HERV-antigens on cells from patients with MS will be determined by confocal microscopy. A flow cytometric/confocal method has been optimized...

  2. A FPGA Implementation of JPEG Baseline Encoder for Wearable Devices.

    Science.gov (United States)

    Li, Yuecheng; Jia, Wenyan; Luan, Bo; Mao, Zhi-Hong; Zhang, Hong; Sun, Mingui

    2015-04-01

    In this paper, an efficient field-programmable gate array (FPGA) implementation of the JPEG baseline image compression encoder is presented for wearable devices in health and wellness applications. In order to gain flexibility in developing FPGA-specific software and balance between real-time performance and resources utilization, A High Level Synthesis (HLS) tool is utilized in our system design. An optimized dataflow configuration with a padding scheme simplifies the timing control for data transfer. Our experiments with a system-on-chip multi-sensor system have verified our FPGA implementation with respect to real-time performance, computational efficiency, and FPGA resource utilization.

  3. Self-encoding Functional Resin Applying for Combinatorial Chemistry and High Throughput Screening

    Institute of Scientific and Technical Information of China (English)

    DU Lei; CHEN Tong-sheng

    2004-01-01

    A novel solid phase organic synthesis resin was synthesized for combinatorial high-throughput screening,which based on FTIR spectra self-encoding functional resin technology. A new deconvolution strategy termed position encoding deconvolution had illustrated and was compared with some popular combinatorial deconvolution strategies in efficiency and information content. The mimic high throughput screening of hexapeptide library successfully proved the applying of the self-encoding functional resin technology and the position encoding deconvolution strategy.

  4. Robust EPI Nyquist Ghost Elimination via Spatial and Temporal Encoding (EPI-GESTE)

    OpenAIRE

    Hoge, W. Scott; Tan, Huan; Kraft, Robert A.

    2010-01-01

    Nyquist ghosts are an inherent artifact in EPI acquisitions. An approach to robustly eliminate Nyquist ghosts is presented that integrates two previous Nyquist ghost correction techniques: temporal domain encoding (Phase Labeling for Additional Coordinate Encoding: PLACE) and spatial domain encoding (Phased Array Ghost Elimination: PAGE). Temporal encoding modulates the EPI acquisition trajectory from frame to frame, enabling one to interleave data to remove inconsistencies that occur between...

  5. Effects of Aging on the Neural Correlates of Successful Item and Source Memory Encoding

    Science.gov (United States)

    Dennis, Nancy A.; Hayes, Scott M.; Prince, Steven E.; Madden, David J.; Huettel, Scott A.; Cabeza, Roberto

    2008-01-01

    To investigate the neural basis of age-related source memory (SM) deficits, young and older adults were scanned with fMRI while encoding faces, scenes, and face-scene pairs. Successful encoding activity was identified by comparing encoding activity for subsequently remembered versus forgotten items or pairs. Age deficits in successful encoding…

  6. Encoder-decoder optimization for brain-computer interfaces.

    Directory of Open Access Journals (Sweden)

    Josh Merel

    2015-06-01

    Full Text Available Neuroprosthetic brain-computer interfaces are systems that decode neural activity into useful control signals for effectors, such as a cursor on a computer screen. It has long been recognized that both the user and decoding system can adapt to increase the accuracy of the end effector. Co-adaptation is the process whereby a user learns to control the system in conjunction with the decoder adapting to learn the user's neural patterns. We provide a mathematical framework for co-adaptation and relate co-adaptation to the joint optimization of the user's control scheme ("encoding model" and the decoding algorithm's parameters. When the assumptions of that framework are respected, co-adaptation cannot yield better performance than that obtainable by an optimal initial choice of fixed decoder, coupled with optimal user learning. For a specific case, we provide numerical methods to obtain such an optimized decoder. We demonstrate our approach in a model brain-computer interface system using an online prosthesis simulator, a simple human-in-the-loop pyschophysics setup which provides a non-invasive simulation of the BCI setting. These experiments support two claims: that users can learn encoders matched to fixed, optimal decoders and that, once learned, our approach yields expected performance advantages.

  7. The pea gene NA encodes ent-kaurenoic acid oxidase.

    Science.gov (United States)

    Davidson, Sandra E; Elliott, Robert C; Helliwell, Chris A; Poole, Andrew T; Reid, James B

    2003-01-01

    The gibberellin (GA)-deficient dwarf na mutant in pea (Pisum sativum) has severely reduced internode elongation, reduced root growth, and decreased leaflet size. However, the seeds develop normally. Two genes, PsKAO1 and PsKAO2, encoding cytochrome P450 monooxygenases of the subfamily CYP88A were isolated. Both PsKAO1 and PsKAO2 had ent-kaurenoic acid oxidase (KAO) activity, catalyzing the three steps of the GA biosynthetic pathway from ent-kaurenoic acid to GA(12) when expressed in yeast (Saccharomyces cerevisiae). In addition to the intermediates ent-7alpha-hydroxykaurenoic acid and GA(12)-aldehyde, some additional products of the pea KAO activity were detected, including ent-6alpha,7alpha-dihydroxykaurenoic acid and 7beta-hydroxykaurenolide. The NA gene encodes PsKAO1, because in two independent mutant alleles, na-1 and na-2, PsKAO1 had altered sequences and the five-base deletion in PsKAO1 associated with the na-1 allele cosegregated with the dwarf na phenotype. PsKAO1 was expressed in the stem, apical bud, leaf, pod, and root, organs in which GA levels have previously been shown to be reduced in na plants. PsKAO2 was expressed only in seeds and this may explain the normal seed development and normal GA biosynthesis in seeds of na plants.

  8. Object recognition memory: neurobiological mechanisms of encoding, consolidation and retrieval.

    Science.gov (United States)

    Winters, Boyer D; Saksida, Lisa M; Bussey, Timothy J

    2008-07-01

    Tests of object recognition memory, or the judgment of the prior occurrence of an object, have made substantial contributions to our understanding of the nature and neurobiological underpinnings of mammalian memory. Only in recent years, however, have researchers begun to elucidate the specific brain areas and neural processes involved in object recognition memory. The present review considers some of this recent research, with an emphasis on studies addressing the neural bases of perirhinal cortex-dependent object recognition memory processes. We first briefly discuss operational definitions of object recognition and the common behavioural tests used to measure it in non-human primates and rodents. We then consider research from the non-human primate and rat literature examining the anatomical basis of object recognition memory in the delayed nonmatching-to-sample (DNMS) and spontaneous object recognition (SOR) tasks, respectively. The results of these studies overwhelmingly favor the view that perirhinal cortex (PRh) is a critical region for object recognition memory. We then discuss the involvement of PRh in the different stages--encoding, consolidation, and retrieval--of object recognition memory. Specifically, recent work in rats has indicated that neural activity in PRh contributes to object memory encoding, consolidation, and retrieval processes. Finally, we consider the pharmacological, cellular, and molecular factors that might play a part in PRh-mediated object recognition memory. Recent studies in rodents have begun to indicate the remarkable complexity of the neural substrates underlying this seemingly simple aspect of declarative memory.

  9. Identification of a Novel UTY‐Encoded Minor Histocompatibility Antigen

    DEFF Research Database (Denmark)

    Mortensen, B. K.; Rasmussen, A. H.; Larsen, Malene Erup;

    2012-01-01

    Minor histocompatibility antigens (mHags) encoded by the Y‐chromosome (H‐Y‐mHags) are known to play a pivotal role in allogeneic haematopoietic cell transplantation (HCT) involving female donors and male recipients. We present a new H‐Y‐mHag, YYNAFHWAI (UTY139–147), encoded by the UTY gene...... and presented by HLA‐A*24:02. Briefly, short peptide stretches encompassing multiple putative H‐Y‐mHags were designed using a bioinformatics predictor of peptide‐HLA binding, NetMHCpan. These peptides were used to screen for peptide‐specific HLA‐restricted T cell responses in peripheral blood mononuclear cells...... degranulation (CD107a). In contrast, no responses were seen when the T cells were stimulated with patient tumour cells alone. CD8+ T cells specific for this new H‐Y‐mHag were found in three of five HLA‐A*24:02‐positive male recipients of female donor HCT grafts available for this study....

  10. pTAR-encoded proteins in plasmid partitioning.

    Science.gov (United States)

    Kalnin, K; Stegalkina, S; Yarmolinsky, M

    2000-04-01

    Partition cassettes, essential for the segregational stability of low-copy-number bacterial plasmids, typically encode two autoregulated proteins and an adjacent cis-acting centromere analog to which one or perhaps both proteins bind. The diminutive partition region of pTAR of Agrobacterium spp. was reported to be exceptional, encoding only a single protein, ParA (D. R. Gallie and C. I. Kado, J. Mol. Biol. 193:465-478, 1987). However, resequencing of the region revealed two small downstream genes, parB and orf-84, of which only parB was found to be essential for partitioning in A. tumefaciens. Purified ParA exhibited a weak ATPase activity that was modestly increased by nonspecific DNA. ParB bound in vitro to repeated sequences present in a region, parS, that possesses centromere and operator functions and within which we identified the primary transcription start site by primer extension. In certain respects the Par proteins behave normally in the foreign host Escherichia coli. In E. coli, as in A. tumefaciens, ParB repressed the partition operon; ParA, inactive alone, augmented this repression. Functional similarities between the partition system of pTAR and those of other plasmids and bacteria are prominent, despite differences in size, organization, and amino acid sequence.

  11. STEGANOGRAFI DENGAN CHAOTIC LEAST SIGNIFICANT BIT ENCODING PADA TELEPON GENGGAM

    Directory of Open Access Journals (Sweden)

    Susany Soplanit

    2007-01-01

    Full Text Available The issues of security in mobile phone in recent days become crucial. Many privacy or secretly data is stored using unsecured protocol or sometimes without the security procedures at all. This will lead to great awareness about security in mobile phone. The effective ways to secure data are steganography and cryptography. The first one concentrate to data hiding in a certain media. In this paper, we present Chaotic Least Significant Bit Encoding (CLSBE as a steganography method in our system design. The experiment results show that hidden messages in PNG form can be retrieved correctly. The implementation of system in emulator works well but depends on mobile phone features and environment. Abstract in Bahasa Indonesia : Telepon genggam saat ini dapat digunakan untuk menyimpan data-data yang bersifat pribadi atau rahasia, oleh karena itu pengamanan data pada telepon genggam akan menjadi hal yang penting di masa ini ataupun di masa yang akan datang. Sistem pengamanan data yang efektif pada telepon genggam selain kriptografi adalah Steganografi yaitu penyembunyian data dalam sebuah media. Dalam perancangan ini metode yang digunakan adalah Chaotic Least Significant Bit Encoding (CLSBE. Hasil pengujian membuktikan bahwa pesan yang tersembunyi dalam citra digital dengan format PNG masih dapat diambil kembali dengan benar. Implementasi pada emulator telah berjalan dengan baik, namun untuk telepon genggam perlu penyesuaian dengan fasilitas pada telepon tersebut. Kata kunci: CLSBE, steganografi, stego-image, cover-image.

  12. Phonological Encoding in Mandarin Chinese: Evidence from Tongue Twisters.

    Science.gov (United States)

    Kember, Heather; Croot, Karen; Patrick, Ellis

    2015-12-01

    Models of connected speech production in Mandarin Chinese must specify how lexical tone, speech segments, and phrase-level prosody are integrated in speech production. This study used tongue twisters to test predictions of the two different models of word form encoding. Tongue twisters were constructed from 5 sets of characters that rotated pairs of initial segments or pairs of tones, or both, across format (ABAB, ABBA), and across position of the characters in four-character tongue twister strings. Fifty two native Mandarin Chinese speakers read aloud 120 tongue twisters, repeating each one six times in a row. They made a total of 3503 (2.34%) segment errors and 1372 (.92%) tone errors. Segment errors occurred on the onsets of the first and third characters in the ABBA but not ABAB segment-alternating tongue twisters, and on the onsets of the second and fourth characters of the tone-alternating tongue twisters. Tone errors were highest on the third and fourth characters in the tone-alternating tongue twisters. The pattern of tone errors is consistent with the claim that tone is associated to a metrical frame prior to segment encoding, while the format by position interaction found for the segment-alternating tongue twisters suggest articulatory gestures oscillate in segment production as proposed by gestural phonology.

  13. MCU encodes the pore conducting mitochondrial calcium currents.

    Science.gov (United States)

    Chaudhuri, Dipayan; Sancak, Yasemin; Mootha, Vamsi K; Clapham, David E

    2013-06-04

    Mitochondrial calcium (Ca(2+)) import is a well-described phenomenon regulating cell survival and ATP production. Of multiple pathways allowing such entry, the mitochondrial Ca(2+) uniporter is a highly Ca(2+)-selective channel complex encoded by several recently-discovered genes. However, the identity of the pore-forming subunit remains to be established, since knockdown of all the candidate uniporter genes inhibit Ca(2+) uptake in imaging assays, and reconstitution experiments have been equivocal. To definitively identify the channel, we use whole-mitoplast voltage-clamping, the technique that originally established the uniporter as a Ca(2+) channel. We show that RNAi-mediated knockdown of the mitochondrial calcium uniporter (MCU) gene reduces mitochondrial Ca(2+) current (I MiCa ), whereas overexpression increases it. Additionally, a classic feature of I MiCa , its sensitivity to ruthenium red inhibition, can be abolished by a point mutation in the putative pore domain without altering current magnitude. These analyses establish that MCU encodes the pore-forming subunit of the uniporter channel. DOI:http://dx.doi.org/10.7554/eLife.00704.001.

  14. Expression of genes encoding extracellular matrix proteins: a macroarray study.

    Science.gov (United States)

    Futyma, Konrad; Miotła, Paweł; Różyńska, Krystyna; Zdunek, Małgorzata; Semczuk, Andrzej; Rechberger, Tomasz; Wojcierowski, Jacek

    2014-12-01

    Endometrial cancer (EC) is one of the most common gynecological malignancies in Poland, with well-established risk factors. Genetic instability and molecular alterations responsible for endometrial carcinogenesis have been systematically investigated. The aim of the present study was to investigate, by means of cDNA macroarrays, the expression profiles of genes encoding extracellular matrix (ECM) proteins in ECs. Tissue specimens were collected during surgical procedures from 40 patients with EC, and control tissue was collected from 9 patients with uterine leiomyomas. RNA was isolated and RT-PCR with radioisotope-labeled cDNA was performed. The levels of ECM protein gene expression in normal endometrial tissues were compared to the expression of these genes in EC specimens. Statistically significant differences in gene expression, stratified by clinical stage of the ECs, were detected for aggrecan, vitronectin, tenascin R, nidogen and two collagen proteins: type VIII chain α1 and type XI chain α2. All of these proteins were overexpressed in stage III endometrial carcinomas compared to levels in stage I and II uterine neoplasms. In conclusion, increased expression of genes encoding ECM proteins may play an important role in facilitating accelerated disease progression of human ECs.

  15. Infants Encode Phonetic Detail during Cross-Situational Word Learning

    Science.gov (United States)

    Escudero, Paola; Mulak, Karen E.; Vlach, Haley A.

    2016-01-01

    Infants often hear new words in the context of more than one candidate referent. In cross-situational word learning (XSWL), word-object mappings are determined by tracking co-occurrences of words and candidate referents across multiple learning events. Research demonstrates that infants can learn words in XSWL paradigms, suggesting that it is a viable model of real-world word learning. However, these studies have all presented infants with words that have no or minimal phonological overlap (e.g., BLICKET and GAX). Words often contain some degree of phonological overlap, and it is unknown whether infants can simultaneously encode fine phonological detail while learning words via XSWL. We tested 12-, 15-, 17-, and 20-month-olds’ XSWL of eight words that, when paired, formed non-minimal pairs (MPs; e.g., BON–DEET) or MPs (e.g., BON–TON, DEET–DIT). The results demonstrated that infants are able to learn word-object mappings and encode them with sufficient phonetic detail as to identify words in both non-minimal and MP contexts. Thus, this work suggests that infants are able to simultaneously discriminate phonetic differences between words and map words to referents in an implicit learning paradigm such as XSWL. PMID:27708605

  16. Spatial encoding and underlying circuitry in scene-selective cortex.

    Science.gov (United States)

    Nasr, Shahin; Devaney, Kathryn J; Tootell, Roger B H

    2013-12-01

    Three cortical areas (Retro-Splenial Cortex (RSC), Transverse Occipital Sulcus (TOS) and Parahippocampal Place Area (PPA)) respond selectively to scenes. However, their wider role in spatial encoding and their functional connectivity remain unclear. Using fMRI, first we tested the responses of these areas during spatial comparison tasks using dot targets on white noise. Activity increased during task performance in both RSC and TOS, but not in PPA. However, the amplitude of task-driven activity and behavioral measures of task demand were correlated only in RSC. A control experiment showed that none of these areas were activated during a comparable shape comparison task. Secondly, we analyzed functional connectivity of these areas during the resting state. Results revealed a significant connection between RSC and frontal association areas (known to be involved in perceptual decision-making). In contrast, TOS showed functional connections dorsally with the Inferior Parietal Sulcus, and ventrally with the Lateral Occipital Complex--but not with RSC and/or frontal association areas. Moreover, RSC and TOS showed differentiable functional connections with the anterior-medial and posterior-lateral parts of PPA, respectively. These results suggest two parallel pathways for spatial encoding, including RSC and TOS respectively. Only the RSC network was involved in active spatial comparisons.

  17. Fast Fractal Image Encoding Based on Special Image Features

    Institute of Scientific and Technical Information of China (English)

    ZHANG Chao; ZHOU Yiming; ZHANG Zengke

    2007-01-01

    The fractal image encoding method has received much attention for its many advantages over other methods,such as high decoding quality at high compression ratios. However, because every range block must be compared to all domain blocks in the codebook to find the best-matched one during the coding procedure, baseline fractal coding (BFC) is quite time consuming. To speed up fractal coding, a new fast fractal encoding algorithm is proposed. This algorithm aims at reducing the size of the search window during the domain-range matching process to minimize the computational cost. A new theorem presented in this paper shows that a special feature of the image can be used to do this work. Based on this theorem, the most inappropriate domain blocks, whose features are not similar to that of the given range block, are excluded before matching. Thus, the best-matched block can be captured much more quickly than in the BFC approachThe experimental results show that the runtime of the proposed method is reduced greatly compared to the BFC method. At the same time,the new algorithm also achieves high reconstructed image quality. In addition,the method can be incorporated with other fast algorithms to achieve better performance.Therefore, the proposed algorithm has a much better application potential than BFC.

  18. Encoding audio motion: spatial impairment in early blind individuals

    Directory of Open Access Journals (Sweden)

    Sara eFinocchietti

    2015-09-01

    Full Text Available The consequence of blindness on auditory spatial localization has been an interesting issue of research in the last decade providing mixed results. Enhanced auditory spatial skills in individuals with visual impairment have been reported by multiple studies, while some aspects of spatial hearing seem to be impaired in the absence of vision. In this study, the ability to encode the trajectory of a 2 dimensional sound motion, reproducing the complete movement, and reaching the correct end-point sound position, is evaluated in 12 early blind individuals, 8 late blind individuals, and 20 age-matched sighted blindfolded controls. Early blind individuals correctly determine the direction of the sound motion on the horizontal axis, but show a clear deficit in encoding the sound motion in the lower side of the plane. On the contrary, late blind individuals and blindfolded controls perform much better with no deficit in the lower side of the plane. In fact the mean localization error resulted 271 ± 10 mm for early blind individuals, 65 ± 4 mm for late blind individuals, and 68 ± 2 mm for sighted blindfolded controls.These results support the hypothesis that i it exists a trade-off between the development of enhanced perceptual abilities and role of vision in the sound localization abilities of early blind individuals, and ii the visual information is fundamental in calibrating some aspects of the representation of auditory space in the brain.

  19. Functional transcriptomics in the post-ENCODE era.

    Science.gov (United States)

    Mudge, Jonathan M; Frankish, Adam; Harrow, Jennifer

    2013-12-01

    The last decade has seen tremendous effort committed to the annotation of the human genome sequence, most notably perhaps in the form of the ENCODE project. One of the major findings of ENCODE, and other genome analysis projects, is that the human transcriptome is far larger and more complex than previously thought. This complexity manifests, for example, as alternative splicing within protein-coding genes, as well as in the discovery of thousands of long noncoding RNAs. It is also possible that significant numbers of human transcripts have not yet been described by annotation projects, while existing transcript models are frequently incomplete. The question as to what proportion of this complexity is truly functional remains open, however, and this ambiguity presents a serious challenge to genome scientists. In this article, we will discuss the current state of human transcriptome annotation, drawing on our experience gained in generating the GENCODE gene annotation set. We highlight the gaps in our knowledge of transcript functionality that remain, and consider the potential computational and experimental strategies that can be used to help close them. We propose that an understanding of the true overlap between transcriptional complexity and functionality will not be gained in the short term. However, significant steps toward obtaining this knowledge can now be taken by using an integrated strategy, combining all of the experimental resources at our disposal.

  20. Properties of virion transactivator proteins encoded by primate cytomegaloviruses

    Directory of Open Access Journals (Sweden)

    Barry Peter A

    2009-05-01

    Full Text Available Abstract Background Human cytomegalovirus (HCMV is a betaherpesvirus that causes severe disease in situations where the immune system is immature or compromised. HCMV immediate early (IE gene expression is stimulated by the virion phosphoprotein pp71, encoded by open reading frame (ORF UL82, and this transactivation activity is important for the efficient initiation of viral replication. It is currently recognized that pp71 acts to overcome cellular intrinsic defences that otherwise block viral IE gene expression, and that interactions of pp71 with the cell proteins Daxx and ATRX are important for this function. A further property of pp71 is the ability to enable prolonged gene expression from quiescent herpes simplex virus type 1 (HSV-1 genomes. Non-human primate cytomegaloviruses encode homologs of pp71, but there is currently no published information that addresses their effects on gene expression and modes of action. Results The UL82 homolog encoded by simian cytomegalovirus (SCMV, strain Colburn, was identified and cloned. This ORF, named S82, was cloned into an HSV-1 vector, as were those from baboon, rhesus monkey and chimpanzee cytomegaloviruses. The use of an HSV-1 vector enabled expression of the UL82 homologs in a range of cell types, and permitted investigation of their abilities to direct prolonged gene expression from quiescent genomes. The results show that all UL82 homologs activate gene expression, and that neither host cell type nor promoter target sequence has major effects on these activities. Surprisingly, the UL82 proteins specified by non-human primate cytomegaloviruses, unlike pp71, did not direct long term expression from quiescent HSV-1 genomes. In addition, significant differences were observed in the intranuclear localization of the UL82 homologs, and in their effects on Daxx. Strikingly, S82 mediated the release of Daxx from nuclear domain 10 substructures much more rapidly than pp71 or the other proteins tested. All

  1. Encoding of Primary Structures of Biological Macromolecules Within a Data Mining Perspective

    Institute of Scientific and Technical Information of China (English)

    Mondher Maddouri; Mourad Elloumi

    2004-01-01

    An encoding method has a direct effect on the quality and the representation of the discovered knowledge in data mining systems. Biological macromolecules are encoded by strings of characters, called primary structures. Knowing that data mining systems usually use relational tables to encode data, we have then to reencode these strings and transform them into relational tables. In this paper, we do a comparative study of the existing static encoding methods, that are based on the Biologist know-how, and our new dynamic encoding one,that is based on the construction of Discriminant and Minimal Substrings (DMS). Different classification methods are used to do this study. The experimental results show that our dynamic encoding method is more efficient than the static ones, to encode biological macromolecules within a data mining perspective.

  2. Comparing Haar-Hilbert and Log-Gabor Based Iris Encoders on Bath Iris Image Database

    CERN Document Server

    Popescu-Bodorin, Nicolaie; 10.1109/SOFA.2010.5565599

    2011-01-01

    This papers introduces a new family of iris encoders which use 2-dimensional Haar Wavelet Transform for noise attenuation, and Hilbert Transform to encode the iris texture. In order to prove the usefulness of the newly proposed iris encoding approach, the recognition results obtained by using these new encoders are compared to those obtained using the classical Log- Gabor iris encoder. Twelve tests involving single/multienrollment and conducted on Bath Iris Image Database are presented here. One of these tests achieves an Equal Error Rate comparable to the lowest value reported so far for this database. New Matlab tools for iris image processing are also released together with this paper: a second version of the Circular Fuzzy Iris Segmentator (CFIS2), a fast Log-Gabor encoder and two Haar-Hilbert based encoders.

  3. Cloning of cDNA Encoding GRA1 Protein of Tachyzoite Toxoplasma Gondii Local Isolate

    Directory of Open Access Journals (Sweden)

    Erma Sulistyaningsih

    2015-10-01

    Full Text Available Gene encoding GRA1 protein is potent DNA-vaccine candidate against toxoplasmosis. The aim of the researchwas to clone the gene encoding GRA1 protein of tachyzoite Toxoplasma gondii local isolate by DNA recombinanttechnology. Tachyzoite was grown in Balb/c mice in vivo. Messenger RNA was isolated from total RNA and itwas used to synthesis cDNA. Complementary DNA encoding GRA1 protein of tachyzoite Toxoplasma gondii localisolate was amplified and cloned in a prokaryote cloning vector. The recombinant GRA1-encoding gene was thendigesting using EcoRI restriction endonuclease and sequencing. The result showed that the recombinant GRA1-encoding gene consisted of DNA sequences encoding all signal peptide and mature peptide of GRA1 protein.Alignment of recombinant GRA1 sequence to gene encoding GRA1 protein of Toxoplasma gondii RH isolate showed100% homologous.Keywords: GRA1 protein, Toxoplasma gondii, tachyzoite, cloning, cDNA

  4. Information transfer via implicit encoding with delay time modulation in a time-delay system

    Energy Technology Data Exchange (ETDEWEB)

    Kye, Won-Ho, E-mail: whkye@kipo.go.kr [Korean Intellectual Property Office, Government Complex Daejeon Building 4, 189, Cheongsa-ro, Seo-gu, Daejeon 302-701 (Korea, Republic of)

    2012-08-20

    A new encoding scheme for information transfer with modulated delay time in a time-delay system is proposed. In the scheme, the message is implicitly encoded into the modulated delay time. The information transfer rate as a function of encoding redundancy in various noise scales is presented and it is analyzed that the implicit encoding scheme (IES) has stronger resistance against channel noise than the explicit encoding scheme (EES). In addition, its advantages in terms of secure communication and feasible applications are discussed. -- Highlights: ► We propose new encoding scheme with delay time modulation. ► The message is implicitly encoded with modulated delay time. ► The proposed scheme shows stronger resistance against channel noise.

  5. Acquiring, encoding, and re-using clinical knowledge in PRODIGY

    Directory of Open Access Journals (Sweden)

    Richard Hall

    2002-11-01

    Full Text Available The development, implementation and maintenance of computer-executable clinical guidelines encompass a series of complex processes. As they are often performed by more than one organisation, this introduces further complexity. Within the PRODIGY project we attempt to control as many aspects of the process as possible, in order to increase the likelihood of achieving success. To illustrate the complexity of the process and many of the inherent problems and solutions, this paper describes the evolution of the PRODIGY knowledge base, describing the steps from acquiring knowledge, through encoding, to the execution of guidelines, and 'closing the loop' by discussing an approach to knowledge re-use. We will also consider some of the wider implications of our work and propose directions for future research and development activities.

  6. Encoding simplicial quantum geometry in group field theories

    Energy Technology Data Exchange (ETDEWEB)

    Oriti, D [Max Planck Institute for Gravitational Physics (Albert Einstein Institute), Am Muehlenberg 1, D-14476 Golm (Germany); Tlas, T, E-mail: daniele.oriti@aei.mpg.d, E-mail: tamer.tlas@aub.edu.l [Department of Mathematics, American Univeristy of Beirut, Bliss Street, Beirut, PO Box 11-0236 (Lebanon)

    2010-07-07

    An extended group field theory formalism for quantum gravity, based on a field that is a function of both group variables, interpreted as discretized connection, and Lie algebra variables, interpreted as discretized triads, has been proposed recently as an attempt to define models with a clearer link with simplicial geometry. In the context of such a formalism, we introduce a new symmetry requirement on the field. This leads, in 3D, to Feynman amplitudes interpreted as simplicial path integrals based on the Regge action, to a proper relation between the discrete connection and the triad vectors appearing in the Regge action, and to a much more satisfactory and transparent encoding of simplicial geometry already at the level of the group field theory action.

  7. Abstract algebra, projective geometry and time encoding of quantum information

    CERN Document Server

    Planat, M R P; Planat, Michel R. P.; Saniga, Metod

    2005-01-01

    Algebraic geometrical concepts are playing an increasing role in quantum applications such as coding, cryptography, tomography and computing. We point out here the prominent role played by Galois fields viewed as cyclotomic extensions of the integers modulo a prime characteristic $p$. They can be used to generate efficient cyclic encoding, for transmitting secrete quantum keys, for quantum state recovery and for error correction in quantum computing. Finite projective planes and their generalization are the geometric counterpart to cyclotomic concepts, their coordinatization involves Galois fields, and they have been used repetitively for enciphering and coding. Finally the characters over Galois fields are fundamental for generating complete sets of mutually unbiased bases, a generic concept of quantum information processing and quantum entanglement. Gauss sums over Galois fields ensure minimum uncertainty under such protocols. Some Galois rings which are cyclotomic extensions of the integers modulo 4 are al...

  8. Coherent ultrafast measurement of time-bin encoded photons

    CERN Document Server

    Donohue, John M; Lavoie, Jonathan; Resch, Kevin J

    2013-01-01

    Time-bin encoding is a robust form of optical quantum information, especially for transmission in optical fibers. To read out the information, the separation of the time bins must be larger than the detector time resolution, typically on the order of nanoseconds for photon counters. In the present work, we demonstrate a technique using a nonlinear interaction between chirped entangled time-bin photons and shaped laser pulses to perform projective measurements on arbitrary time-bin states with picosecond-scale separations. We demonstrate a tomographically-complete set of time-bin qubit projective measurements and show the fidelity of operations is sufficiently high to violate the CHSH-Bell inequality by more than 6 standard deviations.

  9. Small targeted cytotoxics from DNA-encoded chemical libraries.

    Science.gov (United States)

    Samain, Florent; Casi, Giulio

    2015-06-01

    Conventional chemotherapeutic drugs do not selectively localize to tumors, causing undesired toxicities to healthy organs, and precluding the escalation to therapeutically active regimens. The selective delivery at sites of disease of potent effector molecules represents a promising strategy for the treatment of cancer and other diseases. High affinity antibodies towards disease-associated antigens are currently the vehicles of choice for the targeted delivery of payloads. Low molecular weight ligands have the potential to overcome some of the intrinsic limitations associated with antibodies, and have recently been proposed for the development of a novel class of targeted therapeutics. However, the identification of binding molecules, which display high affinity properties and exquisite specificity against protein of therapeutic interest, remains a great challenge. DNA-encoded chemical library technology relies on small molecule libraries of unprecedented size to identify high affinity ligands towards specific target proteins, and could help in the development of next generation targeted cytotoxics.

  10. XOR-FREE Implementation of Convolutional Encoder for Reconfigurable Hardware

    Directory of Open Access Journals (Sweden)

    Gaurav Purohit

    2016-01-01

    Full Text Available This paper presents a novel XOR-FREE algorithm to implement the convolutional encoder using reconfigurable hardware. The approach completely removes the XOR processing of a chosen nonsystematic, feedforward generator polynomial of larger constraint length. The hardware (HW implementation of new architecture uses Lookup Table (LUT for storing the parity bits. The design implements architectural reconfigurability by modifying the generator polynomial of the same constraint length and code rate to reduce the design complexity. The proposed architecture reduces the dynamic power up to 30% and improves the hardware cost and propagation delay up to 20% and 32%, respectively. The performance of the proposed architecture is validated in MATLAB Simulink and tested on Zynq-7 series FPGA.

  11. Ipsilateral directional encoding of joystick movements in human cortex.

    Science.gov (United States)

    Sharma, Mohit; Gaona, Charles; Roland, Jarod; Anderson, Nick; Freudenberg, Zachary; Leuthardt, Eric C

    2009-01-01

    The majority of Brain Computer Interfaces have relied on signals related to primary motor cortex and the operation of the contralateral limb. Recently, the physiology associated with same-sided (ipsilateral) motor movements has been found to have a unique cortical physiology. This study sets out to assess whether more complex motor movements can be discerned utilizing ipsilateral cortical signals. In this study, three invasively monitored human subjects were recorded while performing a center out joystick task with the hand ipsilateral to the hemispheric subdural grid array. It was found that directional tuning was present in ipsilateral cortex. This information was encoded in both distinct anatomic populations and spectral distributions. These findings support the notion that ipsilateral signals may provide added information for BCI operation in the future.

  12. Rapid Automatic Motor Encoding of Competing Reach Options

    Directory of Open Access Journals (Sweden)

    Jason P. Gallivan

    2017-02-01

    Full Text Available Mounting neural evidence suggests that, in situations in which there are multiple potential targets for action, the brain prepares, in parallel, competing movements associated with these targets, prior to implementing one of them. Central to this interpretation is the idea that competing viewed targets, prior to selection, are rapidly and automatically transformed into corresponding motor representations. Here, by applying target-specific, gradual visuomotor rotations and dissociating, unbeknownst to participants, the visual direction of potential targets from the direction of the movements required to reach the same targets, we provide direct evidence for this provocative idea. Our results offer strong empirical support for theories suggesting that competing action options are automatically represented in terms of the movements required to attain them. The rapid motor encoding of potential targets may support the fast optimization of motor costs under conditions of target uncertainty and allow the motor system to inform decisions about target selection.

  13. Encoding nondeterministic fuzzy tree automata into recursive neural networks.

    Science.gov (United States)

    Gori, Marco; Petrosino, Alfredo

    2004-11-01

    Fuzzy neural systems have been a subject of great interest in the last few years, due to their abilities to facilitate the exchange of information between symbolic and subsymbolic domains. However, the models in the literature are not able to deal with structured organization of information, that is typically required by symbolic processing. In many application domains, the patterns are not only structured, but a fuzziness degree is attached to each subsymbolic pattern primitive. The purpose of this paper is to show how recursive neural networks, properly conceived for dealing with structured information, can represent nondeterministic fuzzy frontier-to-root tree automata. Whereas available prior knowledge expressed in terms of fuzzy state transition rules are injected into a recursive network, unknown rules are supposed to be filled in by data-driven learning. We also prove the stability of the encoding algorithm, extending previous results on the injection of fuzzy finite-state dynamics in high-order recurrent networks.

  14. Generating All Partitions: A Comparison Of Two Encodings

    CERN Document Server

    Kelleher, Jerome

    2009-01-01

    Integer partitions may be encoded as either ascending or descending compositions for the purposes of systematic generation. Many algorithms exist to generate all descending compositions, yet none have previously been published to generate all ascending compositions. We develop three new algorithms to generate all ascending compositions and compare these with descending composition generators from the literature. We analyse the new algorithms and provide new and more precise analyses for the descending composition generators. In each case, the ascending composition generation algorithm is substantially more efficient than its descending composition counterpart. We develop a new formula for the partition function p(n) as part of our analysis of the lexicographic succession rule for ascending compositions.

  15. Natural biased coin encoded in the genome determines cell strategy.

    Science.gov (United States)

    Dorri, Faezeh; Mahini, Hamid; Sharifi-Zarchi, Ali; Totonchi, Mehdi; Tusserkani, Ruzbeh; Pezeshk, Hamid; Sadeghi, Mehdi

    2014-01-01

    Decision making at a cellular level determines different fates for isogenic cells. However, it is not yet clear how rational decisions are encoded in the genome, how they are transmitted to their offspring, and whether they evolve and become optimized throughout generations. In this paper, we use a game theoretic approach to explain how rational decisions are made in the presence of cooperators and competitors. Our results suggest the existence of an internal switch that operates as a biased coin. The biased coin is, in fact, a biochemical bistable network of interacting genes that can flip to one of its stable states in response to different environmental stimuli. We present a framework to describe how the positions of attractors in such a gene regulatory network correspond to the behavior of a rational player in a competing environment. We evaluate our model by considering lysis/lysogeny decision making of bacteriophage lambda in E. coli.

  16. Natural biased coin encoded in the genome determines cell strategy.

    Directory of Open Access Journals (Sweden)

    Faezeh Dorri

    Full Text Available Decision making at a cellular level determines different fates for isogenic cells. However, it is not yet clear how rational decisions are encoded in the genome, how they are transmitted to their offspring, and whether they evolve and become optimized throughout generations. In this paper, we use a game theoretic approach to explain how rational decisions are made in the presence of cooperators and competitors. Our results suggest the existence of an internal switch that operates as a biased coin. The biased coin is, in fact, a biochemical bistable network of interacting genes that can flip to one of its stable states in response to different environmental stimuli. We present a framework to describe how the positions of attractors in such a gene regulatory network correspond to the behavior of a rational player in a competing environment. We evaluate our model by considering lysis/lysogeny decision making of bacteriophage lambda in E. coli.

  17. Identification of chromatin marks at TERRA promoter and encoding region.

    Science.gov (United States)

    Negishi, Yutaka; Kawaji, Hideya; Minoda, Aki; Usui, Kengo

    2015-11-27

    TERRA is a long non-coding RNA that is essential for telomere integrity. Although it is transcribed from subtelomeres and telomeres, how it is expressed in heterochromatic region is currently unknown. In this study, we focused our analysis on TERRA-encoding region TelBam3.4 and TelBam3.4-like sequences, and determined their transcription start sites, as well as enrichment of RNA polymerase II and histone modifications. We found that H3K4me3 and H3K9me3 are present at TERRA promoters, whereas H3K27ac and H3K9me3 are present at telomeric repeats. Consistently, we show that presence of active histone modifications H3K4me3 and H3K27ac are correlated to TERRA expression. These results mark an important step towards understanding telomere maintenance and transcription.

  18. Sparse encoding of automatic visual association in hippocampal networks

    DEFF Research Database (Denmark)

    Hulme, Oliver J; Skov, Martin; Chadwick, Martin J

    2014-01-01

    Intelligent action entails exploiting predictions about associations between elements of ones environment. The hippocampus and mediotemporal cortex are endowed with the network topology, physiology, and neurochemistry to automatically and sparsely code sensori-cognitive associations that can...... by these stimuli. Using multivariate Bayesian decoding, we show that human hippocampal and temporal neocortical structures host sparse associative representations that are automatically triggered by visual input. Furthermore, as predicted theoretically, there was a significant increase in sparsity in the Cornu...... Ammonis subfields, relative to the entorhinal cortex. Remarkably, the sparsity of CA encoding correlated significantly with associative memory performance over subjects; elsewhere within the temporal lobe, entorhinal, parahippocampal, perirhinal and fusiform cortices showed the highest model evidence...

  19. Universal quantum computation using all-optical hybrid encoding

    Institute of Scientific and Technical Information of China (English)

    郭奇; 程留永; 王洪福; 张寿

    2015-01-01

    By employing displacement operations, single-photon subtractions, and weak cross-Kerr nonlinearity, we propose an alternative way of implementing several universal quantum logical gates for all-optical hybrid qubits encoded in both single-photon polarization state and coherent state. Since these schemes can be straightforwardly implemented only using local operations without teleportation procedure, therefore, less physical resources and simpler operations are required than the existing schemes. With the help of displacement operations, a large phase shift of the coherent state can be obtained via currently available tiny cross-Kerr nonlinearity. Thus, all of these schemes are nearly deterministic and feasible under current technology conditions, which makes them suitable for large-scale quantum computing.

  20. Dopamine encoding of Pavlovian incentive stimuli diminishes with extended training.

    Science.gov (United States)

    Clark, Jeremy J; Collins, Anne L; Sanford, Christina Akers; Phillips, Paul E M

    2013-02-20

    Dopamine is highly implicated both as a teaching signal in reinforcement learning and in motivating actions to obtain rewards. However, theoretical disconnects remain between the temporal encoding properties of dopamine neurons and the behavioral consequences of its release. Here, we demonstrate in rats that dopamine evoked by Pavlovian cues increases during acquisition, but dissociates from stable conditioned appetitive behavior as this signal returns to preconditioning levels with extended training. Experimental manipulation of the statistical parameters of the behavioral paradigm revealed that this attenuation of cue-evoked dopamine release during the postasymptotic period was attributable to acquired knowledge of the temporal structure of the task. In parallel, conditioned behavior became less dopamine dependent after extended training. Thus, the current work demonstrates that as the presentation of reward-predictive stimuli becomes anticipated through the acquisition of task information, there is a shift in the neurobiological substrates that mediate the motivational properties of these incentive stimuli.

  1. Virus-Encoded microRNAs: Future Therapeutic Targets?

    Institute of Scientific and Technical Information of China (English)

    Peng Qi; Jinxiang Han; Yanqin Lu; Chuanxi Wang; Fanfeng Bu

    2006-01-01

    The discovery of microRNAs (miRNAs) is a remarkable breakthrough in the field of molecular genetics, as miRNAs are key actors which regulate gene expression in diverse cellular processes from unicellular yeast to human. The recent discovery of virus-encoded miRNAs indicates that viruses also use this fundamental mode of gene regulation. Research into viral miRNAs function demonstrates that some miRNAs play an important role in regulating both the viral life cycle and the interaction between viruses and their hosts. The first in vivo "antagomir" study provides an exciting first step towards miRNA therapy, and the potential for ultimately designing molecular medicines based on the modulation of miRNAs seems good.

  2. Late positive slow waves as markers of chunking during encoding

    Science.gov (United States)

    Nogueira, Ana M. L.; Bueno, Orlando F. A.; Manzano, Gilberto M.; Kohn, André F.; Pompéia, Sabine

    2015-01-01

    Electrophysiological markers of chunking of words during encoding have mostly been shown in studies that present pairs of related stimuli. In these cases it is difficult to disentangle cognitive processes that reflect distinctiveness (i.e., conspicuous items because they are related), perceived association between related items and unified representations of various items, or chunking. Here, we propose a paradigm that enables the determination of a separate Event-related Potential (ERP) marker of these cognitive processes using sequentially related word triads. Twenty-three young healthy individuals viewed 80 15-word lists composed of unrelated items except for the three words in the middle serial positions (triads), which could be either unrelated (control list), related perceptually, phonetically or semantically. ERP amplitudes were measured at encoding of each one of the words in the triads. We analyzed two latency intervals (350–400 and 400–800 ms) at midline locations. Behaviorally, we observed a progressive facilitation in the immediate free recall of the words in the triads depending on the relations between their items (control < perceptual < phonetic < semantic), but only semantically related items were recalled as chunks. P300-like deflections were observed for perceptually deviant stimuli. A reduction of amplitude of a component akin to the N400 was found for words that were phonetically and semantically associated with prior items and therefore were not associated to chunking. Positive slow wave (PSW) amplitudes increased as successive phonetically and semantically related items were presented, but they were observed earlier and were more prominent at Fz for semantic associates. PSWs at Fz and Cz also correlated with recall of semantic word chunks. This confirms prior claims that PSWs at Fz are potential markers of chunking which, in the proposed paradigm, were modulated differently from the detection of deviant stimuli and of relations between

  3. Time encoded multicolor fluorescence detection in a microfluidic flow cytometer.

    Science.gov (United States)

    Martini, Joerg; Recht, Michael I; Huck, Malte; Bern, Marshall W; Johnson, Noble M; Kiesel, Peter

    2012-12-07

    We describe an optical detection technique that delivers high signal-to-noise discrimination to enable a multi-parameter flow cytometer that combines high performance, robustness, compactness and low cost. The enabling technique is termed "spatially modulated detection" and generates a time-dependent signal as a continuously fluorescing (bio-) particle traverses an optical transmission pattern along the fluidic channel. Correlating the detected signal with the expected transmission pattern achieves high discrimination of the particle signal from background noise. Additionally, the particle speed and its fluorescence emission characteristics are deduced from the correlation analysis. Our method uses a large excitation/emission volume along the fluidic channel in order to increase the total flux of fluorescence light that originates from a particle while requiring minimal optical alignment. Despite the large excitation/detection volume, the mask pattern enables a high spatial resolution in the micron range. This allows for detection and characterization of particles with a separation (in flow direction) comparable to the dimension of individual particles. In addition, the concept is intrinsically tolerant of non-encoded background fluorescence originating from fluorescent components in solution, fluorescing components of the chamber and contaminants on its surface. The optical detection technique is illustrated with experimental results of multicolor detection with a single large area detector by filtering fluorescence emission of different particles through a patterned color mask. Thereby the particles' fluorescence emission spectrum is encoded in a time dependent intensity signal and color information can be extracted from the correlation analysis. The multicolor detection technique is demonstrated by differentiation of micro-beads loaded with PE (Phycoerythrin) and PE-Cy5 that are excited at 532 nm.

  4. Bubble masks for time-encoded imaging of fast neutrons.

    Energy Technology Data Exchange (ETDEWEB)

    Brubaker, Erik; Brennan, James S.; Marleau, Peter; Nowack, Aaron B.; Steele, John T.; Sweany, Melinda; Throckmorton, Daniel J.

    2013-09-01

    Time-encoded imaging is an approach to directional radiation detection that is being developed at SNL with a focus on fast neutron directional detection. In this technique, a time modulation of a detected neutron signal is inducedtypically, a moving mask that attenuates neutrons with a time structure that depends on the source position. An important challenge in time-encoded imaging is to develop high-resolution two-dimensional imaging capabilities; building a mechanically moving high-resolution mask presents challenges both theoretical and technical. We have investigated an alternative to mechanical masks that replaces the solid mask with a liquid such as mineral oil. Instead of fixed blocks of solid material that move in pre-defined patterns, the oil is contained in tubing structures, and carefully introduced air gapsbubblespropagate through the tubing, generating moving patterns of oil mask elements and air apertures. Compared to current moving-mask techniques, the bubble mask is simple, since mechanical motion is replaced by gravity-driven bubble propagation; it is flexible, since arbitrary bubble patterns can be generated by a software-controlled valve actuator; and it is potentially high performance, since the tubing and bubble size can be tuned for high-resolution imaging requirements. We have built and tested various single-tube mask elements, and will present results on bubble introduction and propagation as a function of tubing size and cross-sectional shape; real-time bubble position tracking; neutron source imaging tests; and reconstruction techniques demonstrated on simple test data as well as a simulated full detector system.

  5. Encoded expansion: an efficient algorithm to discover identical string motifs.

    Directory of Open Access Journals (Sweden)

    Aqil M Azmi

    Full Text Available A major task in computational biology is the discovery of short recurring string patterns known as motifs. Most of the schemes to discover motifs are either stochastic or combinatorial in nature. Stochastic approaches do not guarantee finding the correct motifs, while the combinatorial schemes tend to have an exponential time complexity with respect to motif length. To alleviate the cost, the combinatorial approach exploits dynamic data structures such as trees or graphs. Recently (Karci (2009 Efficient automatic exact motif discovery algorithms for biological sequences, Expert Systems with Applications 36:7952-7963 devised a deterministic algorithm that finds all the identical copies of string motifs of all sizes [Formula: see text] in theoretical time complexity of [Formula: see text] and a space complexity of [Formula: see text] where [Formula: see text] is the length of the input sequence and [Formula: see text] is the length of the longest possible string motif. In this paper, we present a significant improvement on Karci's original algorithm. The algorithm that we propose reports all identical string motifs of sizes [Formula: see text] that occur at least [Formula: see text] times. Our algorithm starts with string motifs of size 2, and at each iteration it expands the candidate string motifs by one symbol throwing out those that occur less than [Formula: see text] times in the entire input sequence. We use a simple array and data encoding to achieve theoretical worst-case time complexity of [Formula: see text] and a space complexity of [Formula: see text] Encoding of the substrings can speed up the process of comparison between string motifs. Experimental results on random and real biological sequences confirm that our algorithm has indeed a linear time complexity and it is more scalable in terms of sequence length than the existing algorithms.

  6. Bacteriophage-encoded shiga toxin gene in atypical bacterial host

    Directory of Open Access Journals (Sweden)

    Casas Veronica

    2011-07-01

    Full Text Available Abstract Background Contamination from fecal bacteria in recreational waters is a major health concern since bacteria capable of causing human disease can be found in animal feces. The Dog Beach area of Ocean Beach in San Diego, California is a beach prone to closures due to high levels of fecal indicator bacteria (FIB. A potential source of these FIB could be the canine feces left behind by owners who do not clean up after their pets. We tested this hypothesis by screening the DNA isolated from canine feces for the bacteriophage-encoded stx gene normally found in the virulent strains of the fecal bacterium Escherichia coli. Results Twenty canine fecal samples were collected, processed for total and bacterial fraction DNA, and screened by PCR for the stx gene. The stx gene was detected in the total and bacterial fraction DNA of one fecal sample. Bacterial isolates were then cultivated from the stx-positive fecal sample. Eighty nine of these canine fecal bacterial isolates were screened by PCR for the stx gene. The stx gene was detected in five of these isolates. Sequencing and phylogenetic analyses of 16S rRNA gene PCR products from the canine fecal bacterial isolates indicated that they were Enterococcus and not E. coli. Conclusions The bacteriophage-encoded stx gene was found in multiple species of bacteria cultivated from canine fecal samples gathered at the shoreline of the Dog Beach area of Ocean Beach in San Diego, California. The canine fecal bacteria carrying the stx gene were not the typical E. coli host and were instead identified through phylogenetic analyses as Enterococcus. This suggests a large degree of horizontal gene transfer of exotoxin genes in recreational waters.

  7. Identification of β-haemolysin-encoding genes in Streptococcus anginosus.

    Science.gov (United States)

    Asam, D; Mauerer, S; Walheim, E; Spellerberg, B

    2013-08-01

    Streptococcus anginosus is an emerging pathogen, but little is known about its virulence factors. To detect the genes responsible for β-haemolysis we performed genomic mutagenesis of the β-haemolytic S. anginosus type strain ATCC 12395 using the vector pGhost9:ISS1. Integration site analysis of 15 non-haemolytic mutants identified a gene cluster with high homology to the genes of the streptolysin S (SLS) encoding sag gene cluster of S. pyogenes. The gene cluster harbours 10 open reading frames displaying significant similarities to the S. pyogenes genes sagA-sagI, with the identities on protein level ranging from 38 to 87%. Complementation assays of S. anginosus sagB and sagD integration mutants with the respective genes confirmed their importance for β-haemolysin production and suggest the presence of post-translational modifications in S. anginosus SLS similar to SLS of S. pyogenes. Characterization of the S. anginosus haemolysin in comparison to the S. pyogenes SLS showed that the haemolysin is surface bound, but in contrast to S. pyogenes neither fetal calf serum nor RNA was able to stabilize the haemolysin of S. anginosus in culture supernatants. Inhibition of β-haemolysis by polyethylene glycol of different sizes was carried out, giving no evidence of a pore-forming haemolytic mechanism. Analysis of a whole genome shotgun sequence of Streptococcus constellatus, a closely related streptococcal species that belongs to the S. anginosus group, revealed a similar sag gene cluster. Employing a genomic mutagenesis strategy we were able to determine an SLS encoding gene cluster in S. anginosus and demonstrate its importance for β-haemolysin production in S. anginosus.

  8. Applicability and efficiency of near-optimal spatial encoding for dynamically adaptive MRI.

    Science.gov (United States)

    Zientara, G P; Panych, L P; Jolesz, F A

    1998-02-01

    Adaptive near-optimal MRI spatial encoding entails, for the acquisition of each image update in a dynamic series, the computation of encodes in the form of a linear algebra-derived orthogonal basis set determined from an image estimate. The origins of adaptive encoding relevant to MRI are reviewed. Sources of error of this approach are identified from the linear algebraic perspective where MRI data acquisition is viewed as the projection of information from the field-of-view onto the encoding basis set. The definitions of ideal and non-ideal encoding follow, with nonideal encoding characterized by the principal angles between two vector spaces. An analysis of the distribution of principal angles is introduced and applied in several example cases to quantitatively describe the suitability of a basis set derived from a specific image estimate for the spatial encoding of a given field-of-view. The robustness of adaptive near-optimal spatial encoding for dynamic MRI is favorably shown by results computed using singular value decomposition encoding that simulates specific instances of worst case data acquisition when all objects have changed or new objects have appeared in the field-of-view. The mathematical analysis and simulations presented clarify the applicability and efficiency of adaptively determined near-optimal spatial encoding throughout a range of circumstances as may typically occur during use of dynamic MRI.

  9. Does long-term object priming depend on the explicit detection of object identity at encoding?

    Science.gov (United States)

    Gomes, Carlos A; Mayes, Andrew

    2015-01-01

    It is currently unclear whether objects have to be explicitly identified at encoding for reliable behavioral long-term object priming to occur. We conducted two experiments that investigated long-term object and non-object priming using a selective-attention encoding manipulation that reduces explicit object identification. In Experiment 1, participants either counted dots flashed within an object picture (shallow encoding) or engaged in an animacy task (deep encoding) at study, whereas, at test, they performed an object-decision task. Priming, as measured by reaction times (RTs), was observed for both types of encoding, and was of equivalent magnitude. In Experiment 2, non-object priming (faster RTs for studied relative to unstudied non-objects) was also obtained under the same selective-attention encoding manipulation as in Experiment 1, and the magnitude of the priming effect was equivalent between experiments. In contrast, we observed a linear decrement in recognition memory accuracy across conditions (deep encoding of Experiment 1 > shallow encoding Experiment 1 > shallow encoding of Experiment 2), suggesting that priming was not contaminated by explicit memory strategies. We argue that our results are more consistent with the identification/production framework than the perceptual/conceptual distinction, and we conclude that priming of pictures largely ignored at encoding can be subserved by the automatic retrieval of two types of instances: one at the motor level and another at an object-decision level.

  10. O-space imaging: Highly efficient parallel imaging using second-order nonlinear fields as encoding gradients with no phase encoding.

    Science.gov (United States)

    Stockmann, Jason P; Ciris, Pelin Aksit; Galiana, Gigi; Tam, Leo; Constable, R Todd

    2010-08-01

    Recent improvements in parallel imaging have been driven by the use of greater numbers of independent surface coils placed so as to minimize aliasing along the phase-encode direction(s). However, gains from increasing the number of coils diminish as coil coupling problems begin to dominate and the ratio of acceleration gain to expense for multiple receiver chains becomes prohibitive. In this work, we redesign the spatial-encoding strategy in order to gain efficiency, achieving a gradient encoding scheme that is complementary to the spatial encoding provided by the receiver coils. This approach leads to "O-space" imaging, wherein the gradient shapes are tailored to an existing surface coil array, making more efficient use of the spatial information contained in the coil profiles. In its simplest form, for each acquired echo the Z2 spherical harmonic is used to project the object onto sets of concentric rings, while the X and Y gradients are used to offset this projection within the imaging plane. The theory is presented, an algorithm is introduced for image reconstruction, and simulations reveal that O-space encoding achieves high encoding efficiency compared to sensitivity encoding (SENSE) radial k-space trajectories, and parallel imaging technique with localized gradients (PatLoc), suggesting that O-space imaging holds great potential for accelerated scanning.

  11. Rejection-free stochastic simulation of BNGL-encoded models

    Energy Technology Data Exchange (ETDEWEB)

    Hlavacek, William S [Los Alamos National Laboratory; Monine, Michael I [Los Alamos National Laboratory; Colvin, Joshua [TRANSLATIONAL GENOM; Posner, Richard G [NORTHERN ARIZONA UNIV.; Von Hoff, Daniel D [TRANSLATIONAL GENOMICS RESEARCH INSTIT.

    2009-01-01

    Formal rules encoded using the BioNetGen language (BNGL) can be used to represent the system-level dynamics of molecular interactions. Rules allow one to compactly and implicitly specify the reaction network implied by a set of molecules and their interactions. Typically, the reaction network implied by a set of rules is large, which makes generation of the underlying rule-defined network expensive. Moreover, the cost of conventional simulation methods typically depends on network size. Together these factors have limited application of the rule-based modeling approach. To overcome this limitation, several methods have recently been developed for determining the reaction dynamics implied by rules while avoiding the expensive step of network generation. The cost of these 'network-free' simulation methods is independent of the number of reactions implied by rules. Software implementing such methods is needed for the analysis of rule-based models of biochemical systems. Here, we present a software tool called RuleMonkey that implements a network-free stochastic simulation method for rule-based models. The method is rejection free, unlike other network-free methods that introduce null events (i.e., steps in the simulation procedure that do not change the state of the reaction system being simulated), and the software is capable of simulating models encoded in BNGL, a general-purpose model-specification language. We verify that RuleMonkey produces correct simulation results, and we compare its performance against DYNSTOC, another BNGL-compliant general-purpose simulator for rule-based models, as well as various problem-specific codes that implement network-free simulation methods. RuleMonkey enables the simulation of models defined by rule sets that imply large-scale reaction networks. It is faster than DYNSTOC for stiff problems, although it requires the use of more computer memory. RuleMonkey is freely available for non-commercial use as a stand

  12. Cloning of Mouse Enamel Matrix Serine Proteinase Encoding Mature Protein

    Institute of Scientific and Technical Information of China (English)

    MU Ya-bing; SUN Hong-chen; ZHANG Ze-bing; OUYANG Jie

    2003-01-01

    Objective: To clone cDNA of enamel matrix serine proteinase (EMSP1) encoding mature protein from mouse dental germs. Methods: Total RNA was isolated from developing incisors and molars of 7 days mouse pups and reverse-transcribed into cDNA. Two pairs of specific primers was designed to obtain the desired gene by Touchdown PCR and Nested PCR. The segment was inserted into Vector pMD-18T, and recombined vectors was transformed into E.coli JM109.The positive clone was chose and analysed by restriction endonuclease mapping and DNA sequencing. Results:700 bp of cDNA of mouse EMSP1 was sueccessfully cloned from mouse tooth germs tissue. The sequence was consistent with that displayed in PubMed. Conclusion:The mouse EMSP1 cDNA encoding mature protein is obtained for further study.%目的:克隆小鼠牙胚组织中釉基质丝氨酸蛋白酶(EMSP1)成熟肽编码区基因.方法:提取出生后7 d昆明种小白鼠切牙、磨牙牙胚总RNA,逆转录为cDNA,设计两对特异性引物,采用Touchdown PCR 和嵌套PCR方法,扩增出小鼠EMSP1起始密码子至终止密码子基因片段.将目的基因连入载体pMD-18T,转化入大肠杆菌JM109,通过蓝白筛选,挑选阳性克隆培养扩增,纯化重组质粒进行限制性酶切和核苷酸序列分析鉴定.结果:限制性酶切图谱和核苷酸序列分析均表明所克隆cDNA为小鼠700 bp的EMSP1成熟肽基因编码.结论:成功地克隆了小鼠编码EMSP1成熟肽基因片段.

  13. Fixed-complexity Sphere Encoder for Multi-user MIMO Systems

    CERN Document Server

    Mohaisen, Manar

    2011-01-01

    In this paper, we propose a fixed-complexity sphere encoder (FSE) for multi-user MIMO (MU-MIMO) systems. The proposed FSE accomplishes a scalable tradeoff between performance and complexity. Also, because it has a parallel tree-search structure, the proposed encoder can be easily pipelined, leading to a tremendous reduction in the precoding latency. The complexity of the proposed encoder is also analyzed, and we propose two techniques that reduce it. Simulation and analytical results demonstrate that in a 4 by 4 MU-MIMO system, the proposed FSE requires only 11.5% of the computational complexity needed by the conventional QRD-M encoder (QRDM-E). Also, the encoding throughput of the proposed encoder is 7.5 times that of the QRDM-E with tolerable degradation in the BER performance, while achieving the optimum diversity order.

  14. Minimal memory requirements for pearl necklace encoders of quantum convolutional codes

    CERN Document Server

    Houshmand, Monireh; Wilde, Mark M

    2010-01-01

    One of the major goals in quantum computer science is to reduce the overhead associated with the implementation of quantum computers, and inevitably, routines for quantum error correction will account for most of this overhead. A particular technique for quantum error correction that may be useful in the outer layers of a concatenated scheme for fault tolerance is quantum convolutional coding. The encoder for a quantum convolutional code has a representation as a convolutional encoder or as a "pearl necklace" encoder. In the pearl necklace representation, it has not been particularly clear in the research literature how much quantum memory such an encoder would require for implementation. Here, we offer an algorithm that answers this question. The algorithm first constructs a weighted, directed acyclic graph where each vertex of the graph corresponds to a gate string in the pearl necklace encoder, and each path through the graph represents a non-commutative path through gates in the encoder. We show that the ...

  15. The prevalence of encoded digital trace evidence in the nonfile space of computer media(,) (.).

    Science.gov (United States)

    Garfinkel, Simson L

    2014-09-01

    Forensically significant digital trace evidence that is frequently present in sectors of digital media not associated with allocated or deleted files. Modern digital forensic tools generally do not decompress such data unless a specific file with a recognized file type is first identified, potentially resulting in missed evidence. Email addresses are encoded differently for different file formats. As a result, trace evidence can be categorized as Plain in File (PF), Encoded in File (EF), Plain Not in File (PNF), or Encoded Not in File (ENF). The tool bulk_extractor finds all of these formats, but other forensic tools do not. A study of 961 storage devices purchased on the secondary market and shows that 474 contained encoded email addresses that were not in files (ENF). Different encoding formats are the result of different application programs that processed different kinds of digital trace evidence. Specific encoding formats explored include BASE64, GZIP, PDF, HIBER, and ZIP.

  16. On the absolute encoders%论绝对编码器

    Institute of Scientific and Technical Information of China (English)

    龚仲华

    2011-01-01

    This article illustrates the features of incremental encoder, resolver, absolute-value encoder, absolute encoder, grating encoder and magnetic grid encoder used on CNC machine tools, and their differences are explained as well, then points out the essence of the absolute rotary encoder and introduces the output method and interface for absolute positions.%说明了数控机床所使用的增量编码器、旋转变压器、绝对值编码器、绝对编码器以及光栅编码器与磁栅编码器的特点与区别,指出了绝对编码器的本质,介绍了绝对位置输出的方式与接口。

  17. On the Properties of Neural Machine Translation: Encoder-Decoder Approaches

    OpenAIRE

    Cho, Kyunghyun; van Merrienboer, Bart; Bahdanau, Dzmitry; Bengio, Yoshua

    2014-01-01

    Neural machine translation is a relatively new approach to statistical machine translation based purely on neural networks. The neural machine translation models often consist of an encoder and a decoder. The encoder extracts a fixed-length representation from a variable-length input sentence, and the decoder generates a correct translation from this representation. In this paper, we focus on analyzing the properties of the neural machine translation using two models; RNN Encoder--Decoder and...

  18. Dual beam encoded extended fractional Fourier transform security hologram with in-built repositioning

    Indian Academy of Sciences (India)

    Amit K Sharma; D P Chhachhia; D Mohan; A K Aggarwal

    2008-01-01

    This paper describes a simple method for making dual beam encoded extended fractional Fourier transform (EFRT) security holograms. The hologram possesses different stages of encoding so that security features are concealed and remain invisible to the counterfeiter. These concealed and encoded anticounterfeit security features in the security hologram can only be read through a key hologram. Key hologram also facilitates in-built repositioning of security hologram. The method of fabrication, the principle of reconstruction and the experimental results are presented.

  19. Structure and function of the DNA ligases encoded by the mammalian LIG3 gene

    OpenAIRE

    Tomkinson, Alan E.; Sallmyr, Annahita

    2013-01-01

    Among the mammalian genes encoding DNA ligases (LIG), the LIG3 gene is unique in that it encodes multiple DNA ligase polypeptides with different cellular functions. Notably, this nuclear gene encodes the only mitochondrial DNA ligase and so is essential for this organelle. In the nucleus, there is significant functional redundancy between DNA ligase IIIα and DNA ligase I in excision repair. In addition, DNA ligase IIIα is essential for DNA replication in the absence of the replicative DNA lig...

  20. Results from laboratory tests of the two-dimensional Time-Encoded Imaging System.

    Energy Technology Data Exchange (ETDEWEB)

    Marleau, Peter; Brennan, James S.; Brubaker, Erik; Gerling, Mark D; Le Galloudec, Nathalie Joelle

    2014-09-01

    A series of laboratory experiments were undertaken to demonstrate the feasibility of two dimensional time-encoded imaging. A prototype two-dimensional time encoded imaging system was designed and constructed. Results from imaging measurements of single and multiple point sources as well as extended source distributions are presented. Time encoded imaging has proven to be a simple method for achieving high resolution two-dimensional imaging with potential to be used in future arms control and treaty verification applications.

  1. Fluorescent proteins as genetically encoded FRET biosensors in life sciences.

    Science.gov (United States)

    Hochreiter, Bernhard; Garcia, Alan Pardo; Schmid, Johannes A

    2015-10-16

    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.

  2. Recombinant Exon-Encoded Resilins for Elastomeric Biomaterials

    Science.gov (United States)

    Qin, Guokui; Rivkin, Amit; Lapidot, Shaul; Hu, Xiao; Arinus, Shira B.; Dgany, Or; Shoseyov, Oded; Kaplan, David L.

    2011-01-01

    Resilin is an elastomeric protein found in specialized regions of the cuticle of most insects, providing outstanding material properties including high resilience and fatigue lifetime for insect flight and jumping needs. Two exons (1 and 3) from the resilin gene in Drosophila melanogaster were cloned and the encoded proteins expressed as soluble products in Escherichia coli. A heat and salt precipitation method was used for efficient purification of the recombinant proteins. The proteins were solution cast from water and formed into rubber-like biomaterials via horseradish peroxidase-mediated cross-linking. Comparative studies of the two proteins expressed from the two different exons were investigated by Fourier Transform Infrared Spectroscopy (FTIR) and Circular Dichrosim (CD) for structural features. Little structural organization was found, suggesting structural order was not induced by the enzyme-mediateed dityrosine cross-links. Atomic Force Microscopy (AFM) was used to study the elastomeric properties of the uncross-linked and cross-linked proteins. The protein from exon 1 exhibited 90% resilience in comparison to 63% for the protein from exon 3, and therefore may be the more critical domain for functional materials to mimic native resilin. Further, the cross-linking of the recombinant exon 1 via the citrate-modified photo-Fenton reaction was explored as an alternative dityrosine mediated polymerization method and resulted in both highly elastic and adhesive materials. The citrate-modified photo-Fenton system may be suitable for in-vivo applications of resilin biomaterials. PMID:21963157

  3. Development of Deduced Protein Database Using Variable Bit Binary Encoding

    Directory of Open Access Journals (Sweden)

    B. Parvathavarthini

    2008-01-01

    Full Text Available A large amount of biological data is semi-structured and stored in any one the following file formats such as flat, XML and relational files. These databases must be integrated with the structured data available in relational or object-oriented databases. The sequence matching process is difficult in such file format, because string comparison takes more computation cost and time. To reduce the memory storage size of amino acid sequence in protein database, a novel probability-based variable bit length encoding technique has been introduced. The number of mapping of triplet CODON for every amino acid evaluates the probability value. Then, a binary tree has been constructed to assign unique bits of binary codes to each amino acid. This derived unique bit pattern of amino acid replaces the existing fixed byte representation. The proof of reduced protein database space has been discussed and it is found to be reduced between 42.86 to 87.17%. To validate our method, we have collected few amino acid sequences of major organisms like Sheep, Lambda phage and etc from NCBI and represented them using proposed method. The comparison shows that of minimum and maximum reduction in storage space are 43.30% and 72.86% respectively. In future the biological data can further be reduced by applying lossless compression on this deduced data.

  4. A genetically encoded, high-signal-to-noise maltose sensor

    Energy Technology Data Exchange (ETDEWEB)

    Marvin, Jonathan S.; Schreiter, Eric R.; Echevarría, Ileabett M.; Looger, Loren L. (Puerto Rico); (HHMI)

    2012-10-23

    We describe the generation of a family of high-signal-to-noise single-wavelength genetically encoded indicators for maltose. This was achieved by insertion of circularly permuted fluorescent proteins into a bacterial periplasmic binding protein (PBP), Escherichia coli maltodextrin-binding protein, resulting in a four-color family of maltose indicators. The sensors were iteratively optimized to have sufficient brightness and maltose-dependent fluorescence increases for imaging, under both one- and two-photon illumination. We demonstrate that maltose affinity of the sensors can be tuned in a fashion largely independent of the fluorescent readout mechanism. Using literature mutations, the binding specificity could be altered to moderate sucrose preference, but with a significant loss of affinity. We use the soluble sensors in individual E. coli bacteria to observe rapid maltose transport across the plasma membrane, and membrane fusion versions of the sensors on mammalian cells to visualize the addition of maltose to extracellular media. The PBP superfamily includes scaffolds specific for a number of analytes whose visualization would be critical to the reverse engineering of complex systems such as neural networks, biosynthetic pathways, and signal transduction cascades. We expect the methodology outlined here to be useful in the development of indicators for many such analytes.

  5. Ion coalescence of neutron encoded TMT 10-plex reporter ions.

    Science.gov (United States)

    Werner, Thilo; Sweetman, Gavain; Savitski, Maria Fälth; Mathieson, Toby; Bantscheff, Marcus; Savitski, Mikhail M

    2014-04-01

    Isobaric mass tag-based quantitative proteomics strategies such as iTRAQ and TMT utilize reporter ions in the low mass range of tandem MS spectra for relative quantification. The recent extension of TMT multiplexing to 10 conditions has been enabled by utilizing neutron encoded tags with reporter ion m/z differences of 6 mDa. The baseline resolution of these closely spaced tags is possible due to the high resolving power of current day mass spectrometers. In this work we evaluated the performance of the TMT10 isobaric mass tags on the Q Exactive Orbitrap mass spectrometers for the first time and demonstrated comparable quantification accuracy and precision to what can be achieved on the Orbitrap Elite mass spectrometers. However, we discovered, upon analysis of complex proteomics samples on the Q Exactive Orbitrap mass spectrometers, that the proximate TMT10 reporter ion pairs become prone to coalescence. The fusion of the different reporter ion signals into a single measurable entity has a detrimental effect on peptide and protein quantification. We established that the main reason for coalescence is the commonly accepted maximum ion target for MS2 spectra of 1e6 on the Q Exactive instruments. The coalescence artifact was completely removed by lowering the maximum ion target for MS2 spectra from 1e6 to 2e5 without any losses in identification depth or quantification quality of proteins.

  6. Atypical Enteropathogenic Escherichia coli Secretes Plasmid Encoded Toxin

    Directory of Open Access Journals (Sweden)

    Rita C. Ruiz

    2014-01-01

    Full Text Available Plasmid encoded toxin (Pet is a serine protease originally described in enteroaggregative Escherichia coli (EAEC prototype strain 042 whose entire characterization was essentially obtained from studies performed with the purified toxin. Here we show that Pet is not exclusive to EAEC. Atypical enteropathogenic Escherichia coli (aEPEC strains, isolated from diarrhea cases, express Pet and its detection in supernatants of infected HEp-2 cells coincides with the appearance of cell damage, which, in turn, were similar to those described with purified Pet. Pet secretion and the cytotoxic effects are time and culture medium dependent. In presence of DMEM supplemented with tryptone cell rounding and detachment were observed after just 5 h of incubation with the bacteria. In the absence of tryptone, the cytotoxic effects were detected only after 24 h of infection. We also show that, in addition to the prototype EAEC, other pet+ EAEC strains, also isolated from diarrhea cases, induce cellular damage in the same degree as the aEPEC. The cytotoxic effects of EAEC and aEPEC strains were significantly reduced in the presence of a serine protease inhibitor or anti-Pet IgG serum. Our results show a common aspect between the aEPEC and EAEC and provide the first evidence pointing to a role of Pet in aEPEC pathogenesis.

  7. Functional correlates of distractor suppression during spatial working memory encoding.

    Science.gov (United States)

    Toepper, M; Gebhardt, H; Beblo, T; Thomas, C; Driessen, M; Bischoff, M; Blecker, C R; Vaitl, D; Sammer, G

    2010-02-17

    Executive working memory operations are related to prefrontal regions in the healthy brain. Moreover, neuroimaging data provide evidence for a functional dissociation of ventrolateral and dorsolateral prefrontal cortex. Most authors either suggest a modality-specific or a function-specific prefrontal cortex organization. In the present study we particularly aimed at the identification of different prefrontal cerebral areas that are involved in executive inhibitory processes during spatial working memory encoding. In an fMRI study (functional magnetic resonance imaging) we examined the neural correlates of spatial working memory processing by varying the amount of executive demands of the task. Twenty healthy volunteers performed the Corsi Block-Tapping test (CBT) during fMRI. The CBT requires the storage and reproduction of spatial target sequences. In a second condition, we presented an adapted version of the Block-Suppression-Test (BST). The BST is based on the original CBT but additionally requires the active suppression of visual distraction within the target sequences. In comparison to the CBT performance, particularly the left dorsolateral prefrontal cortex (BA 9) showed more activity during the BST condition. Our results show that the left dorsolateral prefrontal cortex plays a crucial role for executive controlled inhibition of spatial distraction. Furthermore, our findings are in line with the processing model of a functional dorsolateral-ventrolateral prefrontal cortex organization.

  8. Developmentally distinct MYB genes encode functionally equivalent proteins in Arabidopsis.

    Science.gov (United States)

    Lee, M M; Schiefelbein, J

    2001-05-01

    The duplication and divergence of developmental control genes is thought to have driven morphological diversification during the evolution of multicellular organisms. To examine the molecular basis of this process, we analyzed the functional relationship between two paralogous MYB transcription factor genes, WEREWOLF (WER) and GLABROUS1 (GL1), in Arabidopsis. The WER and GL1 genes specify distinct cell types and exhibit non-overlapping expression patterns during Arabidopsis development. Nevertheless, reciprocal complementation experiments with a series of gene fusions showed that WER and GL1 encode functionally equivalent proteins, and their unique roles in plant development are entirely due to differences in their cis-regulatory sequences. Similar experiments with a distantly related MYB gene (MYB2) showed that its product cannot functionally substitute for WER or GL1. Furthermore, an analysis of the WER and GL1 proteins shows that conserved sequences correspond to specific functional domains. These results provide new insights into the evolution of the MYB gene family in Arabidopsis, and, more generally, they demonstrate that novel developmental gene function may arise solely by the modification of cis-regulatory sequences.

  9. Current View on Phytoplasma Genomes and Encoded Metabolism

    Directory of Open Access Journals (Sweden)

    Michael Kube

    2012-01-01

    Full Text Available Phytoplasmas are specialised bacteria that are obligate parasites of plant phloem tissue and insects. These bacteria have resisted all attempts of cell-free cultivation. Genome research is of particular importance to analyse the genetic endowment of such bacteria. Here we review the gene content of the four completely sequenced ‘Candidatus Phytoplasma’ genomes that include those of ‘Ca. P. asteris’ strains OY-M and AY-WB, ‘Ca. P. australiense,’ and ‘Ca. P. mali’. These genomes are characterized by chromosome condensation resulting in sizes below 900 kb and a G + C content of less than 28%. Evolutionary adaption of the phytoplasmas to nutrient-rich environments resulted in losses of genetic modules and increased host dependency highlighted by the transport systems and limited metabolic repertoire. On the other hand, duplication and integration events enlarged the chromosomes and contribute to genome instability. Present differences in the content of membrane and secreted proteins reflect the host adaptation in the phytoplasma strains. General differences are obvious between different phylogenetic subgroups. ‘Ca. P. mali’ is separated from the other strains by its deviating chromosome organization, the genetic repertoire for recombination and excision repair of nucleotides or the loss of the complete energy-yielding part of the glycolysis. Apart from these differences, comparative analysis exemplified that all four phytoplasmas are likely to encode an alternative pathway to generate pyruvate and ATP.

  10. Mnemons: encoding memory by protein super-assembly

    Directory of Open Access Journals (Sweden)

    Fabrice Caudron

    2015-02-01

    Full Text Available Memory is mainly understood as the recollection of past events. The human brain and its simplest unit, the synapse, belong to the places in which such memories are physically stored. From an experimental point of view, memory can be tested in humans by recall. However, in other organisms, memory is reflected in its use by individuals to learn about and adapt their behavior to their environment. Under this criterion, even unicellular organisms are able to learn from their environments and show the ability to adapt their responses to repeating stimuli. This indicates that they are able to keep track of their histories and use these traces to elaborate adapted responses, making these traces akin to memory encodings. Understanding these phenomena may even help us to dissect part of the rather complex molecular orchestration happening in our synapses. When exposed unsuccessfully to mating pheromone, i.e. when mating does not happen, budding yeast cells become refractory to the mating signal. This refractory state is restricted to the mother cell and not inherited by the daughter cells, even though it is stable for most if not the entire life span of the mother cell. Interestingly, both stability and asymmetric segregation of the acquired state are explained by the molecular mechanism underlying its establishment, which shows important analogies and distinctions to prions. Here we discuss these similarities and differences

  11. Encoding of the cough reflex in anesthetized guinea pigs.

    Science.gov (United States)

    Canning, Brendan J; Mori, Nanako

    2011-02-01

    We have previously described the physiological and morphological properties of the cough receptors and their sites of termination in the airways and centrally in the nucleus tractus solitarius (nTS). In the present study, we have addressed the hypothesis that the primary central synapses of the cough receptors subserve an essential role in the encoding of cough. We found that cough requires sustained, high-frequency (≥8-Hz) afferent nerve activation. We also found evidence for processes that both facilitate (summation, sensitization) and inhibit the initiation of cough. Sensitization of cough occurs with repetitive subthreshold activation of the cough receptors or by coincident activation of C-fibers and/or nTS neurokinin receptor activation. Desensitization of cough evoked by repetitive and/or continuous afferent nerve activation has a rapid onset (nervous system-dependent process. The cough reflex can also be actively inhibited upon activation of other airway afferent nerve subtypes, including slowly adapting receptors and pulmonary C-fibers. The sensitization and desensitization of cough are likely attributable to the prominent, primary, and unique role of N-methyl-d-aspartate receptor-dependent signaling at the central synapses of the cough receptors. These attributes may have direct relevance to the presentation of cough in disease and for the effectiveness of antitussive therapies.

  12. Chromosomally encoded small antisense RNA in Corynebacterium glutamicum.

    Science.gov (United States)

    Zemanová, Martina; Kaderábková, Pavla; Pátek, Miroslav; Knoppová, Monika; Silar, Radoslav; Nesvera, Jan

    2008-02-01

    The first observation of chromosomally encoded small antisense RNA in Corynebacterium glutamicum is reported. Transcription oriented in the reverse direction to the transcription of the genes cg1934 and cg1935 was demonstrated within the chromosomal cg1934-cg1935 intergenic region. The transcription was found to be increased after heat shock. The transcriptional start point of this RNA designated ArnA was localized 21 bp upstream of the cg1935 translational start point by primer extension analysis, when the total RNA was isolated from cells grown at 30 degrees C. After heat shock, the transcriptional start point of an additional species of ArnA RNA was detected 19 bp upstream of the cg1935 translational start point. The stress-response sigma factor SigH was found to be involved in the synthesis of ArnA RNAs. The 3' end of the ArnA RNAs was identified using the 3'-rapid amplification of cDNA ends technique. The length of the two ArnA RNA species was thus determined to be 129 and 131 nt, respectively. The ArnA RNAs were found to overlap the 5'-untranslated region of the transcript of the cg1935 gene coding for a transcriptional regulator of the GntR family. These results suggest that the noncoding ArnA RNAs have a regulatory function.

  13. [Association of schizophrenia with variations in genes encoding transcription factors].

    Science.gov (United States)

    Boyajyan, A S; Atshemyan, S A; Zakharyan, R V

    2015-01-01

    Alterations in neuronal plasticity and immune system play a key role in pathogenesis of schizophrenia. Identification of genetic factors contributing to these alterations will significantly encourage elucidation of molecular etiopathomechanisms of this disorder. Transcription factors c-Fos, c-Jun, and Ier5 are the important regulators of neuronal plasticity and immune response. In the present work we investigated a potential association of schizophrenia with a number of single nucleotide polymorphisms of c-Fos-,c-Jun and Ier5 encoding genes (FOS, JUN, and IER5 respectively). Genotyping of DNA samples of patients with schizophrenia and healthy individuals was performed using polymerase chain reaction with allele specific primers. The results obtained demonstrated association between schizophrenia and FOS rs1063169, FOS rs7101, JUN rs11688, and IER5 rs6425663 polymorphisms. Namely, it was found that the inheritance of FOS rs1063169*T, JUN rs11688*A, and IER5 rs6425663*T minor variants decreases risk for development of schizophrenia whereas the inheritance of FOS rs7101*T minor variant, especially its homozygous form, increases risk for development of this disorder.

  14. Suppressors of RNA silencing encoded by tomato leaf curl betasatellites

    Indian Academy of Sciences (India)

    Richa Shukla; Sunita Dalal; V G Malathi

    2013-03-01

    Virus encoded RNA-silencing suppressors (RSSs) are the key components evolved by the viruses to counter RNA-silencing defense of plants. Whitefly-transmitted begomoviruses infecting tomato crop code for five different proteins, ORF AC4, ORF AC2 and ORF AV2 in DNA-A component, ORF BV1 in DNA-B and ORF C1 in satellite DNA which are predicted to function as silencing suppressors. In the present study suppressor function of ORF C1 of three betasatellites Tomato leaf curl Bangalore betasatellite ToLCBB-[IN:Hess:08], Cotton leaf curl Multan betasatellite CLCuMB–[IN:Sri:02] and Luffa leaf distortion betasatellite LuLDB-[IN:Lu:04] were examined. Agroinfiltration of GFP-silenced Nicotiana tabaccum cv. Xanthi with the cells expressing C1 protein resulted in reversal of silenced GFP expression. GFP-siRNA level was more than 50-fold lower compared to silenced plants in plants infiltrated with C1 gene from ToLCBB. However, in the case of 35S-C1 CLCuMB and 35S-C1 LuLDB construct, although GFP was expressed, siRNA level was not reduced, indicating that the step at which C1 interfere in RNA-silencing pathway is different.

  15. Encoding and storage of spatial information in the retrosplenial cortex.

    Science.gov (United States)

    Czajkowski, Rafał; Jayaprakash, Balaji; Wiltgen, Brian; Rogerson, Thomas; Guzman-Karlsson, Mikael C; Barth, Alison L; Trachtenberg, Joshua T; Silva, Alcino J

    2014-06-10

    The retrosplenial cortex (RSC) is part of a network of interconnected cortical, hippocampal, and thalamic structures harboring spatially modulated neurons. The RSC contains head direction cells and connects to the parahippocampal region and anterior thalamus. Manipulations of the RSC can affect spatial and contextual tasks. A considerable amount of evidence implicates the role of the RSC in spatial navigation, but it is unclear whether this structure actually encodes or stores spatial information. We used a transgenic mouse in which the expression of green fluorescent protein was under the control of the immediate early gene c-fos promoter as well as time-lapse two-photon in vivo imaging to monitor neuronal activation triggered by spatial learning in the Morris water maze. We uncovered a repetitive pattern of cell activation in the RSC consistent with the hypothesis that during spatial learning an experience-dependent memory trace is formed in this structure. In support of this hypothesis, we also report three other observations. First, temporary RSC inactivation disrupts performance in a spatial learning task. Second, we show that overexpressing the transcription factor CREB in the RSC with a viral vector, a manipulation known to enhance memory consolidation in other circuits, results in spatial memory enhancements. Third, silencing the viral CREB-expressing neurons with the allatostatin system occludes the spatial memory enhancement. Taken together, these results indicate that the retrosplenial cortex engages in the formation and storage of memory traces for spatial information.

  16. Remotely operated compact underwater temporally encoded imager: CUTEI

    Science.gov (United States)

    Alley, Derek; Cochenour, Brandon; Mullen, Linda

    2016-05-01

    Remotely operated vehicles (ROVs) typically use traditional optical imaging systems, such as cameras, for high resolution imaging. Cameras are effective in clear water, but have extremely poor performance in degraded visual environments (DVEs) such as turbid coastal waters and harbors. This is due to the multiple scattering of the light from the particulates and organic matter in the water. Laser-based sensors have been developed to enhance optical imaging in DVEs1,3,4,5,6. However, since conventional approaches require that the illuminator and receiver be located on the same platform, the size, weight, and power (SWaP) requirements are incompatible with small ROVs. Researchers at NAVAIR have developed a low cost optical imager utilizing a bistatic geometry where the illuminator and receiver are mounted on separate, smaller platforms. The illuminator steers a modulated laser beam with a microelectromechanical system (MEMS) scanner to sequentially illuminate an underwater object. A distant receiver collects the object reflected laser light and reconstructs the imagery. Communications information, including a synchronization sequence, is encoded onto the modulation which is used by the receiver to build the image. The SWaP of the illuminator's components have been optimized and integrated into a modified version of the OpenROV, a miniature, commercial off-the-shelf ROV. This paper reports on the efforts to reduce the SWaP of the modulated illuminator and the results of testing this system in a laboratory water tank environment.

  17. Spatial encoding of visual words for image classification

    Science.gov (United States)

    Liu, Dong; Wang, Shengsheng; Porikli, Fatih

    2016-05-01

    Appearance-based bag-of-visual words (BoVW) models are employed to represent the frequency of a vocabulary of local features in an image. Due to their versatility, they are widely popular, although they ignore the underlying spatial context and relationships among the features. Here, we present a unified representation that enhances BoVWs with explicit local and global structure models. Three aspects of our method should be noted in comparison to the previous approaches. First, we use a local structure feature that encodes the spatial attributes between a pair of points in a discriminative fashion using class-label information. We introduce a bag-of-structural words (BoSW) model for the given image set and describe each image with this model on its coarsely sampled relevant keypoints. We then combine the codebook histograms of BoVW and BoSW to train a classifier. Rigorous experimental evaluations on four benchmark data sets demonstrate that the unified representation outperforms the conventional models and compares favorably to more sophisticated scene classification techniques.

  18. Co-transcriptional folding is encoded within RNA genes

    Directory of Open Access Journals (Sweden)

    Miklós István

    2004-08-01

    Full Text Available Abstract Background Most of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription. Methods The main aim of this work is to study if and how co-transcriptional folding is encoded within the primary and secondary structure of RNA genes. In order to achieve this, we study the known primary and secondary structures of a comprehensive data set of 361 RNA genes as well as a set of 48 RNA sequences that are known to differ from the originally transcribed sequence units. We detect co-transcriptional folding by defining two measures of directedness which quantify the extend of asymmetry between alternative helices that lie 5' and those that lie 3' of the known helices with which they compete. Results We show with statistical significance that co-transcriptional folding strongly influences RNA sequences in two ways: (1 alternative helices that would compete with the formation of the functional structure during co-transcriptional folding are suppressed and (2 the formation of transient structures which may serve as guidelines for the co-transcriptional folding pathway is encouraged. Conclusions These findings have a number of implications for RNA secondary structure prediction methods and the detection of RNA genes.

  19. Protein Collapse is Encoded in the Folded State Architecture

    CERN Document Server

    Samanta, Himadri S; Hinczewski, Michael; Hori, Naoto; Chakrabarti, Shaon; Thirumalai, D

    2016-01-01

    Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The dependence of the radii of gyration on protein size in the folded and unfolded states obeys the same scaling laws as synthetic polymers. Thus, one might surmise that the mechanism of collapse in proteins and polymers ought to be similar. However, because the number of amino acids in single domain proteins is not significantly greater than about two hundred, it has not been resolved if the unfolded states of proteins are compact under conditions that favor the folded states - a problem at the heart of how proteins fold. By adopting a theory used to derive polymer-scaling laws, we find that the propensity for the unfolded state of a protein to be compact is universal and is encoded in the contact map of the folded state. Remarkably, analysis of over 2000 proteins shows that protei...

  20. Fluorescent Proteins as Genetically Encoded FRET Biosensors in Life Sciences

    Science.gov (United States)

    Hochreiter, Bernhard; Pardo Garcia, Alan; Schmid, Johannes A.

    2015-01-01

    Fluorescence- or Förster resonance energy transfer (FRET) is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a) cleavage; (b) conformational-change; (c) mechanical force and (d) changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them. PMID:26501285

  1. Fluorescent Proteins as Genetically Encoded FRET Biosensors in Life Sciences

    Directory of Open Access Journals (Sweden)

    Bernhard Hochreiter

    2015-10-01

    Full Text Available Fluorescence- or Förster resonance energy transfer (FRET is a measurable physical energy transfer phenomenon between appropriate chromophores, when they are in sufficient proximity, usually within 10 nm. This feature has made them incredibly useful tools for many biomedical studies on molecular interactions. Furthermore, this principle is increasingly exploited for the design of biosensors, where two chromophores are linked with a sensory domain controlling their distance and thus the degree of FRET. The versatility of these FRET-biosensors made it possible to assess a vast amount of biological variables in a fast and standardized manner, allowing not only high-throughput studies but also sub-cellular measurements of biological processes. In this review, we aim at giving an overview over the recent advances in genetically encoded, fluorescent-protein based FRET-biosensors, as these represent the largest and most vividly growing group of FRET-based sensors. For easy understanding, we are grouping them into four categories, depending on their molecular mechanism. These are based on: (a cleavage; (b conformational-change; (c mechanical force and (d changes in the micro-environment. We also address the many issues and considerations that come with the development of FRET-based biosensors, as well as the possibilities that are available to measure them.

  2. Myocardial strains from 3D displacement encoded magnetic resonance imaging

    Directory of Open Access Journals (Sweden)

    Kindberg Katarina

    2012-04-01

    Full Text Available Abstract Background The ability to measure and quantify myocardial motion and deformation provides a useful tool to assist in the diagnosis, prognosis and management of heart disease. The recent development of magnetic resonance imaging methods, such as harmonic phase analysis of tagging and displacement encoding with stimulated echoes (DENSE, make detailed non-invasive 3D kinematic analyses of human myocardium possible in the clinic and for research purposes. A robust analysis method is required, however. Methods We propose to estimate strain using a polynomial function which produces local models of the displacement field obtained with DENSE. Given a specific polynomial order, the model is obtained as the least squares fit of the acquired displacement field. These local models are subsequently used to produce estimates of the full strain tensor. Results The proposed method is evaluated on a numerical phantom as well as in vivo on a healthy human heart. The evaluation showed that the proposed method produced accurate results and showed low sensitivity to noise in the numerical phantom. The method was also demonstrated in vivo by assessment of the full strain tensor and to resolve transmural strain variations. Conclusions Strain estimation within a 3D myocardial volume based on polynomial functions yields accurate and robust results when validated on an analytical model. The polynomial field is capable of resolving the measured material positions from the in vivo data, and the obtained in vivo strains values agree with previously reported myocardial strains in normal human hearts.

  3. Encoding and analyzing aerial imagery using geospatial semantic graphs

    Energy Technology Data Exchange (ETDEWEB)

    Watson, Jean-Paul; Strip, David R.; McLendon, William Clarence,; Parekh, Ojas D.; Diegert, Carl F.; Martin, Shawn Bryan; Rintoul, Mark Daniel

    2014-02-01

    While collection capabilities have yielded an ever-increasing volume of aerial imagery, analytic techniques for identifying patterns in and extracting relevant information from this data have seriously lagged. The vast majority of imagery is never examined, due to a combination of the limited bandwidth of human analysts and limitations of existing analysis tools. In this report, we describe an alternative, novel approach to both encoding and analyzing aerial imagery, using the concept of a geospatial semantic graph. The advantages of our approach are twofold. First, intuitive templates can be easily specified in terms of the domain language in which an analyst converses. These templates can be used to automatically and efficiently search large graph databases, for specific patterns of interest. Second, unsupervised machine learning techniques can be applied to automatically identify patterns in the graph databases, exposing recurring motifs in imagery. We illustrate our approach using real-world data for Anne Arundel County, Maryland, and compare the performance of our approach to that of an expert human analyst.

  4. Optogenetic Monitoring of Synaptic Activity with Genetically Encoded Voltage Indicators

    Science.gov (United States)

    Nakajima, Ryuichi; Jung, Arong; Yoon, Bong-June; Baker, Bradley J.

    2016-01-01

    The age of genetically encoded voltage indicators (GEVIs) has matured to the point that changes in membrane potential can now be observed optically in vivo. Improving the signal size and speed of these voltage sensors has been the primary driving forces during this maturation process. As a result, there is a wide range of probes using different voltage detecting mechanisms and fluorescent reporters. As the use of these probes transitions from optically reporting membrane potential in single, cultured cells to imaging populations of cells in slice and/or in vivo, a new challenge emerges—optically resolving the different types of neuronal activity. While improvements in speed and signal size are still needed, optimizing the voltage range and the subcellular expression (i.e., soma only) of the probe are becoming more important. In this review, we will examine the ability of recently developed probes to report synaptic activity in slice and in vivo. The voltage-sensing fluorescent protein (VSFP) family of voltage sensors, ArcLight, ASAP-1, and the rhodopsin family of probes are all good at reporting changes in membrane potential, but all have difficulty distinguishing subthreshold depolarizations from action potentials and detecting neuronal inhibition when imaging populations of cells. Finally, we will offer a few possible ways to improve the optical resolution of the various types of neuronal activities. PMID:27547183

  5. Experimental implementation of encoded logical qubit operations in a perfect quantum error correcting code.

    Science.gov (United States)

    Zhang, Jingfu; Laflamme, Raymond; Suter, Dieter

    2012-09-07

    Large-scale universal quantum computing requires the implementation of quantum error correction (QEC). While the implementation of QEC has already been demonstrated for quantum memories, reliable quantum computing requires also the application of nontrivial logical gate operations to the encoded qubits. Here, we present examples of such operations by implementing, in addition to the identity operation, the NOT and the Hadamard gate to a logical qubit encoded in a five qubit system that allows correction of arbitrary single-qubit errors. We perform quantum process tomography of the encoded gate operations, demonstrate the successful correction of all possible single-qubit errors, and measure the fidelity of the encoded logical gate operations.

  6. Encoding of High Frequencies Improves with Maturation of Action Potential Generation in Cultured Neocortical Neurons

    Science.gov (United States)

    Nikitin, Evgeny S.; Bal, Natalia V.; Malyshev, Aleksey; Ierusalimsky, Victor N.; Spivak, Yulia; Balaban, Pavel M.; Volgushev, Maxim

    2017-01-01

    The ability of neocortical neurons to detect and encode rapid changes at their inputs is crucial for basic neuronal computations, such as coincidence detection, precise synchronization of activity and spike-timing dependent plasticity. Indeed, populations of cortical neurons can respond to subtle changes of the input very fast, on a millisecond time scale. Theoretical studies and model simulations linked the encoding abilities of neuronal populations to the fast onset dynamics of action potentials (APs). Experimental results support this idea, however mechanisms of fast onset of APs in cortical neurons remain elusive. Studies in neuronal cultures, that are allowing for accurate control over conditions of growth and microenvironment during the development of neurons and provide better access to the spike initiation zone, may help to shed light on mechanisms of AP generation and encoding. Here we characterize properties of AP encoding in neocortical neurons grown for 11–25 days in culture. We show that encoding of high frequencies improves upon culture maturation, which is accompanied by the development of passive electrophysiological properties and AP generation. The onset of APs becomes faster with culture maturation. Statistical analysis using correlations and linear model approaches identified the onset dynamics of APs as a major predictor of age-dependent changes of encoding. Encoding of high frequencies strongly correlated also with the input resistance of neurons. Finally, we show that maturation of encoding properties of neurons in cultures is similar to the maturation of encoding in neurons studied in slices. These results show that maturation of AP generators and encoding is, to a large extent, determined genetically and takes place even without normal micro-environment and activity of the whole brain in vivo. This establishes neuronal cultures as a valid experimental model for studying mechanisms of AP generation and encoding, and their maturation. PMID

  7. Encoding of aversion by dopamine and the nucleus accumbens.

    Science.gov (United States)

    McCutcheon, James E; Ebner, Stephanie R; Loriaux, Amy L; Roitman, Mitchell F

    2012-01-01

    Adaptive motivated behavior requires rapid discrimination between beneficial and harmful stimuli. Such discrimination leads to the generation of either an approach or rejection response, as appropriate, and enables organisms to maximize reward and minimize punishment. Classically, the nucleus accumbens (NAc) and the dopamine projection to it are considered an integral part of the brain's reward circuit, i.e., they direct approach and consumption behaviors and underlie positive reinforcement. This reward-centered framing ignores important evidence about the role of this system in encoding aversive events. One reason for bias toward reward is the difficulty in designing experiments in which animals repeatedly experience punishments; another is the challenge in dissociating the response to an aversive stimulus itself from the reward/relief experienced when an aversive stimulus is terminated. Here, we review studies that employ techniques with sufficient time resolution to measure responses in ventral tegmental area and NAc to aversive stimuli as they are delivered. We also present novel findings showing that the same stimulus - intra-oral infusion of sucrose - has differing effects on NAc shell dopamine release depending on the prior experience. Here, for some rats, sucrose was rendered aversive by explicitly pairing it with malaise in a conditioned taste aversion paradigm. Thereafter, sucrose infusions led to a suppression of dopamine with a similar magnitude and time course to intra-oral infusions of a bitter quinine solution. The results are discussed in the context of regional differences in dopamine signaling and the implications of a pause in phasic dopamine release within the NAc shell. Together with our data, the emerging literature suggests an important role for differential phasic dopamine signaling in aversion vs. reward.

  8. Encoding of aversion by dopamine and the nucleus accumbens

    Directory of Open Access Journals (Sweden)

    James Edgar Mccutcheon

    2012-09-01

    Full Text Available Adaptive motivated behavior requires rapid discrimination between beneficial and harmful stimuli. Such discrimination leads to the generation of either an approach or rejection response, as appropriate, and enables organisms to maximize reward and minimize punishment. Classically, the nucleus accumbens (NAc and the dopamine projection to it are considered an integral part of the brain’s reward circuit, i.e., they direct approach and consumption behaviors and underlie positive reinforcement. This reward-centered framing ignores important evidence about the role of this system in encoding aversive events. One reason for bias towards reward is the difficulty in designing experiments in which animals repeatedly experience punishments; another is the challenge in dissociating the response to an aversive stimulus itself from the reward/relief experienced when an aversive stimulus is terminated. Here, we review studies that employ techniques with sufficient time resolution to measure responses in ventral tegmental area (VTA and NAc to aversive stimuli as they are delivered. We also present novel findings showing that the same stimulus – intraoral infusion of sucrose – has differing effects on NAc shell dopamine release depending on the prior experience. Here, for some rats, sucrose was rendered aversive by explicitly pairing it with malaise in a conditioned taste aversion paradigm. Thereafter, sucrose infusions led to a suppression of dopamine with a similar magnitude and time course to intra-oral infusions of a bitter quinine solution. The results are discussed in the context of regional differences in dopamine signaling and the implications of a pause in phasic dopamine release within the NAc shell. Together with our data, the emerging literature suggests an important role for differential phasic dopamine signaling in aversion versus reward.

  9. Whisker encoding of mechanical events during active tactile exploration

    Directory of Open Access Journals (Sweden)

    Yves eBoubenec

    2012-11-01

    Full Text Available Rats use their whiskers to extract a wealth of information about their immediate environment, such as the shape, position or texture of an object. The information is conveyed to mechanoreceptors located within the whisker follicle in the form of a sequence of whisker deflections induced by the whisker/object contact interaction. How the whiskers filter and shape the mechanical information and effectively participate in the coding of tactile features remains an open question to date. In the present article, a biomechanical model was developed that provides predictions of the whisker dynamics during active tactile exploration, amenable to quantitative experimental comparison. This model is based on a decomposition of the whisker profile into a slow, quasi-static sequence and rapid resonant small-scale vibrations. It was applied to the typical situation of a rat whisking across an object. Having derived the quasi-static sequence of whisker deformation, the resonant properties of the whisker were analyzed, taking into account the boundary conditions imposed by the whisker/surface contact. We then focused on two elementary mechanical events that are expected to trigger neural responses, namely (i the whisker/object first contact and (ii the whisker detachment from the object. Both events were found to trigger a deflection wave propagating upward to the mystacial pad at constant velocity of 3-5m/s. This yielded a characteristic mechanical signature at the whisker base, in the form of a large peak of negative curvature occurring 4ms after the event was triggered. The dependence in amplitude and lag of this mechanical signal with the main contextual parameters (such as radial or angular distance was investigated. The model was validated experimentally by comparing its predictions to high-speed video recordings of shock-induced whisker deflections performed on anesthetized rats. The consequences of these results on possible tactile encoding schemes are

  10. Mobile antibiotic resistance encoding elements promote their own diversity.

    Directory of Open Access Journals (Sweden)

    Geneviève Garriss

    2009-12-01

    Full Text Available Integrating conjugative elements (ICEs are a class of bacterial mobile genetic elements that disseminate via conjugation and then integrate into the host cell genome. The SXT/R391 family of ICEs consists of more than 30 different elements that all share the same integration site in the host chromosome but often encode distinct properties. These elements contribute to the spread of antibiotic resistance genes in several gram-negative bacteria including Vibrio cholerae, the agent of cholera. Here, using comparative analyses of the genomes of several SXT/R391 ICEs, we found evidence that the genomes of these elements have been shaped by inter-ICE recombination. We developed a high throughput semi-quantitative method to explore the genetic determinants involved in hybrid ICE formation. Recombinant ICE formation proved to be relatively frequent, and to depend on host (recA and ICE (s065 and s066 loci, which can independently and potentially cooperatively mediate hybrid ICE formation. s065 and s066, which are found in all SXT/R391 ICEs, are orthologues of the bacteriophage lambda Red recombination genes bet and exo, and the s065/s066 recombination system is the first Red-like recombination pathway to be described in a conjugative element. Neither ICE excision nor conjugative transfer proved to be essential for generation of hybrid ICEs. Instead conjugation facilitates the segregation of hybrids and could provide a means to select for functional recombinant ICEs containing novel combinations of genes conferring resistance to antibiotics. Thus, ICEs promote their own diversity and can yield novel mobile elements capable of disseminating new combinations of antibiotic resistance genes.

  11. A computational model of dysfunctional facial encoding in congenital prosopagnosia.

    Science.gov (United States)

    Stollhoff, Rainer; Kennerknecht, Ingo; Elze, Tobias; Jost, Jürgen

    2011-08-01

    Congenital prosopagnosia is a selective deficit in face identification that is present from birth. Previously, behavioral deficits in face recognition and differences in the neuroanatomical structure and functional activation of face processing areas have been documented mostly in separate studies. Here, we propose a neural network model of congenital prosopagnosia which relates behavioral and neuropsychological studies of prosopagnosia to theoretical models of information processing. In this study we trained a neural network with two different algorithms to represent face images. First, we introduced a predisposition towards a decreased network connectivity implemented as a temporal independent component analysis (ICA). This predisposition induced a featural representation of faces in terms of isolated face parts. Second, we trained the network for optimal information encoding using spatial ICA, which led to holistic representations of faces. The network model was then tested empirically in an experiment with ten prosopagnosic and twenty age-matched controls. Participants had to discriminate between faces that were changed either according to the prosopagnosic model of featural representation or to the control model of holistic representation. Compared to controls prosopagnosic participants were impaired only in discriminating holistic changes of faces but showed no impairment in detecting featural changes. In summary, the proposed model presents an empirically testable account of congenital prosopagnosia that links the critical features--a lack of holistic processing at the computational level and a sparse structural connectivity at the implementation level. More generally, our results point to structural differences in the network connectivity as the cause of the face processing deficit in congenital prosopagnosia.

  12. Whisker encoding of mechanical events during active tactile exploration

    Science.gov (United States)

    Boubenec, Yves; Shulz, Daniel E.; Debrégeas, Georges

    2012-01-01

    encoding schemes are briefly discussed. PMID:23133410

  13. Quantum holographic encoding in a two-dimensional electron gas

    Energy Technology Data Exchange (ETDEWEB)

    Moon, Christopher

    2010-05-26

    The advent of bottom-up atomic manipulation heralded a new horizon for attainable information density, as it allowed a bit of information to be represented by a single atom. The discrete spacing between atoms in condensed matter has thus set a rigid limit on the maximum possible information density. While modern technologies are still far from this scale, all theoretical downscaling of devices terminates at this spatial limit. Here, however, we break this barrier with electronic quantum encoding scaled to subatomic densities. We use atomic manipulation to first construct open nanostructures - 'molecular holograms' - which in turn concentrate information into a medium free of lattice constraints: the quantum states of a two-dimensional degenerate Fermi gas of electrons. The information embedded in the holograms is transcoded at even smaller length scales into an atomically uniform area of a copper surface, where it is densely projected into both two spatial degrees of freedom and a third holographic dimension mapped to energy. In analogy to optical volume holography, this requires precise amplitude and phase engineering of electron wavefunctions to assemble pages of information volumetrically. This data is read out by mapping the energy-resolved electron density of states with a scanning tunnelling microscope. As the projection and readout are both extremely near-field, and because we use native quantum states rather than an external beam, we are not limited by lensing or collimation and can create electronically projected objects with features as small as {approx}0.3 nm. These techniques reach unprecedented densities exceeding 20 bits/nm{sup 2} and place tens of bits into a single fermionic state.

  14. Cloning of two genes encoding Rab7 in Paramecium.

    Science.gov (United States)

    Surmacz, Liliana; Wiejak, Jolanta; Wyroba, Elzbieta

    2006-01-01

    Rab7 is a small GTPase that plays a crucial role in the regulation of transport from early to late endosomes and lysosomes, phagosome maturation and in lysosomal biogenesis in mammalian cells. It contains conserved and unique sequence elements that mediate its function. Two Rab7 genes, Rab7a (703 bp) and Rab7b (707 bp) were identified in the unicellular eukaryote Paramecium by PCR amplification. They contain three short introns of different lengths (28-32 bp) and sequence located at identical positions in both genes. The presence of two Rab7 genes in the Paramecium genome was confirmed by Southern hybridization analysis performed with six different restriction enzymes. Expression of both genes was assessed by Northern blot and RT-PCR. Two transcripts of 1.8 and 2.2 kb were identified by hybridization analysis. The cloned complementary DNAs, both of 618 nucleotides in length, encode polypeptides of 206 amino acids that are 97.6% identical and differ in their C-termini. The predicted protein sequences of Rab7a and Rab7b contain all characteristic domains essential for Rab function: the effector domain (YRATVGADF) and four GTP-binding consensus sequences (GDSGVGKT, WDTAGQ, NKLD, SAK) as well as the prenylation motif (-CC) at the C-terminus indispensable for Rab binding to the membrane. Similarity searches revealed 81.6-82.1% homology of Paramecium Rab7 isoforms to human Rab7 and a lack of an insert typical for the Kinetoplastida - the species that appeared earlier in evolution. Paramecium is the first free-living lower eukaryote in which homologues of Rab7 have been identified that exhibit features similar to those of mammalian Rab7.

  15. Genome-wide identification of structural variants in genes encoding drug targets

    DEFF Research Database (Denmark)

    Rasmussen, Henrik Berg; Dahmcke, Christina Mackeprang

    2012-01-01

    The objective of the present study was to identify structural variants of drug target-encoding genes on a genome-wide scale. We also aimed at identifying drugs that are potentially amenable for individualization of treatments based on knowledge about structural variation in the genes encoding the...

  16. The Role of Memory Activation in Creating False Memories of Encoding Context

    Science.gov (United States)

    Arndt, Jason

    2010-01-01

    Using 3 experiments, I examined false memory for encoding context by presenting Deese-Roediger-McDermott themes (Deese, 1959; Roediger & McDermott, 1995) in usual-looking fonts and by testing related, but unstudied, lure items in a font that was shown during encoding. In 2 of the experiments, testing lure items in the font used to study their…

  17. Physical exercise during encoding improves vocabulary learning in young female adults: a neuroendocrinological study.

    Directory of Open Access Journals (Sweden)

    Maren Schmidt-Kassow

    Full Text Available Acute physical activity has been repeatedly shown to improve various cognitive functions. However, there have been no investigations comparing the effects of exercise during verbal encoding versus exercise prior to encoding on long-term memory performance. In this current psychoneuroendocrinological study we aim to test whether light to moderate ergometric bicycling during vocabulary encoding enhances subsequent recall compared to encoding during physical rest and encoding after being physically active. Furthermore, we examined the kinetics of brain-derived neurotrophic factor (BDNF in serum which has been previously shown to correlate with learning performance. We also controlled for the BDNF val66met polymorphism. We found better vocabulary test performance for subjects that were physically active during the encoding phase compared to sedentary subjects. Post-hoc tests revealed that this effect was particularly present in initially low performers. BDNF in serum and BDNF genotype failed to account for the current result. Our data indicates that light to moderate simultaneous physical activity during encoding, but not prior to encoding, is beneficial for subsequent recall of new items.

  18. Least-squares reverse time migration of marine data with frequency-selection encoding

    KAUST Repository

    Dai, Wei

    2013-06-24

    The phase-encoding technique can sometimes increase the efficiency of the least-squares reverse time migration (LSRTM) by more than one order of magnitude. However, traditional random encoding functions require all the encoded shots to share the same receiver locations, thus limiting the usage to seismic surveys with a fixed spread geometry. We implement a frequency-selection encoding strategy that accommodates data with a marine streamer geometry. The encoding functions are delta functions in the frequency domain, so that all the encoded shots have unique nonoverlapping frequency content, and the receivers can distinguish the wavefield from each shot with a unique frequency band. Because the encoding functions are orthogonal to each other, there will be no crosstalk between different shots during modeling and migration. With the frequency-selection encoding method, the computational efficiency of LSRTM is increased so that its cost is comparable to conventional RTM for the Marmousi2 model and a marine data set recorded in the Gulf of Mexico. With more iterations, the LSRTM image quality is further improved by suppressing migration artifacts, balancing reflector amplitudes, and enhancing the spatial resolution. We conclude that LSRTM with frequency-selection is an efficient migration method that can sometimes produce more focused images than conventional RTM. © 2013 Society of Exploration Geophysicists.

  19. On the relationships between generative encodings, regularity, and learning abilities when evolving plastic artificial neural networks.

    Directory of Open Access Journals (Sweden)

    Paul Tonelli

    Full Text Available A major goal of bio-inspired artificial intelligence is to design artificial neural networks with abilities that resemble those of animal nervous systems. It is commonly believed that two keys for evolving nature-like artificial neural networks are (1 the developmental process that links genes to nervous systems, which enables the evolution of large, regular neural networks, and (2 synaptic plasticity, which allows neural networks to change during their lifetime. So far, these two topics have been mainly studied separately. The present paper shows that they are actually deeply connected. Using a simple operant conditioning task and a classic evolutionary algorithm, we compare three ways to encode plastic neural networks: a direct encoding, a developmental encoding inspired by computational neuroscience models, and a developmental encoding inspired by morphogen gradients (similar to HyperNEAT. Our results suggest that using a developmental encoding could improve the learning abilities of evolved, plastic neural networks. Complementary experiments reveal that this result is likely the consequence of the bias of developmental encodings towards regular structures: (1 in our experimental setup, encodings that tend to produce more regular networks yield networks with better general learning abilities; (2 whatever the encoding is, networks that are the more regular are statistically those that have the best learning abilities.

  20. Selective Memories: Infants' Encoding Is Enhanced in Selection via Suppression

    Science.gov (United States)

    Markant, Julie; Amso, Dima

    2013-01-01

    The present study examined the hypothesis that inhibitory visual selection mechanisms play a vital role in memory by limiting distractor interference during item encoding. In Experiment 1a we used a modified spatial cueing task in which 9-month-old infants encoded multiple category exemplars in the contexts of an attention orienting mechanism…

  1. A grammar of space in Baure: A study on the linguistic encoding of spacial reference

    NARCIS (Netherlands)

    Admiraal, F.

    2016-01-01

    Cross-linguistic research has shown that languages vary greatly in the way they encode spatial reference. However, it has also shown that patterns can be identified in this variety of linguistic encodings. This dissertation focuses on the key components of spatial language in Baure, a critically end

  2. On the relationships between generative encodings, regularity, and learning abilities when evolving plastic artificial neural networks.

    Science.gov (United States)

    Tonelli, Paul; Mouret, Jean-Baptiste

    2013-01-01

    A major goal of bio-inspired artificial intelligence is to design artificial neural networks with abilities that resemble those of animal nervous systems. It is commonly believed that two keys for evolving nature-like artificial neural networks are (1) the developmental process that links genes to nervous systems, which enables the evolution of large, regular neural networks, and (2) synaptic plasticity, which allows neural networks to change during their lifetime. So far, these two topics have been mainly studied separately. The present paper shows that they are actually deeply connected. Using a simple operant conditioning task and a classic evolutionary algorithm, we compare three ways to encode plastic neural networks: a direct encoding, a developmental encoding inspired by computational neuroscience models, and a developmental encoding inspired by morphogen gradients (similar to HyperNEAT). Our results suggest that using a developmental encoding could improve the learning abilities of evolved, plastic neural networks. Complementary experiments reveal that this result is likely the consequence of the bias of developmental encodings towards regular structures: (1) in our experimental setup, encodings that tend to produce more regular networks yield networks with better general learning abilities; (2) whatever the encoding is, networks that are the more regular are statistically those that have the best learning abilities.

  3. How Do Expert Soccer Players Encode Visual Information to Make Decisions in Simulated Game Situations?

    Science.gov (United States)

    Poplu, Gerald; Ripoll, Hubert; Mavromatis, Sebastien; Baratgin, Jean

    2008-01-01

    The aim of this study was to determine what visual information expert soccer players encode when they are asked to make a decision. We used a repetition-priming paradigm to test the hypothesis that experts encode a soccer pattern's structure independently of the players' physical characteristics (i.e., posture and morphology). The participants…

  4. Nonlinear Trellis Description for Convolutionally Encoded Transmission Over ISI-channels with Applications for CPM

    CERN Document Server

    Schuh, Fabian

    2012-01-01

    In this paper we propose a matched decoding scheme for convolutionally encoded transmission over intersymbol interference (ISI) channels and devise a nonlinear trellis description. As an application we show that for coded continuous phase modulation (CPM) using a non-coherent receiver the number of states of the super trellis can be significantly reduced by means of a matched non-linear trellis encoder.

  5. Memory for Emotional Words in the First and the Second Language: Effects of the Encoding Task

    Science.gov (United States)

    Ferre, Pilar; Sanchez-Casas, Rosa; Fraga, Isabel

    2013-01-01

    Emotional words are better remembered than neutral words in the first language. Ferre, Garcia, Fraga, Sanchez-Casas and Molero (2010) found this emotional effect also for second language words by using an encoding task focused on emotionality. The aim of the present study was to test whether the same effect can also be observed with encoding tasks…

  6. The Role of Executive Control of Attention and Selective Encoding for Preschoolers' Learning

    Science.gov (United States)

    Roderer, Thomas; Krebs, Saskia; Schmid, Corinne; Roebers, Claudia M.

    2012-01-01

    Selectivity in encoding, aspects of attentional control and their contribution to learning performance were explored in a sample of preschoolers. While the children are performing a learning task, their encoding of relevant and attention towards irrelevant information was recorded through an eye-tracking device. Recognition of target items was…

  7. 47 CFR 11.12 - Two-tone Attention Signal encoder and decoder.

    Science.gov (United States)

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Two-tone Attention Signal encoder and decoder... SYSTEM (EAS) General § 11.12 Two-tone Attention Signal encoder and decoder. Existing two-tone Attention... Attention Signal decoder will no longer be required and the two-tone Attention Signal will be used...

  8. Confabulation in Alzheimer's disease: poor encoding and retrieval of over-learned information.

    Science.gov (United States)

    Attali, Eve; De Anna, Francesca; Dubois, Bruno; Dalla Barba, Gianfranco

    2009-01-01

    Patients who confabulate retrieve personal habits, repeated events or over-learned information and mistake them for actually experienced, specific unique events. Although some hypotheses favour a disruption of frontal/executive functions operating at retrieval, the respective involvement of encoding and retrieval processes in confabulation is still controversial. The present study sought to investigate experimentally the involvement of encoding and retrieval processes and the interference of over-learned information in the confabulation of Alzheimer's disease patients. Twenty Alzheimer's disease patients and 20 normal controls encoded and retrieved unknown stories, well-known fairy tales (e.g. Snow White) and modified well-known fairy tales (e.g. Little Red Riding Hood is not eaten by the wolf) under three experimental conditions: (i) full attention at encoding and at retrieval; (ii) divided attention at encoding (i.e. performing an attention demanding secondary task) and full attention at retrieval; (iii) full attention at encoding and divided attention at retrieval. We found that confabulations in Alzheimer's disease patients were more frequent for the modified well-known fairy tales and when encoding was weakened by a concurrent secondary task (61%), compared with the other types of stories and experimental conditions. Confabulations in the modified fairy tales always consisted of elements of the original version of the fairy tale (e.g. Little Red Riding Hood is eaten by the wolf). This is the first experimental evidence showing that poor encoding and over-learned information are involved in confabulation in Alzheimer's disease.

  9. Learning-based encoding with soft assignment for age estimation under unconstrained imaging conditions

    NARCIS (Netherlands)

    Alnajar, F.; Shan, C.; Gevers, T.; Geusebroek, J.M.

    2012-01-01

    In this paper we propose to adopt a learning-based encoding method for age estimation under unconstrained imaging conditions. A similar approach [Cao et al., 2010] is applied to face recognition in real-life face images. However, the feature vectors are encoded in hard manner i.e. each feature vecto

  10. In vivo single-shot (13)C spectroscopic imaging of hyperpolarized metabolites by spatiotemporal encoding

    DEFF Research Database (Denmark)

    Schmidt, Rita; Laustsen, Christoffer; Dumez, Jean-Nicolas;

    2014-01-01

    on spatiotemporal encoding (SPEN) principles, to derive chemical-shift images within a sub-second period. By contrast to EPSI, SPEN does not require oscillating acquisition gradients to deliver chemical-shift information: its signal encodes both spatial as well as chemical shift information, at no extra cost...

  11. Repeated quantum error correction on a continuously encoded qubit by real-time feedback

    Science.gov (United States)

    Cramer, J.; Kalb, N.; Rol, M. A.; Hensen, B.; Blok, M. S.; Markham, M.; Twitchen, D. J.; Hanson, R.; Taminiau, T. H.

    2016-05-01

    Reliable quantum information processing in the face of errors is a major fundamental and technological challenge. Quantum error correction protects quantum states by encoding a logical quantum bit (qubit) in multiple physical qubits. To be compatible with universal fault-tolerant computations, it is essential that states remain encoded at all times and that errors are actively corrected. Here we demonstrate such active error correction on a continuously protected logical qubit using a diamond quantum processor. We encode the logical qubit in three long-lived nuclear spins, repeatedly detect phase errors by non-destructive measurements, and apply corrections by real-time feedback. The actively error-corrected qubit is robust against errors and encoded quantum superposition states are preserved beyond the natural dephasing time of the best physical qubit in the encoding. These results establish a powerful platform to investigate error correction under different types of noise and mark an important step towards fault-tolerant quantum information processing.

  12. Chemical ligation methods for the tagging of DNA-encoded chemical libraries.

    Science.gov (United States)

    Keefe, Anthony D; Clark, Matthew A; Hupp, Christopher D; Litovchick, Alexander; Zhang, Ying

    2015-06-01

    The generation of DNA-encoded chemical libraries requires the unimolecular association of multiple encoding oligonucleotides with encoded chemical entities during combinatorial synthesis processes. This has traditionally been achieved using enzymatic ligation. We discuss a range of chemical ligation methods that provide alternatives to enzymatic ligation. These chemical ligation methods include the generation of modified internucleotide linkages that support polymerase translocation and other modified linkages that while not supporting the translocation of polymerases can also be used to generate individual cDNA molecules containing encoded chemical information specifying individual library members. We also describe which of these approaches have been successfully utilized for the preparation of DNA-encoded chemical libraries and those that were subsequently used for the discovery of inhibitors.

  13. VHDL Implementation of different Turbo Encoder using Log-MAP Decoder

    CERN Document Server

    Gupta, Akash Kumar

    2010-01-01

    Turbo code is a great achievement in the field of communication system. It can be created by connecting a turbo encoder and a decoder serially. A Turbo encoder is build with parallel concatenation of two simple convolutional codes. By varying the number of memory element (encoder configuration), code rate (1/2 or 1/3), block size of data and iteration, we can achieve better BER performance. Turbo code also consists of interleaver unit and its BER performance also depends on interleaver size. Turbo Decoder can be implemented using different algorithm, but Log -MAP decoding algorithm is less computationaly complex with respect to MAP (maximux a posteriori) algorithm, without compromising its BER performance, nearer to Shannon limit. A register transfer level (RTL) turbo encoder is designed and simulated using VHDL (Very high speed integrated circuit Hardware Description Language). In this paper VHDL model of different turbo encoder are implemented using Log MAP decoder and its performance are compared and verif...

  14. Functional properties of Virus-Encoded and Virus-Regulated 7TM Receptors

    DEFF Research Database (Denmark)

    Spiess, Katja; Rosenkilde, Mette Marie

    2014-01-01

    During co-evolution with their hosts, viruses have developed several survival strategies that involve exploitation of 7TM receptors. These include virus-encoded 7TM receptors and ligands and viral regulation of endogenous receptors. Many functional properties have been ascribed to virus-exploited 7......-herpesvirus-encoded BILF1 receptors, the human cytomegalovirus (HCMV)-encoded US28 receptor and the Epstein-Barr virus (EBV)-regulated EBI2 (or GPR183), 2) the tissue tropism and virus-dissemination properties, exemplified by the murine CMV-encoded M33, and 3) the tumorigenic properties, exemplified...... by the human herpesvirus 8 (HHV8)-encoded ORF74, HCMV-US28 and EBV-BILF1. Given the general high “druggability” of 7TM receptors, and the recent progress in the understanding of in particular immune evasive functions of the virus-exploited 7TM receptors, we put a special emphasis on the progress of novel anti...

  15. Correspondence between stimulus encoding- and maintenance-related neural processes underlies successful working memory.

    Science.gov (United States)

    Cohen, Jessica R; Sreenivasan, Kartik K; D'Esposito, Mark

    2014-03-01

    The ability to actively maintain information in working memory (WM) is vital for goal-directed behavior, but the mechanisms underlying this process remain elusive. We hypothesized that successful WM relies upon a correspondence between the neural processes associated with stimulus encoding and the neural processes associated with maintenance. Using functional magnetic resonance imaging, we identified regional activity and inter-regional connectivity during stimulus encoding and the maintenance of those stimuli when they were no longer present. We compared correspondence in these neural processes across encoding and maintenance epochs with WM performance. Critically, greater correspondence between encoding and maintenance in 1) regional activity in the lateral prefrontal cortex (PFC) and 2) connectivity between lateral PFC and extrastriate cortex was associated with increased performance. These findings suggest that the conservation of neural processes across encoding and maintenance supports the integrity of representations in WM.

  16. Repeated quantum error correction on a continuously encoded qubit by real-time feedback.

    Science.gov (United States)

    Cramer, J; Kalb, N; Rol, M A; Hensen, B; Blok, M S; Markham, M; Twitchen, D J; Hanson, R; Taminiau, T H

    2016-05-05

    Reliable quantum information processing in the face of errors is a major fundamental and technological challenge. Quantum error correction protects quantum states by encoding a logical quantum bit (qubit) in multiple physical qubits. To be compatible with universal fault-tolerant computations, it is essential that states remain encoded at all times and that errors are actively corrected. Here we demonstrate such active error correction on a continuously protected logical qubit using a diamond quantum processor. We encode the logical qubit in three long-lived nuclear spins, repeatedly detect phase errors by non-destructive measurements, and apply corrections by real-time feedback. The actively error-corrected qubit is robust against errors and encoded quantum superposition states are preserved beyond the natural dephasing time of the best physical qubit in the encoding. These results establish a powerful platform to investigate error correction under different types of noise and mark an important step towards fault-tolerant quantum information processing.

  17. The role of attention in automatization: does attention operate at encoding, or retrieval, or both?

    Science.gov (United States)

    Boronat, C B; Logan, G D

    1997-01-01

    In this research, we investigated whether attention operates in the encoding of automatized information, the retrieval of automatized information, or in both cases. Subjects searched two-word displays for members of a target category in focused-attention or divided-attention conditions that were crossed with block (training vs. transfer). To see whether subjects encoded all available items or only attended items, we compared performance for subjects in different training conditions but in the same transfer condition. Subjects encoded attended items. To see whether subjects retrieved all the items they had in memory, or only items associated with that to which they were attending at retrieval, we compared performance for subjects in the same training conditions but in different transfer conditions. Subjects retrieved attended items. Attention was found to operate at both encoding and retrieval. These findings support the instance theory of automaticity, which predicts the role of attention at encoding and retrieval.

  18. SERK1 links somatic embryogenesis to brassinosteroid signalling

    NARCIS (Netherlands)

    Kwaaitaal, M.A.C.J.

    2007-01-01

    Somatic embryogenesis, the phenomenon where a somatic cell supplied with the right cues can re-initiate embryogenesis, reveals the underlying totipotent character of plant cells. The acquisition of this totipotent state coincides with the expression of the Somatic Embryogenesis Receptor Kinase (SERK

  19. Visualizing brassinosteroid receptor hetero-oligomers in Arabidopsis roots

    NARCIS (Netherlands)

    Bücherl, C.A.

    2013-01-01

    Living matter is continuously challenged by the dynamics of its environment and intrinsic fluctuations. In the course of evolution, cells have developed mechanisms to detect and adapt to environmental and endogenous cues by the use of a wide array of receptors (Afzal et al., 2008). These receptors p

  20. CAG-encoded polyglutamine length polymorphism in the human genome

    Directory of Open Access Journals (Sweden)

    Hayden Michael R

    2007-05-01

    Full Text Available Abstract Background Expansion of polyglutamine-encoding CAG trinucleotide repeats has been identified as the pathogenic mutation in nine different genes associated with neurodegenerative disorders. The majority of individuals clinically diagnosed with spinocerebellar ataxia do not have mutations within known disease genes, and it is likely that additional ataxias or Huntington disease-like disorders will be found to be caused by this common mutational mechanism. We set out to determine the length distributions of CAG-polyglutamine tracts for the entire human genome in a set of healthy individuals in order to characterize the nature of polyglutamine repeat length variation across the human genome, to establish the background against which pathogenic repeat expansions can be detected, and to prioritize candidate genes for repeat expansion disorders. Results We found that repeats, including those in known disease genes, have unique distributions of glutamine tract lengths, as measured by fragment analysis of PCR-amplified repeat regions. This emphasizes the need to characterize each distribution and avoid making generalizations between loci. The best predictors of known disease genes were occurrence of a long CAG-tract uninterrupted by CAA codons in their reference genome sequence, and high glutamine tract length variance in the normal population. We used these parameters to identify eight priority candidate genes for polyglutamine expansion disorders. Twelve CAG-polyglutamine repeats were invariant and these can likely be excluded as candidates. We outline some confusion in the literature about this type of data, difficulties in comparing such data between publications, and its application to studies of disease prevalence in different populations. Analysis of Gene Ontology-based functions of CAG-polyglutamine-containing genes provided a visual framework for interpretation of these genes' functions. All nine known disease genes were involved in DNA